diff --git a/.github/workflows/pkgdown-gh-pages.yaml b/.github/workflows/pkgdown-gh-pages.yaml
index 7df698d..d7193da 100644
--- a/.github/workflows/pkgdown-gh-pages.yaml
+++ b/.github/workflows/pkgdown-gh-pages.yaml
@@ -1,42 +1,42 @@
-# Alternative pkgdown workflow using gh-pages branch deployment
-# This workflow builds the pkgdown site and deploys to gh-pages branch
-# rather than using the newer GitHub Actions deployment method
-
-on:
-  push:
-    branches: [main]
-  workflow_dispatch:
-
-name: pkgdown-gh-pages
-
-jobs:
-  pkgdown:
-    runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    permissions:
-      contents: write
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::pkgdown, local::.
-          needs: website
-
-      - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
-        shell: Rscript {0}
-
-      - name: Deploy to GitHub Pages
-        uses: JamesIves/github-pages-deploy-action@v4
-        with:
-          folder: docs
-          branch: gh-pages
+# Alternative pkgdown workflow using gh-pages branch deployment
+# This workflow builds the pkgdown site and deploys to gh-pages branch
+# rather than using the newer GitHub Actions deployment method
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+name: pkgdown-gh-pages
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub Pages
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: docs
+          branch: gh-pages
           clean: true
\ No newline at end of file
diff --git a/inst/examples/create-putior-hex.R b/inst/examples/create-putior-hex.R
index 53320e0..a5683fc 100644
--- a/inst/examples/create-putior-hex.R
+++ b/inst/examples/create-putior-hex.R
@@ -1,223 +1,223 @@
-# Create putior hex sticker - Recommended ggplot2 approach
-# This script recreates the putior hex sticker using pure ggplot2
-
-library(ggplot2)
-library(dplyr)
-
-# Function to create hexagon coordinates
-create_hexagon <- function(center_x = 0.5, center_y = 0.5, size = 0.45) {
-  angles <- seq(30, 330, by = 60) * pi / 180
-  data.frame(
-    x = center_x + size * cos(angles),
-    y = center_y + size * sin(angles)
-  )
-}
-
-# Create network data (mimicking the original design)
-create_network_data <- function() {
-  set.seed(42)  # For reproducibility
-  
-  # Node positions (right side of hex)
-  nodes <- data.frame(
-    x = c(0.65, 0.75, 0.85, 0.7, 0.8, 0.6, 0.9),
-    y = c(0.8, 0.7, 0.6, 0.5, 0.4, 0.6, 0.7),
-    size = c(4, 3.5, 3, 3.5, 3, 2.5, 2.5),
-    id = 1:7
-  )
-  
-  # Connections between nodes
-  edges <- data.frame(
-    from = c(1, 1, 2, 3, 4, 6),
-    to = c(2, 4, 3, 5, 5, 7)
-  ) %>%
-    left_join(nodes, by = c("from" = "id")) %>%
-    rename(x_from = x, y_from = y) %>%
-    select(-size) %>%
-    left_join(nodes, by = c("to" = "id")) %>%
-    rename(x_to = x, y_to = y) %>%
-    select(-size)
-  
-  list(nodes = nodes, edges = edges)
-}
-
-# Create document stack data
-create_document_data <- function() {
-  # Three stacked documents (left side of hex)
-  data.frame(
-    x = c(0.25, 0.23, 0.27),      # Slightly offset x positions
-    y = c(0.65, 0.62, 0.68),      # Slightly offset y positions  
-    width = c(0.12, 0.12, 0.12),  # Document width
-    height = c(0.15, 0.15, 0.15), # Document height
-    layer = c(1, 2, 3)            # Stacking order
-  )
-}
-
-# Main function to create the hex sticker
-create_putior_hex <- function() {
-  # Get data
-  hex_shape <- create_hexagon()
-  network_data <- create_network_data()
-  doc_data <- create_document_data()
-  
-  # Color palette
-  bg_color <- "#6B5B95"      # Main purple
-  bg_light <- "#8B7BA5"      # Lighter purple for gradient
-  border_color <- "#000000"   # Black border
-  text_color <- "#FFFFFF"     # White text
-  node_color <- "#FFFFFF"     # White nodes
-  doc_color <- "#FFFFFF"      # White documents
-  
-  # Create the plot
-  p <- ggplot() +
-    
-    # Background gradient effect (multiple layers for gradient simulation)
-    geom_polygon(data = hex_shape, 
-                 aes(x, y), 
-                 fill = bg_light, 
-                 color = NA,
-                 alpha = 0.8) +
-    
-    geom_polygon(data = hex_shape, 
-                 aes(x, y), 
-                 fill = bg_color, 
-                 color = NA,
-                 alpha = 0.6) +
-    
-    # Hexagon border
-    geom_polygon(data = hex_shape, 
-                 aes(x, y), 
-                 fill = NA, 
-                 color = border_color, 
-                 size = 1.5) +
-    
-    # Network edges
-    geom_segment(data = network_data$edges,
-                 aes(x = x_from, y = y_from, 
-                     xend = x_to, yend = y_to),
-                 color = text_color, 
-                 alpha = 0.4, 
-                 size = 0.8) +
-    
-    # Network nodes
-    geom_point(data = network_data$nodes,
-               aes(x, y, size = size),
-               color = node_color, 
-               alpha = 0.9) +
-    
-    # Document stack (back to front)
-    geom_rect(data = arrange(doc_data, layer),
-              aes(xmin = x - width/2, xmax = x + width/2,
-                  ymin = y - height/2, ymax = y + height/2),
-              fill = doc_color, 
-              color = bg_color,
-              alpha = 0.95,
-              size = 0.5) +
-    
-    # Document text annotations
-    annotate("text", 
-             x = doc_data$x[1], 
-             y = doc_data$y[1] + 0.02, 
-             label = "# put", 
-             size = 3, 
-             color = bg_color,
-             family = "mono",
-             fontface = "bold") +
-    
-    # Package name
-    annotate("text", 
-             x = 0.5, 
-             y = 0.15, 
-             label = "putior", 
-             size = 12, 
-             color = text_color,
-             fontface = "bold") +
-    
-    # Styling
-    scale_size_identity() +
-    coord_fixed(ratio = 1) +
-    xlim(0, 1) +
-    ylim(0, 1) +
-    theme_void() +
-    theme(
-      plot.background = element_blank(),
-      panel.background = element_blank(),
-      plot.margin = margin(0, 0, 0, 0)
-    )
-  
-  return(p)
-}
-
-# Alternative version with enhanced gradient effect
-create_putior_hex_enhanced <- function() {
-  # Similar to above but with more sophisticated gradient
-  hex_shape <- create_hexagon()
-  network_data <- create_network_data()
-  doc_data <- create_document_data()
-  
-  # Create multiple gradient layers
-  gradient_layers <- data.frame(
-    layer = 1:5,
-    alpha = c(0.2, 0.25, 0.3, 0.35, 0.4),
-    color = c("#8B7BA5", "#7B6B95", "#6B5B95", "#5B4B85", "#4B3B75")
-  )
-  
-  p <- ggplot()
-  
-  # Add gradient layers
-  for(i in 1:nrow(gradient_layers)) {
-    p <- p +
-      geom_polygon(data = hex_shape, 
-                   aes(x, y), 
-                   fill = gradient_layers$color[i], 
-                   color = NA,
-                   alpha = gradient_layers$alpha[i])
-  }
-  
-  # Add remaining elements (same as basic version)
-  p <- p +
-    geom_polygon(data = hex_shape, aes(x, y), 
-                 fill = NA, color = "#000000", size = 1.5) +
-    # ... (add other elements)
-    
-    theme_void() +
-    coord_fixed()
-  
-  return(p)
-}
-
-# Function to save the hex sticker
-save_putior_hex <- function(plot, filename = "putior_hex", 
-                           width = 2, height = 2, dpi = 300) {
-  
-  # Save as PNG (for package use)
-  ggsave(paste0(filename, ".png"), plot, 
-         width = width, height = height, dpi = dpi,
-         bg = "transparent")
-  
-  # Save as SVG (for scalability) 
-  ggsave(paste0(filename, ".svg"), plot,
-         width = width, height = height,
-         bg = "transparent")
-  
-  cat("Hex sticker saved as:", paste0(filename, c(".png", ".svg")), "\n")
-}
-
-# Usage example:
-if (FALSE) {  # Set to TRUE to run
-  # Create the hex sticker
-  hex_plot <- create_putior_hex()
-  
-  # Preview
-  print(hex_plot)
-  
-  # Save to files
-  save_putior_hex(hex_plot, "putior_hex_ggplot2")
-}
-
-# Notes for further customization:
-# 1. Adjust node positions in create_network_data() to match original exactly
-# 2. Fine-tune colors to match original purple gradient
-# 3. Add more sophisticated document shapes if needed
-# 4. Consider using ggraph for more complex network layouts
-# 5. Use showtext package for custom fonts if required
+# Create putior hex sticker - Recommended ggplot2 approach
+# This script recreates the putior hex sticker using pure ggplot2
+
+library(ggplot2)
+library(dplyr)
+
+# Function to create hexagon coordinates
+create_hexagon <- function(center_x = 0.5, center_y = 0.5, size = 0.45) {
+  angles <- seq(30, 330, by = 60) * pi / 180
+  data.frame(
+    x = center_x + size * cos(angles),
+    y = center_y + size * sin(angles)
+  )
+}
+
+# Create network data (mimicking the original design)
+create_network_data <- function() {
+  set.seed(42)  # For reproducibility
+  
+  # Node positions (right side of hex)
+  nodes <- data.frame(
+    x = c(0.65, 0.75, 0.85, 0.7, 0.8, 0.6, 0.9),
+    y = c(0.8, 0.7, 0.6, 0.5, 0.4, 0.6, 0.7),
+    size = c(4, 3.5, 3, 3.5, 3, 2.5, 2.5),
+    id = 1:7
+  )
+  
+  # Connections between nodes
+  edges <- data.frame(
+    from = c(1, 1, 2, 3, 4, 6),
+    to = c(2, 4, 3, 5, 5, 7)
+  ) %>%
+    left_join(nodes, by = c("from" = "id")) %>%
+    rename(x_from = x, y_from = y) %>%
+    select(-size) %>%
+    left_join(nodes, by = c("to" = "id")) %>%
+    rename(x_to = x, y_to = y) %>%
+    select(-size)
+  
+  list(nodes = nodes, edges = edges)
+}
+
+# Create document stack data
+create_document_data <- function() {
+  # Three stacked documents (left side of hex)
+  data.frame(
+    x = c(0.25, 0.23, 0.27),      # Slightly offset x positions
+    y = c(0.65, 0.62, 0.68),      # Slightly offset y positions  
+    width = c(0.12, 0.12, 0.12),  # Document width
+    height = c(0.15, 0.15, 0.15), # Document height
+    layer = c(1, 2, 3)            # Stacking order
+  )
+}
+
+# Main function to create the hex sticker
+create_putior_hex <- function() {
+  # Get data
+  hex_shape <- create_hexagon()
+  network_data <- create_network_data()
+  doc_data <- create_document_data()
+  
+  # Color palette
+  bg_color <- "#6B5B95"      # Main purple
+  bg_light <- "#8B7BA5"      # Lighter purple for gradient
+  border_color <- "#000000"   # Black border
+  text_color <- "#FFFFFF"     # White text
+  node_color <- "#FFFFFF"     # White nodes
+  doc_color <- "#FFFFFF"      # White documents
+  
+  # Create the plot
+  p <- ggplot() +
+    
+    # Background gradient effect (multiple layers for gradient simulation)
+    geom_polygon(data = hex_shape, 
+                 aes(x, y), 
+                 fill = bg_light, 
+                 color = NA,
+                 alpha = 0.8) +
+    
+    geom_polygon(data = hex_shape, 
+                 aes(x, y), 
+                 fill = bg_color, 
+                 color = NA,
+                 alpha = 0.6) +
+    
+    # Hexagon border
+    geom_polygon(data = hex_shape, 
+                 aes(x, y), 
+                 fill = NA, 
+                 color = border_color, 
+                 size = 1.5) +
+    
+    # Network edges
+    geom_segment(data = network_data$edges,
+                 aes(x = x_from, y = y_from, 
+                     xend = x_to, yend = y_to),
+                 color = text_color, 
+                 alpha = 0.4, 
+                 size = 0.8) +
+    
+    # Network nodes
+    geom_point(data = network_data$nodes,
+               aes(x, y, size = size),
+               color = node_color, 
+               alpha = 0.9) +
+    
+    # Document stack (back to front)
+    geom_rect(data = arrange(doc_data, layer),
+              aes(xmin = x - width/2, xmax = x + width/2,
+                  ymin = y - height/2, ymax = y + height/2),
+              fill = doc_color, 
+              color = bg_color,
+              alpha = 0.95,
+              size = 0.5) +
+    
+    # Document text annotations
+    annotate("text", 
+             x = doc_data$x[1], 
+             y = doc_data$y[1] + 0.02, 
+             label = "# put", 
+             size = 3, 
+             color = bg_color,
+             family = "mono",
+             fontface = "bold") +
+    
+    # Package name
+    annotate("text", 
+             x = 0.5, 
+             y = 0.15, 
+             label = "putior", 
+             size = 12, 
+             color = text_color,
+             fontface = "bold") +
+    
+    # Styling
+    scale_size_identity() +
+    coord_fixed(ratio = 1) +
+    xlim(0, 1) +
+    ylim(0, 1) +
+    theme_void() +
+    theme(
+      plot.background = element_blank(),
+      panel.background = element_blank(),
+      plot.margin = margin(0, 0, 0, 0)
+    )
+  
+  return(p)
+}
+
+# Alternative version with enhanced gradient effect
+create_putior_hex_enhanced <- function() {
+  # Similar to above but with more sophisticated gradient
+  hex_shape <- create_hexagon()
+  network_data <- create_network_data()
+  doc_data <- create_document_data()
+  
+  # Create multiple gradient layers
+  gradient_layers <- data.frame(
+    layer = 1:5,
+    alpha = c(0.2, 0.25, 0.3, 0.35, 0.4),
+    color = c("#8B7BA5", "#7B6B95", "#6B5B95", "#5B4B85", "#4B3B75")
+  )
+  
+  p <- ggplot()
+  
+  # Add gradient layers
+  for(i in 1:nrow(gradient_layers)) {
+    p <- p +
+      geom_polygon(data = hex_shape, 
+                   aes(x, y), 
+                   fill = gradient_layers$color[i], 
+                   color = NA,
+                   alpha = gradient_layers$alpha[i])
+  }
+  
+  # Add remaining elements (same as basic version)
+  p <- p +
+    geom_polygon(data = hex_shape, aes(x, y), 
+                 fill = NA, color = "#000000", size = 1.5) +
+    # ... (add other elements)
+    
+    theme_void() +
+    coord_fixed()
+  
+  return(p)
+}
+
+# Function to save the hex sticker
+save_putior_hex <- function(plot, filename = "putior_hex", 
+                           width = 2, height = 2, dpi = 300) {
+  
+  # Save as PNG (for package use)
+  ggsave(paste0(filename, ".png"), plot, 
+         width = width, height = height, dpi = dpi,
+         bg = "transparent")
+  
+  # Save as SVG (for scalability) 
+  ggsave(paste0(filename, ".svg"), plot,
+         width = width, height = height,
+         bg = "transparent")
+  
+  cat("Hex sticker saved as:", paste0(filename, c(".png", ".svg")), "\n")
+}
+
+# Usage example:
+if (FALSE) {  # Set to TRUE to run
+  # Create the hex sticker
+  hex_plot <- create_putior_hex()
+  
+  # Preview
+  print(hex_plot)
+  
+  # Save to files
+  save_putior_hex(hex_plot, "putior_hex_ggplot2")
+}
+
+# Notes for further customization:
+# 1. Adjust node positions in create_network_data() to match original exactly
+# 2. Fine-tune colors to match original purple gradient
+# 3. Add more sophisticated document shapes if needed
+# 4. Consider using ggraph for more complex network layouts
+# 5. Use showtext package for custom fonts if required
 # 6. Add drop shadow effects with additional polygon layers
\ No newline at end of file
diff --git a/inst/examples/data-science-workflow.R b/inst/examples/data-science-workflow.R
index 596f565..eb80818 100644
--- a/inst/examples/data-science-workflow.R
+++ b/inst/examples/data-science-workflow.R
@@ -1,228 +1,228 @@
-# Data Science Workflow Example: Modular Functions with source()
-# ==============================================================================
-# This example demonstrates the most common data science pattern: modularizing
-# functions into separate scripts and orchestrating them in a main workflow.
-#
-# To run this example:
-#   source(system.file("examples", "data-science-workflow.R", package = "putior"))
-# ==============================================================================
-
-library(putior)
-
-cat("🔬 Data Science Workflow Example: Modular source() Pattern\n")
-cat(paste(rep("=", 60), collapse = ""), "\n\n")
-
-# Create example directory structure
-temp_dir <- file.path(tempdir(), "putior_datascience_example")
-dir.create(temp_dir, showWarnings = FALSE)
-
-cat("📁 Creating modular data science workflow...\n")
-
-# utils.R - Utility functions
-utils_script <- c(
-  "# Data utilities - sourced by main workflow",
-  "# put label:\"Data Utilities\", node_type:\"input\"",
-  "# output defaults to 'utils.R' - this script provides itself",
-  "",
-  "load_and_clean <- function(file_path) {",
-  "  cat(\"Loading data from:\", file_path, \"\\n\")",
-  "  # Simulate loading CSV data",
-  "  data <- data.frame(",
-  "    id = 1:100,",
-  "    value = rnorm(100, 50, 10),",
-  "    category = sample(c(\"A\", \"B\", \"C\"), 100, replace = TRUE),",
-  "    date = seq.Date(as.Date(\"2024-01-01\"), by = \"day\", length.out = 100)",
-  "  )",
-  "  ",
-  "  # Clean data",
-  "  data <- data[complete.cases(data), ]",
-  "  cat(\"Cleaned data:\", nrow(data), \"rows\\n\")",
-  "  return(data)",
-  "}",
-  "",
-  "validate_data <- function(data) {",
-  "  cat(\"Validating data quality...\\n\")",
-  "  stopifnot(nrow(data) > 0)",
-  "  stopifnot(all(c(\"id\", \"value\", \"category\") %in% names(data)))",
-  "  cat(\"Data validation passed\\n\")",
-  "  return(data)",
-  "}",
-  "",
-  "save_data <- function(data, file_path) {",
-  "  write.csv(data, file_path, row.names = FALSE)",
-  "  cat(\"Data saved to:\", file_path, \"\\n\")",
-  "}"
-)
-
-# analysis.R - Analysis functions that depend on utils.R
-analysis_script <- c(
-  "# Analysis functions - sourced by main workflow, depends on utils.R",
-  "# put label:\"Statistical Analysis\", node_type:\"process\", input:\"utils.R\"",
-  "# input: utils.R because we use utility functions",
-  "# output defaults to 'analysis.R'",
-  "",
-  "perform_descriptive_analysis <- function(data) {",
-  "  cat(\"Performing descriptive analysis...\\n\")",
-  "  # Uses validate_data() from utils.R",
-  "  data <- validate_data(data)",
-  "  ",
-  "  summary_stats <- list(",
-  "    mean_value = mean(data$value),",
-  "    sd_value = sd(data$value),",
-  "    n_categories = length(unique(data$category)),",
-  "    date_range = range(data$date)",
-  "  )",
-  "  ",
-  "  cat(\"Analysis complete:\\n\")",
-  "  cat(\"  Mean value:\", round(summary_stats$mean_value, 2), \"\\n\")",
-  "  cat(\"  Categories:\", summary_stats$n_categories, \"\\n\")",
-  "  return(summary_stats)",
-  "}",
-  "",
-  "perform_category_analysis <- function(data) {",
-  "  cat(\"Analyzing by category...\\n\")",
-  "  # Group analysis",
-  "  category_stats <- aggregate(data$value, by = list(data$category), FUN = mean)",
-  "  names(category_stats) <- c(\"category\", \"mean_value\")",
-  "  return(category_stats)",
-  "}"
-)
-
-# visualization.R - Plotting functions that depend on analysis.R
-visualization_script <- c(
-  "# Visualization functions - sourced by main workflow, depends on analysis.R",
-  "# put label:\"Data Visualization\", node_type:\"process\", input:\"analysis.R\"",
-  "# input: analysis.R because we use analysis results",
-  "# output defaults to 'visualization.R'",
-  "",
-  "create_summary_plot <- function(data, output_dir) {",
-  "  cat(\"Creating summary visualizations...\\n\")",
-  "  ",
-  "  # Create simple plots",
-  "  png(file.path(output_dir, \"value_histogram.png\"))",
-  "  hist(data$value, main = \"Distribution of Values\", col = \"lightblue\")",
-  "  dev.off()",
-  "  ",
-  "  png(file.path(output_dir, \"category_boxplot.png\"))",
-  "  boxplot(value ~ category, data = data, main = \"Values by Category\")",
-  "  dev.off()",
-  "  ",
-  "  cat(\"Plots saved to:\", output_dir, \"\\n\")",
-  "}",
-  "",
-  "create_analysis_report <- function(summary_stats, category_stats, output_file) {",
-  "  cat(\"Generating analysis report...\\n\")",
-  "  ",
-  "  report <- c(",
-  "    \"# Data Analysis Report\",",
-  "    paste(\"Generated:\", Sys.time()),",
-  "    \"\",",
-  "    \"## Summary Statistics\",",
-  "    paste(\"- Mean value:\", round(summary_stats$mean_value, 2)),",
-  "    paste(\"- Standard deviation:\", round(summary_stats$sd_value, 2)),",
-  "    paste(\"- Number of categories:\", summary_stats$n_categories),",
-  "    \"\",",
-  "    \"## Category Analysis\",",
-  "    paste(capture.output(print(category_stats)), collapse = \"\\n\")",
-  "  )",
-  "  ",
-  "  writeLines(report, output_file)",
-  "  cat(\"Report saved to:\", output_file, \"\\n\")",
-  "}"
-)
-
-# main.R - Main workflow orchestrator
-main_script <- c(
-  "# Main data science workflow - orchestrates the entire analysis",
-  "# put label:\"Data Science Pipeline\", node_type:\"process\", input:\"utils.R,analysis.R,visualization.R\", output:\"analysis_report.md,plots/\"",
-  "",
-  "# Source all function modules",
-  "source(\"utils.R\")         # Load data utility functions",
-  "source(\"analysis.R\")      # Load statistical analysis functions", 
-  "source(\"visualization.R\") # Load visualization functions",
-  "",
-  "cat(\"🚀 Starting data science pipeline...\\n\\n\")",
-  "",
-  "# Step 1: Data loading and cleaning",
-  "cat(\"Step 1: Data Loading & Cleaning\\n\")",
-  "raw_data <- load_and_clean(\"input_data.csv\")  # Uses utils.R",
-  "",
-  "# Step 2: Statistical analysis",
-  "cat(\"\\nStep 2: Statistical Analysis\\n\")",
-  "summary_stats <- perform_descriptive_analysis(raw_data)  # Uses analysis.R",
-  "category_stats <- perform_category_analysis(raw_data)    # Uses analysis.R",
-  "",
-  "# Step 3: Data visualization",
-  "cat(\"\\nStep 3: Data Visualization\\n\")",
-  "plots_dir <- \"plots\"",
-  "dir.create(plots_dir, showWarnings = FALSE)",
-  "create_summary_plot(raw_data, plots_dir)  # Uses visualization.R",
-  "",
-  "# Step 4: Report generation",
-  "cat(\"\\nStep 4: Report Generation\\n\")",
-  "create_analysis_report(summary_stats, category_stats, \"analysis_report.md\")  # Uses visualization.R",
-  "",
-  "cat(\"\\n✅ Data science pipeline complete!\\n\")",
-  "cat(\"📊 Results available in: analysis_report.md and plots/\\n\")"
-)
-
-# Write all files
-writeLines(utils_script, file.path(temp_dir, "utils.R"))
-writeLines(analysis_script, file.path(temp_dir, "analysis.R"))
-writeLines(visualization_script, file.path(temp_dir, "visualization.R"))
-writeLines(main_script, file.path(temp_dir, "main.R"))
-
-cat("✅ Created modular data science workflow files\n\n")
-
-# Extract and visualize the workflow
-cat("🔍 Extracting modular workflow structure...\n")
-workflow <- put(temp_dir)
-
-cat("\n📊 Workflow structure:\n")
-cat(paste(rep("-", 55), collapse = ""), "\n")
-
-# Display the relationships
-for (i in seq_len(nrow(workflow))) {
-  row <- workflow[i, ]
-  cat(sprintf("%-20s: %s\n", "File", row$file_name))
-  cat(sprintf("%-20s: %s\n", "Label", row$label))
-  cat(sprintf("%-20s: %s\n", "Type", ifelse(is.na(row$node_type), "process", row$node_type)))
-  cat(sprintf("%-20s: %s\n", "Dependencies", ifelse(is.na(row$input), "none", row$input)))
-  cat(sprintf("%-20s: %s\n", "Provides", row$output))
-  cat(paste(rep("-", 55), collapse = ""), "\n")
-}
-
-# Generate diagram
-cat("\n🎨 Modular workflow diagram:\n")
-cat(paste(rep("-", 55), collapse = ""), "\n")
-put_diagram(workflow, 
-            theme = "github", 
-            show_files = TRUE,
-            title = "Data Science Modular Workflow")
-
-cat("\n\n💡 Data Science Pattern Insights:\n")
-cat(paste(rep("=", 55), collapse = ""), "\n")
-cat("1. 📦 MODULARITY: Functions organized by purpose (utils, analysis, viz)\n")
-cat("2. 🔗 DEPENDENCIES: Clear dependency chain (utils → analysis → viz → main)\n")
-cat("3. ♻️  REUSABILITY: Utility functions can be reused across projects\n")
-cat("4. 🔄 SOURCE FLOW: Scripts are sourced INTO the main workflow\n")
-cat("5. 📊 DATA + CODE: Main script handles data, modules provide functions\n\n")
-
-cat("📝 Best Practices Demonstrated:\n")
-cat("• Separate concerns: data handling vs. analysis vs. visualization\n")
-cat("• Clear dependencies: each module declares what it needs\n")
-cat("• Function encapsulation: reusable, testable code modules\n")
-cat("• Orchestration: main script coordinates the entire pipeline\n\n")
-
-cat("🗂️ Example files created in:\n")
-cat("   ", temp_dir, "\n\n")
-
-cat("🚀 Try running the workflow:\n")
-cat("   setwd(\"", temp_dir, "\")\n", sep = "")
-cat("   source(\"main.R\")\n\n")
-
-cat("✅ Data science workflow example complete!\n")
-
-# Clean up
-cat("🧹 Cleaning up...\n")
+# Data Science Workflow Example: Modular Functions with source()
+# ==============================================================================
+# This example demonstrates the most common data science pattern: modularizing
+# functions into separate scripts and orchestrating them in a main workflow.
+#
+# To run this example:
+#   source(system.file("examples", "data-science-workflow.R", package = "putior"))
+# ==============================================================================
+
+library(putior)
+
+cat("🔬 Data Science Workflow Example: Modular source() Pattern\n")
+cat(paste(rep("=", 60), collapse = ""), "\n\n")
+
+# Create example directory structure
+temp_dir <- file.path(tempdir(), "putior_datascience_example")
+dir.create(temp_dir, showWarnings = FALSE)
+
+cat("📁 Creating modular data science workflow...\n")
+
+# utils.R - Utility functions
+utils_script <- c(
+  "# Data utilities - sourced by main workflow",
+  "# put label:\"Data Utilities\", node_type:\"input\"",
+  "# output defaults to 'utils.R' - this script provides itself",
+  "",
+  "load_and_clean <- function(file_path) {",
+  "  cat(\"Loading data from:\", file_path, \"\\n\")",
+  "  # Simulate loading CSV data",
+  "  data <- data.frame(",
+  "    id = 1:100,",
+  "    value = rnorm(100, 50, 10),",
+  "    category = sample(c(\"A\", \"B\", \"C\"), 100, replace = TRUE),",
+  "    date = seq.Date(as.Date(\"2024-01-01\"), by = \"day\", length.out = 100)",
+  "  )",
+  "  ",
+  "  # Clean data",
+  "  data <- data[complete.cases(data), ]",
+  "  cat(\"Cleaned data:\", nrow(data), \"rows\\n\")",
+  "  return(data)",
+  "}",
+  "",
+  "validate_data <- function(data) {",
+  "  cat(\"Validating data quality...\\n\")",
+  "  stopifnot(nrow(data) > 0)",
+  "  stopifnot(all(c(\"id\", \"value\", \"category\") %in% names(data)))",
+  "  cat(\"Data validation passed\\n\")",
+  "  return(data)",
+  "}",
+  "",
+  "save_data <- function(data, file_path) {",
+  "  write.csv(data, file_path, row.names = FALSE)",
+  "  cat(\"Data saved to:\", file_path, \"\\n\")",
+  "}"
+)
+
+# analysis.R - Analysis functions that depend on utils.R
+analysis_script <- c(
+  "# Analysis functions - sourced by main workflow, depends on utils.R",
+  "# put label:\"Statistical Analysis\", node_type:\"process\", input:\"utils.R\"",
+  "# input: utils.R because we use utility functions",
+  "# output defaults to 'analysis.R'",
+  "",
+  "perform_descriptive_analysis <- function(data) {",
+  "  cat(\"Performing descriptive analysis...\\n\")",
+  "  # Uses validate_data() from utils.R",
+  "  data <- validate_data(data)",
+  "  ",
+  "  summary_stats <- list(",
+  "    mean_value = mean(data$value),",
+  "    sd_value = sd(data$value),",
+  "    n_categories = length(unique(data$category)),",
+  "    date_range = range(data$date)",
+  "  )",
+  "  ",
+  "  cat(\"Analysis complete:\\n\")",
+  "  cat(\"  Mean value:\", round(summary_stats$mean_value, 2), \"\\n\")",
+  "  cat(\"  Categories:\", summary_stats$n_categories, \"\\n\")",
+  "  return(summary_stats)",
+  "}",
+  "",
+  "perform_category_analysis <- function(data) {",
+  "  cat(\"Analyzing by category...\\n\")",
+  "  # Group analysis",
+  "  category_stats <- aggregate(data$value, by = list(data$category), FUN = mean)",
+  "  names(category_stats) <- c(\"category\", \"mean_value\")",
+  "  return(category_stats)",
+  "}"
+)
+
+# visualization.R - Plotting functions that depend on analysis.R
+visualization_script <- c(
+  "# Visualization functions - sourced by main workflow, depends on analysis.R",
+  "# put label:\"Data Visualization\", node_type:\"process\", input:\"analysis.R\"",
+  "# input: analysis.R because we use analysis results",
+  "# output defaults to 'visualization.R'",
+  "",
+  "create_summary_plot <- function(data, output_dir) {",
+  "  cat(\"Creating summary visualizations...\\n\")",
+  "  ",
+  "  # Create simple plots",
+  "  png(file.path(output_dir, \"value_histogram.png\"))",
+  "  hist(data$value, main = \"Distribution of Values\", col = \"lightblue\")",
+  "  dev.off()",
+  "  ",
+  "  png(file.path(output_dir, \"category_boxplot.png\"))",
+  "  boxplot(value ~ category, data = data, main = \"Values by Category\")",
+  "  dev.off()",
+  "  ",
+  "  cat(\"Plots saved to:\", output_dir, \"\\n\")",
+  "}",
+  "",
+  "create_analysis_report <- function(summary_stats, category_stats, output_file) {",
+  "  cat(\"Generating analysis report...\\n\")",
+  "  ",
+  "  report <- c(",
+  "    \"# Data Analysis Report\",",
+  "    paste(\"Generated:\", Sys.time()),",
+  "    \"\",",
+  "    \"## Summary Statistics\",",
+  "    paste(\"- Mean value:\", round(summary_stats$mean_value, 2)),",
+  "    paste(\"- Standard deviation:\", round(summary_stats$sd_value, 2)),",
+  "    paste(\"- Number of categories:\", summary_stats$n_categories),",
+  "    \"\",",
+  "    \"## Category Analysis\",",
+  "    paste(capture.output(print(category_stats)), collapse = \"\\n\")",
+  "  )",
+  "  ",
+  "  writeLines(report, output_file)",
+  "  cat(\"Report saved to:\", output_file, \"\\n\")",
+  "}"
+)
+
+# main.R - Main workflow orchestrator
+main_script <- c(
+  "# Main data science workflow - orchestrates the entire analysis",
+  "# put label:\"Data Science Pipeline\", node_type:\"process\", input:\"utils.R,analysis.R,visualization.R\", output:\"analysis_report.md,plots/\"",
+  "",
+  "# Source all function modules",
+  "source(\"utils.R\")         # Load data utility functions",
+  "source(\"analysis.R\")      # Load statistical analysis functions", 
+  "source(\"visualization.R\") # Load visualization functions",
+  "",
+  "cat(\"🚀 Starting data science pipeline...\\n\\n\")",
+  "",
+  "# Step 1: Data loading and cleaning",
+  "cat(\"Step 1: Data Loading & Cleaning\\n\")",
+  "raw_data <- load_and_clean(\"input_data.csv\")  # Uses utils.R",
+  "",
+  "# Step 2: Statistical analysis",
+  "cat(\"\\nStep 2: Statistical Analysis\\n\")",
+  "summary_stats <- perform_descriptive_analysis(raw_data)  # Uses analysis.R",
+  "category_stats <- perform_category_analysis(raw_data)    # Uses analysis.R",
+  "",
+  "# Step 3: Data visualization",
+  "cat(\"\\nStep 3: Data Visualization\\n\")",
+  "plots_dir <- \"plots\"",
+  "dir.create(plots_dir, showWarnings = FALSE)",
+  "create_summary_plot(raw_data, plots_dir)  # Uses visualization.R",
+  "",
+  "# Step 4: Report generation",
+  "cat(\"\\nStep 4: Report Generation\\n\")",
+  "create_analysis_report(summary_stats, category_stats, \"analysis_report.md\")  # Uses visualization.R",
+  "",
+  "cat(\"\\n✅ Data science pipeline complete!\\n\")",
+  "cat(\"📊 Results available in: analysis_report.md and plots/\\n\")"
+)
+
+# Write all files
+writeLines(utils_script, file.path(temp_dir, "utils.R"))
+writeLines(analysis_script, file.path(temp_dir, "analysis.R"))
+writeLines(visualization_script, file.path(temp_dir, "visualization.R"))
+writeLines(main_script, file.path(temp_dir, "main.R"))
+
+cat("✅ Created modular data science workflow files\n\n")
+
+# Extract and visualize the workflow
+cat("🔍 Extracting modular workflow structure...\n")
+workflow <- put(temp_dir)
+
+cat("\n📊 Workflow structure:\n")
+cat(paste(rep("-", 55), collapse = ""), "\n")
+
+# Display the relationships
+for (i in seq_len(nrow(workflow))) {
+  row <- workflow[i, ]
+  cat(sprintf("%-20s: %s\n", "File", row$file_name))
+  cat(sprintf("%-20s: %s\n", "Label", row$label))
+  cat(sprintf("%-20s: %s\n", "Type", ifelse(is.na(row$node_type), "process", row$node_type)))
+  cat(sprintf("%-20s: %s\n", "Dependencies", ifelse(is.na(row$input), "none", row$input)))
+  cat(sprintf("%-20s: %s\n", "Provides", row$output))
+  cat(paste(rep("-", 55), collapse = ""), "\n")
+}
+
+# Generate diagram
+cat("\n🎨 Modular workflow diagram:\n")
+cat(paste(rep("-", 55), collapse = ""), "\n")
+put_diagram(workflow, 
+            theme = "github", 
+            show_files = TRUE,
+            title = "Data Science Modular Workflow")
+
+cat("\n\n💡 Data Science Pattern Insights:\n")
+cat(paste(rep("=", 55), collapse = ""), "\n")
+cat("1. 📦 MODULARITY: Functions organized by purpose (utils, analysis, viz)\n")
+cat("2. 🔗 DEPENDENCIES: Clear dependency chain (utils → analysis → viz → main)\n")
+cat("3. ♻️  REUSABILITY: Utility functions can be reused across projects\n")
+cat("4. 🔄 SOURCE FLOW: Scripts are sourced INTO the main workflow\n")
+cat("5. 📊 DATA + CODE: Main script handles data, modules provide functions\n\n")
+
+cat("📝 Best Practices Demonstrated:\n")
+cat("• Separate concerns: data handling vs. analysis vs. visualization\n")
+cat("• Clear dependencies: each module declares what it needs\n")
+cat("• Function encapsulation: reusable, testable code modules\n")
+cat("• Orchestration: main script coordinates the entire pipeline\n\n")
+
+cat("🗂️ Example files created in:\n")
+cat("   ", temp_dir, "\n\n")
+
+cat("🚀 Try running the workflow:\n")
+cat("   setwd(\"", temp_dir, "\")\n", sep = "")
+cat("   source(\"main.R\")\n\n")
+
+cat("✅ Data science workflow example complete!\n")
+
+# Clean up
+cat("🧹 Cleaning up...\n")
 unlink(temp_dir, recursive = TRUE)
\ No newline at end of file
diff --git a/inst/examples/diagram-example.R b/inst/examples/diagram-example.R
index f5270b0..7cf59d1 100644
--- a/inst/examples/diagram-example.R
+++ b/inst/examples/diagram-example.R
@@ -1,228 +1,228 @@
-# Putior Diagram Example: Workflow Visualization with Mermaid
-# ==============================================================================
-# This example demonstrates putior's visualization capabilities by creating
-# a sample workflow and generating elegant mermaid diagrams.
-#
-# To run this example:
-#   source(system.file("examples", "diagram-example.R", package = "putior"))
-# ==============================================================================
-
-library(putior)
-
-cat("🎨 Putior Diagram Example: Workflow Visualization\n")
-cat(paste(rep("=", 50), collapse = ""), "\n\n")
-
-# Create a sample workflow for demonstration
-temp_dir <- file.path(tempdir(), "putior_diagram_example")
-dir.create(temp_dir, showWarnings = FALSE)
-
-cat("📁 Creating sample workflow files...\n")
-
-# File 1: Data Collection (Python)
-data_collection <- c(
-  "# Data Collection from Multiple Sources",
-  "# put id:\"fetch_sales\", label:\"Fetch Sales Data\", node_type:\"input\", output:\"raw_sales.csv\"",
-  "# put id:\"fetch_customers\", label:\"Fetch Customer Data\", node_type:\"input\", output:\"raw_customers.csv\"",
-  "",
-  "import pandas as pd",
-  "import requests",
-  "",
-  "# Fetch sales data",
-  "sales_data = fetch_api_data('/sales')",
-  "sales_data.to_csv('raw_sales.csv')",
-  "",
-  "# Fetch customer data", 
-  "customer_data = fetch_api_data('/customers')",
-  "customer_data.to_csv('raw_customers.csv')"
-)
-
-# File 2: Data Processing (R)
-data_processing <- c(
-  "# Data Cleaning and Integration", 
-  "# put id:\"clean_sales\", label:\"Clean Sales Data\", node_type:\"process\", input:\"raw_sales.csv\", output:\"clean_sales.csv\"",
-  "# put id:\"clean_customers\", label:\"Clean Customer Data\", node_type:\"process\", input:\"raw_customers.csv\", output:\"clean_customers.csv\"",
-  "# put id:\"merge_data\", label:\"Merge Datasets\", node_type:\"process\", input:\"clean_sales.csv,clean_customers.csv\", output:\"merged_data.csv\"",
-  "",
-  "library(dplyr)",
-  "library(readr)",
-  "",
-  "# Clean sales data",
-  "sales <- read_csv('raw_sales.csv') %>%",
-  "  filter(!is.na(amount)) %>%",
-  "  mutate(date = as.Date(date))",
-  "write_csv(sales, 'clean_sales.csv')",
-  "",
-  "# Clean customer data",
-  "customers <- read_csv('raw_customers.csv') %>%",
-  "  filter(!is.na(customer_id))",
-  "write_csv(customers, 'clean_customers.csv')",
-  "",
-  "# Merge datasets",
-  "merged <- sales %>%",
-  "  left_join(customers, by = 'customer_id')",
-  "write_csv(merged, 'merged_data.csv')"
-)
-
-# File 3: Analysis and Decision Making (R)
-analysis <- c(
-  "# Statistical Analysis and Decision Making",
-  "# put id:\"analyze_trends\", label:\"Analyze Trends\", node_type:\"process\", input:\"merged_data.csv\", output:\"trend_analysis.rds\"",
-  "# put id:\"quality_check\", label:\"Data Quality Check\", node_type:\"decision\", input:\"merged_data.csv\", output:\"quality_report.json\"",
-  "# put id:\"generate_insights\", label:\"Generate Insights\", node_type:\"process\", input:\"trend_analysis.rds\", output:\"insights.rds\"",
-  "",
-  "library(dplyr)",
-  "",
-  "# Analyze trends",
-  "data <- read_csv('merged_data.csv')",
-  "trends <- analyze_time_series(data)",
-  "saveRDS(trends, 'trend_analysis.rds')",
-  "",
-  "# Quality check",
-  "quality <- check_data_quality(data)",
-  "write_json(quality, 'quality_report.json')",
-  "",
-  "# Generate insights",
-  "trends <- readRDS('trend_analysis.rds')",
-  "insights <- generate_business_insights(trends)",
-  "saveRDS(insights, 'insights.rds')"
-)
-
-# File 4: Reporting (R)
-reporting <- c(
-  "# Report Generation and Distribution",
-  "# put id:\"create_dashboard\", label:\"Create Dashboard\", node_type:\"output\", input:\"insights.rds\", output:\"dashboard.html\"",
-  "# put id:\"executive_summary\", label:\"Executive Summary\", node_type:\"output\", input:\"insights.rds\", output:\"executive_summary.pdf\"",
-  "# put id:\"data_export\", label:\"Export Data\", node_type:\"output\", input:\"merged_data.csv\", output:\"final_dataset.xlsx\"",
-  "",
-  "library(rmarkdown)",
-  "library(plotly)",
-  "",
-  "# Create interactive dashboard",
-  "insights <- readRDS('insights.rds')",
-  "render('dashboard_template.Rmd', output_file = 'dashboard.html')",
-  "",
-  "# Generate executive summary", 
-  "render('executive_template.Rmd', output_file = 'executive_summary.pdf')",
-  "",
-  "# Export final dataset",
-  "data <- read_csv('merged_data.csv')",
-  "write_xlsx(data, 'final_dataset.xlsx')"
-)
-
-# Write all files
-writeLines(data_collection, file.path(temp_dir, "01_collect_data.py"))
-writeLines(data_processing, file.path(temp_dir, "02_process_data.R"))
-writeLines(analysis, file.path(temp_dir, "03_analyze_data.R"))
-writeLines(reporting, file.path(temp_dir, "04_generate_reports.R"))
-
-cat("✅ Created", length(list.files(temp_dir)), "workflow files\n\n")
-
-# Extract workflow using putior
-cat("🔍 Extracting workflow with putior...\n")
-workflow <- put(temp_dir)
-
-cat("📊 Found", nrow(workflow), "workflow nodes:\n")
-for (i in seq_len(nrow(workflow))) {
-  row <- workflow[i, ]
-  cat("  -", row$id, "(", row$node_type, "): ", row$label, "\n")
-}
-
-cat("\n", paste(rep("=", 50), collapse = ""), "\n")
-cat("🎨 DIAGRAM EXAMPLES\n")
-cat(paste(rep("=", 50), collapse = ""), "\n\n")
-
-# Example 1: Basic diagram
-cat("📋 Example 1: Basic Top-Down Diagram\n")
-cat(paste(rep("-", 40), collapse = ""), "\n")
-put_diagram(workflow)
-
-cat("\n📋 Example 2: Horizontal Layout with File Labels\n")
-cat(paste(rep("-", 40), collapse = ""), "\n")
-put_diagram(workflow, 
-            direction = "LR", 
-            show_files = TRUE, 
-            title = "Data Processing Pipeline")
-
-cat("\n📋 Example 3: Detailed Labels with Styling\n")
-cat(paste(rep("-", 40), collapse = ""), "\n")
-put_diagram(workflow, 
-            node_labels = "both", 
-            style_nodes = TRUE,
-            title = "Complete Workflow Analysis")
-
-cat("\n📋 Example 4: Process-Only View\n")
-cat(paste(rep("-", 40), collapse = ""), "\n")
-# Filter to show only process nodes
-process_workflow <- workflow[workflow$node_type == "process", ]
-put_diagram(process_workflow, 
-            direction = "LR",
-            title = "Data Processing Steps")
-
-# Example 5: Save to file
-cat("\n💾 Example 5: Saving Diagram to File\n")
-cat(paste(rep("-", 40), collapse = ""), "\n")
-output_file <- file.path(temp_dir, "workflow_diagram.md")
-put_diagram(workflow, 
-            output = "file", 
-            file = output_file,
-            title = "Sales Data Analysis Workflow",
-            show_files = TRUE,
-            style_nodes = TRUE)
-
-cat("📄 Diagram saved to:", output_file, "\n")
-cat("   You can view this in any markdown viewer or GitHub!\n\n")
-
-# Show workflow statistics
-cat("📈 Workflow Statistics:\n")
-cat("   Total nodes:", nrow(workflow), "\n")
-cat("   Input nodes:", sum(workflow$node_type == "input", na.rm = TRUE), "\n")
-cat("   Process nodes:", sum(workflow$node_type == "process", na.rm = TRUE), "\n")
-cat("   Output nodes:", sum(workflow$node_type == "output", na.rm = TRUE), "\n")
-cat("   Decision nodes:", sum(workflow$node_type == "decision", na.rm = TRUE), "\n")
-
-# Show file flow
-cat("\n🔄 Data Flow:\n")
-inputs <- unique(workflow$input[!is.na(workflow$input)])
-outputs <- unique(workflow$output[!is.na(workflow$output)])
-intermediate <- intersect(inputs, outputs)
-external_inputs <- setdiff(inputs, outputs)
-final_outputs <- setdiff(outputs, inputs)
-
-if (length(external_inputs) > 0) {
-  cat("   External inputs:", paste(external_inputs, collapse = ", "), "\n")
-}
-if (length(intermediate) > 0) {
-  cat("   Intermediate files:", paste(intermediate, collapse = ", "), "\n")
-}
-if (length(final_outputs) > 0) {
-  cat("   Final outputs:", paste(final_outputs, collapse = ", "), "\n")
-}
-
-cat("\n", paste(rep("=", 50), collapse = ""), "\n")
-cat("🎯 USAGE TIPS\n")
-cat(paste(rep("=", 50), collapse = ""), "\n\n")
-
-cat("💡 The generated mermaid diagrams can be used in:\n")
-cat("   • GitHub README files (native rendering)\n")
-cat("   • GitLab documentation\n") 
-cat("   • Jupyter notebooks\n")
-cat("   • R Markdown documents\n")
-cat("   • Quarto documents\n")
-cat("   • Any markdown viewer that supports mermaid\n\n")
-
-cat("🔧 Customization options:\n")
-cat("   • direction: 'TD', 'LR', 'BT', 'RL'\n")
-cat("   • node_labels: 'name', 'label', 'both'\n")
-cat("   • show_files: TRUE/FALSE (show file names on arrows)\n")
-cat("   • style_nodes: TRUE/FALSE (color-code by node type)\n")
-cat("   • output: 'console', 'file', 'clipboard'\n\n")
-
-cat("📋 Copy any diagram above and paste it into:\n")
-cat("   • GitHub markdown files\n")
-cat("   • Mermaid live editor: https://mermaid.live\n")
-cat("   • VS Code with mermaid extension\n\n")
-
-cat("🗂️ Example files created in:\n")
-cat("   ", temp_dir, "\n\n")
-
+# Putior Diagram Example: Workflow Visualization with Mermaid
+# ==============================================================================
+# This example demonstrates putior's visualization capabilities by creating
+# a sample workflow and generating elegant mermaid diagrams.
+#
+# To run this example:
+#   source(system.file("examples", "diagram-example.R", package = "putior"))
+# ==============================================================================
+
+library(putior)
+
+cat("🎨 Putior Diagram Example: Workflow Visualization\n")
+cat(paste(rep("=", 50), collapse = ""), "\n\n")
+
+# Create a sample workflow for demonstration
+temp_dir <- file.path(tempdir(), "putior_diagram_example")
+dir.create(temp_dir, showWarnings = FALSE)
+
+cat("📁 Creating sample workflow files...\n")
+
+# File 1: Data Collection (Python)
+data_collection <- c(
+  "# Data Collection from Multiple Sources",
+  "# put id:\"fetch_sales\", label:\"Fetch Sales Data\", node_type:\"input\", output:\"raw_sales.csv\"",
+  "# put id:\"fetch_customers\", label:\"Fetch Customer Data\", node_type:\"input\", output:\"raw_customers.csv\"",
+  "",
+  "import pandas as pd",
+  "import requests",
+  "",
+  "# Fetch sales data",
+  "sales_data = fetch_api_data('/sales')",
+  "sales_data.to_csv('raw_sales.csv')",
+  "",
+  "# Fetch customer data", 
+  "customer_data = fetch_api_data('/customers')",
+  "customer_data.to_csv('raw_customers.csv')"
+)
+
+# File 2: Data Processing (R)
+data_processing <- c(
+  "# Data Cleaning and Integration", 
+  "# put id:\"clean_sales\", label:\"Clean Sales Data\", node_type:\"process\", input:\"raw_sales.csv\", output:\"clean_sales.csv\"",
+  "# put id:\"clean_customers\", label:\"Clean Customer Data\", node_type:\"process\", input:\"raw_customers.csv\", output:\"clean_customers.csv\"",
+  "# put id:\"merge_data\", label:\"Merge Datasets\", node_type:\"process\", input:\"clean_sales.csv,clean_customers.csv\", output:\"merged_data.csv\"",
+  "",
+  "library(dplyr)",
+  "library(readr)",
+  "",
+  "# Clean sales data",
+  "sales <- read_csv('raw_sales.csv') %>%",
+  "  filter(!is.na(amount)) %>%",
+  "  mutate(date = as.Date(date))",
+  "write_csv(sales, 'clean_sales.csv')",
+  "",
+  "# Clean customer data",
+  "customers <- read_csv('raw_customers.csv') %>%",
+  "  filter(!is.na(customer_id))",
+  "write_csv(customers, 'clean_customers.csv')",
+  "",
+  "# Merge datasets",
+  "merged <- sales %>%",
+  "  left_join(customers, by = 'customer_id')",
+  "write_csv(merged, 'merged_data.csv')"
+)
+
+# File 3: Analysis and Decision Making (R)
+analysis <- c(
+  "# Statistical Analysis and Decision Making",
+  "# put id:\"analyze_trends\", label:\"Analyze Trends\", node_type:\"process\", input:\"merged_data.csv\", output:\"trend_analysis.rds\"",
+  "# put id:\"quality_check\", label:\"Data Quality Check\", node_type:\"decision\", input:\"merged_data.csv\", output:\"quality_report.json\"",
+  "# put id:\"generate_insights\", label:\"Generate Insights\", node_type:\"process\", input:\"trend_analysis.rds\", output:\"insights.rds\"",
+  "",
+  "library(dplyr)",
+  "",
+  "# Analyze trends",
+  "data <- read_csv('merged_data.csv')",
+  "trends <- analyze_time_series(data)",
+  "saveRDS(trends, 'trend_analysis.rds')",
+  "",
+  "# Quality check",
+  "quality <- check_data_quality(data)",
+  "write_json(quality, 'quality_report.json')",
+  "",
+  "# Generate insights",
+  "trends <- readRDS('trend_analysis.rds')",
+  "insights <- generate_business_insights(trends)",
+  "saveRDS(insights, 'insights.rds')"
+)
+
+# File 4: Reporting (R)
+reporting <- c(
+  "# Report Generation and Distribution",
+  "# put id:\"create_dashboard\", label:\"Create Dashboard\", node_type:\"output\", input:\"insights.rds\", output:\"dashboard.html\"",
+  "# put id:\"executive_summary\", label:\"Executive Summary\", node_type:\"output\", input:\"insights.rds\", output:\"executive_summary.pdf\"",
+  "# put id:\"data_export\", label:\"Export Data\", node_type:\"output\", input:\"merged_data.csv\", output:\"final_dataset.xlsx\"",
+  "",
+  "library(rmarkdown)",
+  "library(plotly)",
+  "",
+  "# Create interactive dashboard",
+  "insights <- readRDS('insights.rds')",
+  "render('dashboard_template.Rmd', output_file = 'dashboard.html')",
+  "",
+  "# Generate executive summary", 
+  "render('executive_template.Rmd', output_file = 'executive_summary.pdf')",
+  "",
+  "# Export final dataset",
+  "data <- read_csv('merged_data.csv')",
+  "write_xlsx(data, 'final_dataset.xlsx')"
+)
+
+# Write all files
+writeLines(data_collection, file.path(temp_dir, "01_collect_data.py"))
+writeLines(data_processing, file.path(temp_dir, "02_process_data.R"))
+writeLines(analysis, file.path(temp_dir, "03_analyze_data.R"))
+writeLines(reporting, file.path(temp_dir, "04_generate_reports.R"))
+
+cat("✅ Created", length(list.files(temp_dir)), "workflow files\n\n")
+
+# Extract workflow using putior
+cat("🔍 Extracting workflow with putior...\n")
+workflow <- put(temp_dir)
+
+cat("📊 Found", nrow(workflow), "workflow nodes:\n")
+for (i in seq_len(nrow(workflow))) {
+  row <- workflow[i, ]
+  cat("  -", row$id, "(", row$node_type, "): ", row$label, "\n")
+}
+
+cat("\n", paste(rep("=", 50), collapse = ""), "\n")
+cat("🎨 DIAGRAM EXAMPLES\n")
+cat(paste(rep("=", 50), collapse = ""), "\n\n")
+
+# Example 1: Basic diagram
+cat("📋 Example 1: Basic Top-Down Diagram\n")
+cat(paste(rep("-", 40), collapse = ""), "\n")
+put_diagram(workflow)
+
+cat("\n📋 Example 2: Horizontal Layout with File Labels\n")
+cat(paste(rep("-", 40), collapse = ""), "\n")
+put_diagram(workflow, 
+            direction = "LR", 
+            show_files = TRUE, 
+            title = "Data Processing Pipeline")
+
+cat("\n📋 Example 3: Detailed Labels with Styling\n")
+cat(paste(rep("-", 40), collapse = ""), "\n")
+put_diagram(workflow, 
+            node_labels = "both", 
+            style_nodes = TRUE,
+            title = "Complete Workflow Analysis")
+
+cat("\n📋 Example 4: Process-Only View\n")
+cat(paste(rep("-", 40), collapse = ""), "\n")
+# Filter to show only process nodes
+process_workflow <- workflow[workflow$node_type == "process", ]
+put_diagram(process_workflow, 
+            direction = "LR",
+            title = "Data Processing Steps")
+
+# Example 5: Save to file
+cat("\n💾 Example 5: Saving Diagram to File\n")
+cat(paste(rep("-", 40), collapse = ""), "\n")
+output_file <- file.path(temp_dir, "workflow_diagram.md")
+put_diagram(workflow, 
+            output = "file", 
+            file = output_file,
+            title = "Sales Data Analysis Workflow",
+            show_files = TRUE,
+            style_nodes = TRUE)
+
+cat("📄 Diagram saved to:", output_file, "\n")
+cat("   You can view this in any markdown viewer or GitHub!\n\n")
+
+# Show workflow statistics
+cat("📈 Workflow Statistics:\n")
+cat("   Total nodes:", nrow(workflow), "\n")
+cat("   Input nodes:", sum(workflow$node_type == "input", na.rm = TRUE), "\n")
+cat("   Process nodes:", sum(workflow$node_type == "process", na.rm = TRUE), "\n")
+cat("   Output nodes:", sum(workflow$node_type == "output", na.rm = TRUE), "\n")
+cat("   Decision nodes:", sum(workflow$node_type == "decision", na.rm = TRUE), "\n")
+
+# Show file flow
+cat("\n🔄 Data Flow:\n")
+inputs <- unique(workflow$input[!is.na(workflow$input)])
+outputs <- unique(workflow$output[!is.na(workflow$output)])
+intermediate <- intersect(inputs, outputs)
+external_inputs <- setdiff(inputs, outputs)
+final_outputs <- setdiff(outputs, inputs)
+
+if (length(external_inputs) > 0) {
+  cat("   External inputs:", paste(external_inputs, collapse = ", "), "\n")
+}
+if (length(intermediate) > 0) {
+  cat("   Intermediate files:", paste(intermediate, collapse = ", "), "\n")
+}
+if (length(final_outputs) > 0) {
+  cat("   Final outputs:", paste(final_outputs, collapse = ", "), "\n")
+}
+
+cat("\n", paste(rep("=", 50), collapse = ""), "\n")
+cat("🎯 USAGE TIPS\n")
+cat(paste(rep("=", 50), collapse = ""), "\n\n")
+
+cat("💡 The generated mermaid diagrams can be used in:\n")
+cat("   • GitHub README files (native rendering)\n")
+cat("   • GitLab documentation\n") 
+cat("   • Jupyter notebooks\n")
+cat("   • R Markdown documents\n")
+cat("   • Quarto documents\n")
+cat("   • Any markdown viewer that supports mermaid\n\n")
+
+cat("🔧 Customization options:\n")
+cat("   • direction: 'TD', 'LR', 'BT', 'RL'\n")
+cat("   • node_labels: 'name', 'label', 'both'\n")
+cat("   • show_files: TRUE/FALSE (show file names on arrows)\n")
+cat("   • style_nodes: TRUE/FALSE (color-code by node type)\n")
+cat("   • output: 'console', 'file', 'clipboard'\n\n")
+
+cat("📋 Copy any diagram above and paste it into:\n")
+cat("   • GitHub markdown files\n")
+cat("   • Mermaid live editor: https://mermaid.live\n")
+cat("   • VS Code with mermaid extension\n\n")
+
+cat("🗂️ Example files created in:\n")
+cat("   ", temp_dir, "\n\n")
+
 cat("🎨 Happy workflow visualization with putior! 🚀\n")
\ No newline at end of file
diff --git a/inst/examples/generate-readme-examples.R b/inst/examples/generate-readme-examples.R
index 632cffe..0b853c5 100644
--- a/inst/examples/generate-readme-examples.R
+++ b/inst/examples/generate-readme-examples.R
@@ -1,183 +1,183 @@
-#!/usr/bin/env Rscript
-# Generate README.md examples using putior itself
-# This ensures examples always show current themes and styling
-
-library(putior)
-
-cat("🔧 Generating README examples with putior...\n")
-
-# =============================================================================
-# Example 1: Basic Quick Start Workflow
-# =============================================================================
-cat("📊 Generating basic workflow example...\n")
-
-basic_workflow <- data.frame(
-  file_name = c("01_fetch_data.R", "02_clean_data.py"),
-  id = c("fetch_sales", "clean_data"),
-  label = c("Fetch Sales Data", "Clean and Process"),
-  node_type = c("input", "process"),
-  input = c(NA, "sales_data.csv"),
-  output = c("sales_data.csv", "clean_sales.csv"),
-  stringsAsFactors = FALSE
-)
-
-basic_example <- put_diagram(basic_workflow, theme = "github", output = "none")
-
-# =============================================================================
-# Example 2: Workflow Boundaries Demo  
-# =============================================================================
-cat("⚡ Generating workflow boundaries examples...\n")
-
-boundary_workflow <- data.frame(
-  file_name = c("start.R", "extract.R", "transform.R", "end.R"),
-  id = c("pipeline_start", "extract_data", "transform_data", "pipeline_end"),
-  label = c("Data Pipeline Start", "Extract Raw Data", "Transform Data", "Pipeline Complete"),
-  node_type = c("start", "process", "process", "end"),
-  input = c(NA, "raw_config.json", "raw_data.csv", "clean_data.csv"),
-  output = c("raw_config.json", "raw_data.csv", "clean_data.csv", NA),
-  stringsAsFactors = FALSE
-)
-
-# With boundaries (default)
-boundary_with <- put_diagram(boundary_workflow, 
-                           show_workflow_boundaries = TRUE, 
-                           theme = "github", 
-                           output = "none")
-
-# Without boundaries  
-boundary_without <- put_diagram(boundary_workflow, 
-                              show_workflow_boundaries = FALSE, 
-                              theme = "github", 
-                              output = "none")
-
-# =============================================================================
-# Example 3: Data Science Pipeline
-# =============================================================================
-cat("📈 Generating data science pipeline example...\n")
-
-datascience_workflow <- data.frame(
-  file_name = c("01_fetch_sales.R", "02_fetch_customers.R", "03_clean_sales.py", 
-                "04_merge_data.R", "05_analyze.py", "06_report.R"),
-  id = c("fetch_sales", "fetch_customers", "clean_sales", "merge_data", "analyze", "report"),
-  label = c("Fetch Sales Data", "Fetch Customer Data", "Clean Sales Data", 
-            "Merge Datasets", "Statistical Analysis", "Generate Final Report"),
-  node_type = c("input", "input", "process", "process", "process", "output"),
-  input = c(NA, NA, "sales_data.csv", "customers.csv,clean_sales.csv", "merged_data.csv", "analysis_results.csv"),
-  output = c("sales_data.csv", "customers.csv", "clean_sales.csv", "merged_data.csv", "analysis_results.csv", "final_report.pdf"),
-  stringsAsFactors = FALSE
-)
-
-datascience_example <- put_diagram(datascience_workflow, theme = "github", output = "none")
-
-# =============================================================================
-# Example 4: Theme Showcase
-# =============================================================================
-cat("🎨 Generating theme examples...\n")
-
-theme_workflow <- data.frame(
-  file_name = c("fetch.R", "process.R", "report.R"),
-  id = c("fetch_data", "clean_data", "generate_report"),
-  label = c("Fetch API Data", "Clean and Validate", "Generate Final Report"),
-  node_type = c("input", "process", "output"),
-  input = c(NA, "raw_data.csv", "clean_data.csv"),
-  output = c("raw_data.csv", "clean_data.csv", "final_report.html"),
-  stringsAsFactors = FALSE
-)
-
-# Generate all theme examples
-themes <- c("light", "dark", "auto", "github", "minimal")
-theme_examples <- list()
-
-for (theme in themes) {
-  cat("  🎨 Generating", theme, "theme...\n")
-  theme_examples[[theme]] <- put_diagram(theme_workflow, 
-                                        theme = theme, 
-                                        output = "none")
-}
-
-# =============================================================================
-# Example 5: Modular Source Workflow
-# =============================================================================
-cat("📦 Generating modular source workflow...\n")
-
-modular_workflow <- data.frame(
-  file_name = c("utils.R", "analysis.R", "main.R"),
-  id = c("utils", "analysis", "main"),
-  label = c("Data Utilities", "Statistical Analysis", "Main Analysis Pipeline"),
-  node_type = c("input", "process", "process"),
-  input = c(NA, "utils.R", "utils.R,analysis.R"),
-  output = c("utils.R", "analysis.R", "results.csv"),
-  stringsAsFactors = FALSE
-)
-
-# Simple mode
-modular_simple <- put_diagram(modular_workflow, theme = "github", output = "none")
-
-# Artifact mode
-modular_artifacts <- put_diagram(modular_workflow, 
-                                show_artifacts = TRUE, 
-                                theme = "github", 
-                                output = "none")
-
-# =============================================================================
-# Example 6: Simple vs Artifact Comparison
-# =============================================================================
-cat("🔄 Generating simple vs artifact comparison...\n")
-
-comparison_workflow <- data.frame(
-  file_name = c("load.R", "process.R", "analyze.R"),
-  id = c("load", "process", "analyze"),
-  label = c("Load Data", "Process Data", "Analyze"),
-  node_type = c("input", "process", "output"),
-  input = c(NA, "raw_data.csv", "clean_data.csv"),
-  output = c("raw_data.csv", "clean_data.csv", "results.json"),
-  stringsAsFactors = FALSE
-)
-
-# Simple mode
-comparison_simple <- put_diagram(comparison_workflow, 
-                                show_artifacts = FALSE, 
-                                theme = "github", 
-                                output = "none")
-
-# Artifact mode
-comparison_artifacts <- put_diagram(comparison_workflow, 
-                                   show_artifacts = TRUE, 
-                                   theme = "github", 
-                                   output = "none")
-
-# =============================================================================
-# Output Results
-# =============================================================================
-cat("\n✅ Generated all examples!\n\n")
-
-cat("📋 Example outputs:\n")
-cat("==================\n")
-
-examples <- list(
-  "Basic Workflow" = basic_example,
-  "Boundaries Enabled" = boundary_with,
-  "Boundaries Disabled" = boundary_without,
-  "Data Science Pipeline" = datascience_example,
-  "Modular Simple" = modular_simple,
-  "Modular Artifacts" = modular_artifacts,
-  "Comparison Simple" = comparison_simple,
-  "Comparison Artifacts" = comparison_artifacts
-)
-
-# Add theme examples
-for (theme in themes) {
-  examples[[paste("Theme:", theme)]] <- theme_examples[[theme]]
-}
-
-# Save examples to a structured list for potential README integration
-saveRDS(examples, "readme_examples.rds")
-
-cat("💾 Saved examples to readme_examples.rds\n")
-cat("🎯 Ready for README integration!\n")
-
-# Print first example as demonstration
-cat("\n📖 Sample output (Basic Workflow):\n")
-cat("```mermaid\n")
-cat(basic_example)
+#!/usr/bin/env Rscript
+# Generate README.md examples using putior itself
+# This ensures examples always show current themes and styling
+
+library(putior)
+
+cat("🔧 Generating README examples with putior...\n")
+
+# =============================================================================
+# Example 1: Basic Quick Start Workflow
+# =============================================================================
+cat("📊 Generating basic workflow example...\n")
+
+basic_workflow <- data.frame(
+  file_name = c("01_fetch_data.R", "02_clean_data.py"),
+  id = c("fetch_sales", "clean_data"),
+  label = c("Fetch Sales Data", "Clean and Process"),
+  node_type = c("input", "process"),
+  input = c(NA, "sales_data.csv"),
+  output = c("sales_data.csv", "clean_sales.csv"),
+  stringsAsFactors = FALSE
+)
+
+basic_example <- put_diagram(basic_workflow, theme = "github", output = "none")
+
+# =============================================================================
+# Example 2: Workflow Boundaries Demo  
+# =============================================================================
+cat("⚡ Generating workflow boundaries examples...\n")
+
+boundary_workflow <- data.frame(
+  file_name = c("start.R", "extract.R", "transform.R", "end.R"),
+  id = c("pipeline_start", "extract_data", "transform_data", "pipeline_end"),
+  label = c("Data Pipeline Start", "Extract Raw Data", "Transform Data", "Pipeline Complete"),
+  node_type = c("start", "process", "process", "end"),
+  input = c(NA, "raw_config.json", "raw_data.csv", "clean_data.csv"),
+  output = c("raw_config.json", "raw_data.csv", "clean_data.csv", NA),
+  stringsAsFactors = FALSE
+)
+
+# With boundaries (default)
+boundary_with <- put_diagram(boundary_workflow, 
+                           show_workflow_boundaries = TRUE, 
+                           theme = "github", 
+                           output = "none")
+
+# Without boundaries  
+boundary_without <- put_diagram(boundary_workflow, 
+                              show_workflow_boundaries = FALSE, 
+                              theme = "github", 
+                              output = "none")
+
+# =============================================================================
+# Example 3: Data Science Pipeline
+# =============================================================================
+cat("📈 Generating data science pipeline example...\n")
+
+datascience_workflow <- data.frame(
+  file_name = c("01_fetch_sales.R", "02_fetch_customers.R", "03_clean_sales.py", 
+                "04_merge_data.R", "05_analyze.py", "06_report.R"),
+  id = c("fetch_sales", "fetch_customers", "clean_sales", "merge_data", "analyze", "report"),
+  label = c("Fetch Sales Data", "Fetch Customer Data", "Clean Sales Data", 
+            "Merge Datasets", "Statistical Analysis", "Generate Final Report"),
+  node_type = c("input", "input", "process", "process", "process", "output"),
+  input = c(NA, NA, "sales_data.csv", "customers.csv,clean_sales.csv", "merged_data.csv", "analysis_results.csv"),
+  output = c("sales_data.csv", "customers.csv", "clean_sales.csv", "merged_data.csv", "analysis_results.csv", "final_report.pdf"),
+  stringsAsFactors = FALSE
+)
+
+datascience_example <- put_diagram(datascience_workflow, theme = "github", output = "none")
+
+# =============================================================================
+# Example 4: Theme Showcase
+# =============================================================================
+cat("🎨 Generating theme examples...\n")
+
+theme_workflow <- data.frame(
+  file_name = c("fetch.R", "process.R", "report.R"),
+  id = c("fetch_data", "clean_data", "generate_report"),
+  label = c("Fetch API Data", "Clean and Validate", "Generate Final Report"),
+  node_type = c("input", "process", "output"),
+  input = c(NA, "raw_data.csv", "clean_data.csv"),
+  output = c("raw_data.csv", "clean_data.csv", "final_report.html"),
+  stringsAsFactors = FALSE
+)
+
+# Generate all theme examples
+themes <- c("light", "dark", "auto", "github", "minimal")
+theme_examples <- list()
+
+for (theme in themes) {
+  cat("  🎨 Generating", theme, "theme...\n")
+  theme_examples[[theme]] <- put_diagram(theme_workflow, 
+                                        theme = theme, 
+                                        output = "none")
+}
+
+# =============================================================================
+# Example 5: Modular Source Workflow
+# =============================================================================
+cat("📦 Generating modular source workflow...\n")
+
+modular_workflow <- data.frame(
+  file_name = c("utils.R", "analysis.R", "main.R"),
+  id = c("utils", "analysis", "main"),
+  label = c("Data Utilities", "Statistical Analysis", "Main Analysis Pipeline"),
+  node_type = c("input", "process", "process"),
+  input = c(NA, "utils.R", "utils.R,analysis.R"),
+  output = c("utils.R", "analysis.R", "results.csv"),
+  stringsAsFactors = FALSE
+)
+
+# Simple mode
+modular_simple <- put_diagram(modular_workflow, theme = "github", output = "none")
+
+# Artifact mode
+modular_artifacts <- put_diagram(modular_workflow, 
+                                show_artifacts = TRUE, 
+                                theme = "github", 
+                                output = "none")
+
+# =============================================================================
+# Example 6: Simple vs Artifact Comparison
+# =============================================================================
+cat("🔄 Generating simple vs artifact comparison...\n")
+
+comparison_workflow <- data.frame(
+  file_name = c("load.R", "process.R", "analyze.R"),
+  id = c("load", "process", "analyze"),
+  label = c("Load Data", "Process Data", "Analyze"),
+  node_type = c("input", "process", "output"),
+  input = c(NA, "raw_data.csv", "clean_data.csv"),
+  output = c("raw_data.csv", "clean_data.csv", "results.json"),
+  stringsAsFactors = FALSE
+)
+
+# Simple mode
+comparison_simple <- put_diagram(comparison_workflow, 
+                                show_artifacts = FALSE, 
+                                theme = "github", 
+                                output = "none")
+
+# Artifact mode
+comparison_artifacts <- put_diagram(comparison_workflow, 
+                                   show_artifacts = TRUE, 
+                                   theme = "github", 
+                                   output = "none")
+
+# =============================================================================
+# Output Results
+# =============================================================================
+cat("\n✅ Generated all examples!\n\n")
+
+cat("📋 Example outputs:\n")
+cat("==================\n")
+
+examples <- list(
+  "Basic Workflow" = basic_example,
+  "Boundaries Enabled" = boundary_with,
+  "Boundaries Disabled" = boundary_without,
+  "Data Science Pipeline" = datascience_example,
+  "Modular Simple" = modular_simple,
+  "Modular Artifacts" = modular_artifacts,
+  "Comparison Simple" = comparison_simple,
+  "Comparison Artifacts" = comparison_artifacts
+)
+
+# Add theme examples
+for (theme in themes) {
+  examples[[paste("Theme:", theme)]] <- theme_examples[[theme]]
+}
+
+# Save examples to a structured list for potential README integration
+saveRDS(examples, "readme_examples.rds")
+
+cat("💾 Saved examples to readme_examples.rds\n")
+cat("🎯 Ready for README integration!\n")
+
+# Print first example as demonstration
+cat("\n📖 Sample output (Basic Workflow):\n")
+cat("```mermaid\n")
+cat(basic_example)
 cat("\n```\n")
\ No newline at end of file
diff --git a/inst/examples/hex-sticker-research.R b/inst/examples/hex-sticker-research.R
index bb31d8d..4b87d58 100644
--- a/inst/examples/hex-sticker-research.R
+++ b/inst/examples/hex-sticker-research.R
@@ -1,199 +1,199 @@
-# Research on creating reproducible hex stickers for putior
-# Comparing different approaches for creating complex hex stickers
-
-# Required libraries
-library(ggplot2)
-library(grid)
-library(ggraph)
-library(igraph)
-library(showtext)
-
-# Approach 1: hexSticker package (requires installation)
-# The hexSticker package is the standard tool for creating hex stickers
-# Pros:
-# - Purpose-built for hex stickers
-# - Handles fonts, borders, and positioning automatically
-# - Supports both ggplot2 plots and images as input
-# - Built-in hexagon shape
-# Cons:
-# - Limited customization for complex designs
-# - May need workarounds for multiple elements
-# - Package not currently installed
-
-# Example structure (would work if hexSticker was installed):
-# library(hexSticker)
-# # Create a base plot with network visualization
-# g <- make_graph(~ 1-2-3-4-5, 1-3, 1-4, 2-5)
-# p <- ggraph(g, layout = 'fr') +
-#   geom_edge_link(color = "white", alpha = 0.5) +
-#   geom_node_point(color = "white", size = 3) +
-#   theme_void()
-# 
-# sticker(p, 
-#         package = "putior",
-#         p_size = 20,
-#         s_x = 1,
-#         s_y = 0.8,
-#         s_width = 1.3,
-#         s_height = 1,
-#         h_fill = "#6B5B95",
-#         h_color = "#000000",
-#         filename = "hex_hexsticker.png")
-
-# Approach 2: Pure ggplot2 with custom hexagon
-# Pros:
-# - Full control over every element
-# - No additional dependencies beyond ggplot2
-# - Can layer multiple elements easily
-# - Supports gradients via scale_fill_gradient
-# Cons:
-# - More code required
-# - Need to manually create hexagon shape
-# - Font handling more complex
-
-create_hexagon <- function(center_x = 0, center_y = 0, size = 1) {
-  angles <- seq(30, 330, by = 60) * pi / 180
-  data.frame(
-    x = center_x + size * cos(angles),
-    y = center_y + size * sin(angles)
-  )
-}
-
-# Create network data
-set.seed(42)
-nodes <- data.frame(
-  x = c(0.3, 0.7, 0.5, 0.2, 0.8, 0.4, 0.6),
-  y = c(0.7, 0.7, 0.5, 0.3, 0.3, 0.4, 0.6),
-  size = c(3, 3, 2, 2, 2, 1.5, 1.5)
-)
-
-edges <- data.frame(
-  x = c(0.3, 0.3, 0.7, 0.5, 0.2, 0.4),
-  y = c(0.7, 0.7, 0.7, 0.5, 0.3, 0.4),
-  xend = c(0.5, 0.2, 0.8, 0.4, 0.4, 0.6),
-  yend = c(0.5, 0.3, 0.3, 0.4, 0.4, 0.6)
-)
-
-# Create document icons data
-docs <- data.frame(
-  x = c(0.15, 0.12, 0.18),
-  y = c(0.75, 0.72, 0.78),
-  label = c("# put", "# put", "# put"),
-  size = c(4, 3.5, 3)
-)
-
-# Create ggplot2 hex sticker
-hex_ggplot <- ggplot() +
-  # Hexagon background with gradient effect
-  geom_polygon(data = create_hexagon(0.5, 0.5, 0.48),
-               aes(x, y), fill = "#6B5B95", color = NA) +
-  geom_polygon(data = create_hexagon(0.5, 0.5, 0.5),
-               aes(x, y), fill = NA, color = "black", size = 2) +
-  # Network edges
-  geom_segment(data = edges,
-               aes(x = x, y = y, xend = xend, yend = yend),
-               color = "white", alpha = 0.3, size = 0.5) +
-  # Network nodes
-  geom_point(data = nodes,
-             aes(x, y, size = size),
-             color = "white", alpha = 0.8) +
-  # Document icons (simplified as rectangles with text)
-  geom_rect(data = docs,
-            aes(xmin = x - 0.03, xmax = x + 0.03,
-                ymin = y - 0.02, ymax = y + 0.02),
-            fill = "white", alpha = 0.9) +
-  geom_text(data = docs,
-            aes(x, y, label = label, size = size),
-            color = "#6B5B95", family = "mono") +
-  # Package name
-  annotate("text", x = 0.5, y = 0.1, label = "putior",
-           size = 8, color = "white", fontface = "bold") +
-  # Styling
-  scale_size_identity() +
-  coord_fixed() +
-  theme_void() +
-  theme(plot.margin = margin(0, 0, 0, 0))
-
-# Approach 3: Grid graphics
-# Pros:
-# - Low-level control
-# - Can create exact shapes and gradients
-# - Efficient for complex custom graphics
-# Cons:
-# - Steeper learning curve
-# - More verbose code
-# - Less integration with data visualization tools
-
-create_hex_grid <- function() {
-  grid.newpage()
-  
-  # Define hexagon vertices
-  angles <- seq(30, 330, by = 60) * pi / 180
-  hex_x <- 0.5 + 0.4 * cos(angles)
-  hex_y <- 0.5 + 0.4 * sin(angles)
-  
-  # Create gradient background
-  gradient <- linearGradient(
-    colours = c("#4B4B6B", "#6B5B95", "#8B7BA5"),
-    x1 = 0, y1 = 1, x2 = 0, y2 = 0
-  )
-  
-  # Draw hexagon with gradient
-  grid.polygon(x = hex_x, y = hex_y,
-               gp = gpar(fill = "#6B5B95", col = "black", lwd = 3))
-  
-  # Add network elements
-  # ... (would add circles, lines, text using grid functions)
-  
-  # Add text
-  grid.text("putior", x = 0.5, y = 0.1,
-            gp = gpar(col = "white", fontsize = 24, fontface = "bold"))
-}
-
-# Approach 4: Hybrid approach - ggplot2 + hexSticker
-# Pros:
-# - Best of both worlds
-# - Create complex plot in ggplot2, use hexSticker for final formatting
-# - Handles fonts and borders well
-# Cons:
-# - Requires hexSticker package
-
-# Approach 5: Using additional packages
-# - ggraph: Excellent for network visualizations
-# - patchwork: Combine multiple plots
-# - ggforce: Additional geoms for complex shapes
-# - gganimate: For animated hex stickers
-
-# Recommendation for putior hex sticker:
-# 
-# Given the requirements:
-# 1. Multiple document/file icons
-# 2. Network/graph visualization
-# 3. Gradient background
-# 4. Text elements
-# 
-# Best approach: Pure ggplot2 or ggplot2 + hexSticker
-# 
-# Pure ggplot2 advantages:
-# - No additional dependencies
-# - Full control over all elements
-# - Can create gradient effects with multiple polygons
-# - Easy to maintain and modify
-# 
-# Implementation strategy:
-# 1. Create hexagon shape as polygon
-# 2. Layer gradient effect with multiple semi-transparent polygons
-# 3. Use ggraph or manual positioning for network elements
-# 4. Add document shapes as rectangles or custom polygons
-# 5. Use annotate() or geom_text() for text elements
-# 6. Export with ggsave() at appropriate resolution
-
-# Example implementation starter:
-create_putior_hex <- function() {
-  # This would be the full implementation
-  # combining all elements shown above
-  # with proper styling and positioning
-}
-
-# Save examples
+# Research on creating reproducible hex stickers for putior
+# Comparing different approaches for creating complex hex stickers
+
+# Required libraries
+library(ggplot2)
+library(grid)
+library(ggraph)
+library(igraph)
+library(showtext)
+
+# Approach 1: hexSticker package (requires installation)
+# The hexSticker package is the standard tool for creating hex stickers
+# Pros:
+# - Purpose-built for hex stickers
+# - Handles fonts, borders, and positioning automatically
+# - Supports both ggplot2 plots and images as input
+# - Built-in hexagon shape
+# Cons:
+# - Limited customization for complex designs
+# - May need workarounds for multiple elements
+# - Package not currently installed
+
+# Example structure (would work if hexSticker was installed):
+# library(hexSticker)
+# # Create a base plot with network visualization
+# g <- make_graph(~ 1-2-3-4-5, 1-3, 1-4, 2-5)
+# p <- ggraph(g, layout = 'fr') +
+#   geom_edge_link(color = "white", alpha = 0.5) +
+#   geom_node_point(color = "white", size = 3) +
+#   theme_void()
+# 
+# sticker(p, 
+#         package = "putior",
+#         p_size = 20,
+#         s_x = 1,
+#         s_y = 0.8,
+#         s_width = 1.3,
+#         s_height = 1,
+#         h_fill = "#6B5B95",
+#         h_color = "#000000",
+#         filename = "hex_hexsticker.png")
+
+# Approach 2: Pure ggplot2 with custom hexagon
+# Pros:
+# - Full control over every element
+# - No additional dependencies beyond ggplot2
+# - Can layer multiple elements easily
+# - Supports gradients via scale_fill_gradient
+# Cons:
+# - More code required
+# - Need to manually create hexagon shape
+# - Font handling more complex
+
+create_hexagon <- function(center_x = 0, center_y = 0, size = 1) {
+  angles <- seq(30, 330, by = 60) * pi / 180
+  data.frame(
+    x = center_x + size * cos(angles),
+    y = center_y + size * sin(angles)
+  )
+}
+
+# Create network data
+set.seed(42)
+nodes <- data.frame(
+  x = c(0.3, 0.7, 0.5, 0.2, 0.8, 0.4, 0.6),
+  y = c(0.7, 0.7, 0.5, 0.3, 0.3, 0.4, 0.6),
+  size = c(3, 3, 2, 2, 2, 1.5, 1.5)
+)
+
+edges <- data.frame(
+  x = c(0.3, 0.3, 0.7, 0.5, 0.2, 0.4),
+  y = c(0.7, 0.7, 0.7, 0.5, 0.3, 0.4),
+  xend = c(0.5, 0.2, 0.8, 0.4, 0.4, 0.6),
+  yend = c(0.5, 0.3, 0.3, 0.4, 0.4, 0.6)
+)
+
+# Create document icons data
+docs <- data.frame(
+  x = c(0.15, 0.12, 0.18),
+  y = c(0.75, 0.72, 0.78),
+  label = c("# put", "# put", "# put"),
+  size = c(4, 3.5, 3)
+)
+
+# Create ggplot2 hex sticker
+hex_ggplot <- ggplot() +
+  # Hexagon background with gradient effect
+  geom_polygon(data = create_hexagon(0.5, 0.5, 0.48),
+               aes(x, y), fill = "#6B5B95", color = NA) +
+  geom_polygon(data = create_hexagon(0.5, 0.5, 0.5),
+               aes(x, y), fill = NA, color = "black", size = 2) +
+  # Network edges
+  geom_segment(data = edges,
+               aes(x = x, y = y, xend = xend, yend = yend),
+               color = "white", alpha = 0.3, size = 0.5) +
+  # Network nodes
+  geom_point(data = nodes,
+             aes(x, y, size = size),
+             color = "white", alpha = 0.8) +
+  # Document icons (simplified as rectangles with text)
+  geom_rect(data = docs,
+            aes(xmin = x - 0.03, xmax = x + 0.03,
+                ymin = y - 0.02, ymax = y + 0.02),
+            fill = "white", alpha = 0.9) +
+  geom_text(data = docs,
+            aes(x, y, label = label, size = size),
+            color = "#6B5B95", family = "mono") +
+  # Package name
+  annotate("text", x = 0.5, y = 0.1, label = "putior",
+           size = 8, color = "white", fontface = "bold") +
+  # Styling
+  scale_size_identity() +
+  coord_fixed() +
+  theme_void() +
+  theme(plot.margin = margin(0, 0, 0, 0))
+
+# Approach 3: Grid graphics
+# Pros:
+# - Low-level control
+# - Can create exact shapes and gradients
+# - Efficient for complex custom graphics
+# Cons:
+# - Steeper learning curve
+# - More verbose code
+# - Less integration with data visualization tools
+
+create_hex_grid <- function() {
+  grid.newpage()
+  
+  # Define hexagon vertices
+  angles <- seq(30, 330, by = 60) * pi / 180
+  hex_x <- 0.5 + 0.4 * cos(angles)
+  hex_y <- 0.5 + 0.4 * sin(angles)
+  
+  # Create gradient background
+  gradient <- linearGradient(
+    colours = c("#4B4B6B", "#6B5B95", "#8B7BA5"),
+    x1 = 0, y1 = 1, x2 = 0, y2 = 0
+  )
+  
+  # Draw hexagon with gradient
+  grid.polygon(x = hex_x, y = hex_y,
+               gp = gpar(fill = "#6B5B95", col = "black", lwd = 3))
+  
+  # Add network elements
+  # ... (would add circles, lines, text using grid functions)
+  
+  # Add text
+  grid.text("putior", x = 0.5, y = 0.1,
+            gp = gpar(col = "white", fontsize = 24, fontface = "bold"))
+}
+
+# Approach 4: Hybrid approach - ggplot2 + hexSticker
+# Pros:
+# - Best of both worlds
+# - Create complex plot in ggplot2, use hexSticker for final formatting
+# - Handles fonts and borders well
+# Cons:
+# - Requires hexSticker package
+
+# Approach 5: Using additional packages
+# - ggraph: Excellent for network visualizations
+# - patchwork: Combine multiple plots
+# - ggforce: Additional geoms for complex shapes
+# - gganimate: For animated hex stickers
+
+# Recommendation for putior hex sticker:
+# 
+# Given the requirements:
+# 1. Multiple document/file icons
+# 2. Network/graph visualization
+# 3. Gradient background
+# 4. Text elements
+# 
+# Best approach: Pure ggplot2 or ggplot2 + hexSticker
+# 
+# Pure ggplot2 advantages:
+# - No additional dependencies
+# - Full control over all elements
+# - Can create gradient effects with multiple polygons
+# - Easy to maintain and modify
+# 
+# Implementation strategy:
+# 1. Create hexagon shape as polygon
+# 2. Layer gradient effect with multiple semi-transparent polygons
+# 3. Use ggraph or manual positioning for network elements
+# 4. Add document shapes as rectangles or custom polygons
+# 5. Use annotate() or geom_text() for text elements
+# 6. Export with ggsave() at appropriate resolution
+
+# Example implementation starter:
+create_putior_hex <- function() {
+  # This would be the full implementation
+  # combining all elements shown above
+  # with proper styling and positioning
+}
+
+# Save examples
 # ggsave("hex_ggplot.png", hex_ggplot, width = 2, height = 2, dpi = 300)
\ No newline at end of file
diff --git a/inst/examples/multiline-example.R b/inst/examples/multiline-example.R
index 8eb5cf4..953c8d8 100644
--- a/inst/examples/multiline-example.R
+++ b/inst/examples/multiline-example.R
@@ -1,77 +1,77 @@
-# Multiline PUT Annotation Example
-# 
-# This example demonstrates how to use multiline annotations 
-# for better code style compliance when dealing with long lists
-# of input/output files.
-
-library(putior)
-
-# Create temporary directory for example
-temp_dir <- tempdir()
-example_dir <- file.path(temp_dir, "multiline_example")
-dir.create(example_dir, showWarnings = FALSE)
-
-# Example 1: Traditional single-line annotation (can get very long)
-single_line_content <- c(
-  "# Traditional approach - can be very long and violate style guidelines",
-  "# put id:\"data_merger\", label:\"Merge Multiple Data Sources\", node_type:\"process\", input:\"sales_data.csv,customer_data.csv,product_data.csv,inventory_data.csv,returns_data.csv\", output:\"merged_dataset.csv\"",
-  "",
-  "# Simulate data merging code",
-  "cat(\"Merging multiple data sources...\\n\")"
-)
-
-# Example 2: Multiline annotation (more readable and style-compliant)
-multiline_content <- c(
-  "# Multiline approach - readable and follows style guidelines",
-  "# put id:\"data_processor\", \\",
-  "#    label:\"Advanced Data Processing Pipeline\", \\",
-  "#    node_type:\"process\", \\",
-  "#    input:\"raw_sales.csv,customer_profiles.csv,product_catalog.csv,inventory_status.csv,returns_log.csv\", \\",
-  "#    output:\"processed_dataset.csv,summary_report.csv\"",
-  "",
-  "# Simulate advanced processing code",
-  "cat(\"Processing data with complex transformations...\\n\")",
-  "",
-  "# Another multiline example",
-  "# put id:\"visualization_generator\", \\",
-  "#    label:\"Generate Comprehensive Visualizations\", \\",
-  "#    node_type:\"output\", \\",
-  "#    input:\"processed_dataset.csv,summary_report.csv\", \\",
-  "#    output:\"dashboard.html,charts.png,summary_plots.pdf\"",
-  "",
-  "cat(\"Generating visualizations...\\n\")"
-)
-
-# Write example files
-writeLines(single_line_content, file.path(example_dir, "01_single_line.R"))
-writeLines(multiline_content, file.path(example_dir, "02_multiline.R"))
-
-# Extract workflow from both approaches
-cat("\\n=== Extracting PUT annotations ===\\n")
-workflow <- put(example_dir)
-
-# Display results
-cat("\\nFound", nrow(workflow), "annotations:\\n")
-for (i in 1:nrow(workflow)) {
-  cat("\\n", i, ". ID:", workflow$id[i], "\\n")
-  cat("   Label:", workflow$label[i], "\\n")
-  cat("   Input:", workflow$input[i], "\\n")
-  cat("   Output:", workflow$output[i], "\\n")
-}
-
-# Generate diagram
-cat("\\n=== Generated Mermaid Diagram ===\\n")
-diagram <- put_diagram(workflow, theme = "minimal")
-cat(diagram)
-
-# Key benefits of multiline annotations:
-cat("\\n\\n=== Benefits of Multiline Annotations ===\\n")
-cat("1. Better code readability\\n")
-cat("2. Compliance with style guidelines (e.g., styler)\\n")
-cat("3. Easier maintenance of long parameter lists\\n")
-cat("4. Consistent indentation with surrounding code\\n")
-cat("5. No change to existing functionality\\n")
-
-# Cleanup
-unlink(example_dir, recursive = TRUE)
+# Multiline PUT Annotation Example
+# 
+# This example demonstrates how to use multiline annotations 
+# for better code style compliance when dealing with long lists
+# of input/output files.
+
+library(putior)
+
+# Create temporary directory for example
+temp_dir <- tempdir()
+example_dir <- file.path(temp_dir, "multiline_example")
+dir.create(example_dir, showWarnings = FALSE)
+
+# Example 1: Traditional single-line annotation (can get very long)
+single_line_content <- c(
+  "# Traditional approach - can be very long and violate style guidelines",
+  "# put id:\"data_merger\", label:\"Merge Multiple Data Sources\", node_type:\"process\", input:\"sales_data.csv,customer_data.csv,product_data.csv,inventory_data.csv,returns_data.csv\", output:\"merged_dataset.csv\"",
+  "",
+  "# Simulate data merging code",
+  "cat(\"Merging multiple data sources...\\n\")"
+)
+
+# Example 2: Multiline annotation (more readable and style-compliant)
+multiline_content <- c(
+  "# Multiline approach - readable and follows style guidelines",
+  "# put id:\"data_processor\", \\",
+  "#    label:\"Advanced Data Processing Pipeline\", \\",
+  "#    node_type:\"process\", \\",
+  "#    input:\"raw_sales.csv,customer_profiles.csv,product_catalog.csv,inventory_status.csv,returns_log.csv\", \\",
+  "#    output:\"processed_dataset.csv,summary_report.csv\"",
+  "",
+  "# Simulate advanced processing code",
+  "cat(\"Processing data with complex transformations...\\n\")",
+  "",
+  "# Another multiline example",
+  "# put id:\"visualization_generator\", \\",
+  "#    label:\"Generate Comprehensive Visualizations\", \\",
+  "#    node_type:\"output\", \\",
+  "#    input:\"processed_dataset.csv,summary_report.csv\", \\",
+  "#    output:\"dashboard.html,charts.png,summary_plots.pdf\"",
+  "",
+  "cat(\"Generating visualizations...\\n\")"
+)
+
+# Write example files
+writeLines(single_line_content, file.path(example_dir, "01_single_line.R"))
+writeLines(multiline_content, file.path(example_dir, "02_multiline.R"))
+
+# Extract workflow from both approaches
+cat("\\n=== Extracting PUT annotations ===\\n")
+workflow <- put(example_dir)
+
+# Display results
+cat("\\nFound", nrow(workflow), "annotations:\\n")
+for (i in 1:nrow(workflow)) {
+  cat("\\n", i, ". ID:", workflow$id[i], "\\n")
+  cat("   Label:", workflow$label[i], "\\n")
+  cat("   Input:", workflow$input[i], "\\n")
+  cat("   Output:", workflow$output[i], "\\n")
+}
+
+# Generate diagram
+cat("\\n=== Generated Mermaid Diagram ===\\n")
+diagram <- put_diagram(workflow, theme = "minimal")
+cat(diagram)
+
+# Key benefits of multiline annotations:
+cat("\\n\\n=== Benefits of Multiline Annotations ===\\n")
+cat("1. Better code readability\\n")
+cat("2. Compliance with style guidelines (e.g., styler)\\n")
+cat("3. Easier maintenance of long parameter lists\\n")
+cat("4. Consistent indentation with surrounding code\\n")
+cat("5. No change to existing functionality\\n")
+
+# Cleanup
+unlink(example_dir, recursive = TRUE)
 cat("\\nExample completed! Temporary files cleaned up.\\n")
\ No newline at end of file
diff --git a/inst/examples/reprex.R b/inst/examples/reprex.R
index 8faba4d..edbc6a0 100644
--- a/inst/examples/reprex.R
+++ b/inst/examples/reprex.R
@@ -1,201 +1,201 @@
-# Putior Package Example: Workflow Extraction
-# ==============================================================================
-# This example demonstrates putior's core functionality by creating a sample
-# multi-language data workflow and extracting its structure using PUT annotations.
-#
-# To run this example:
-#   source(system.file("examples", "reprex.R", package = "putior"))
-# ==============================================================================
-
-library(putior)
-
-# Create temporary directory for example files
-temp_dir <- file.path(tempdir(), "putior_workflow_example")
-dir.create(temp_dir, showWarnings = FALSE)
-
-cat("Creating example workflow in:", temp_dir, "\n")
-
-# ==============================================================================
-# CREATE SAMPLE WORKFLOW FILES
-# ==============================================================================
-
-# File 1: Data Collection (Python script)
-# Demonstrates: input node with output annotation
-file1_lines <- c(
-  "# Data Collection Script",
-  "# put id:\"collect_data\", label:\"Collect Raw Data\", node_type:\"input\", output:\"raw_data.csv\"",
-  "",
-  "import pandas as pd",
-  "import requests",
-  "",
-  "def collect_sales_data():",
-  "    \"\"\"Collect sales data from API\"\"\"",
-  "    # Simulate API call",
-  "    data = pd.DataFrame({",
-  "        \"date\": [\"2024-01-01\", \"2024-01-02\", \"2024-01-03\"],",
-  "        \"sales\": [100, 150, 120],",
-  "        \"region\": [\"North\", \"South\", \"East\"]",
-  "    })",
-  "    data.to_csv(\"raw_data.csv\", index=False)",
-  "    return data",
-  "",
-  "if __name__ == \"__main__\":",
-  "    collect_sales_data()"
-)
-
-# File 2: Data Processing (R script)
-# Demonstrates: process node with input and output annotations
-file2_lines <- c(
-  "# Data Processing Script",
-  "# put id:\"process_data\", label:\"Clean and Transform Data\", node_type:\"process\", input:\"raw_data.csv\", output:\"processed_data.csv\"",
-  "",
-  "library(dplyr)",
-  "library(readr)",
-  "",
-  "# Read raw data",
-  "raw_data <- read_csv(\"raw_data.csv\")",
-  "",
-  "# Clean and process data",
-  "processed_data <- raw_data %>%",
-  "  mutate(",
-  "    date = as.Date(date),",
-  "    sales_category = case_when(",
-  "      sales < 110 ~ \"Low\",",
-  "      sales < 140 ~ \"Medium\",",
-  "      TRUE ~ \"High\"",
-  "    )",
-  "  ) %>%",
-  "  arrange(date)",
-  "",
-  "# Save processed data",
-  "write_csv(processed_data, \"processed_data.csv\")"
-)
-
-# File 3: Analysis and Reporting (R script)
-# Demonstrates: multiple PUT annotations in one file
-file3_lines <- c(
-  "# Analysis and Reporting Script",
-  "# put id:\"create_report\", label:\"Generate Sales Report\", node_type:\"output\", input:\"processed_data.csv\", output:\"sales_report.html\"",
-  "# put id:\"create_summary\", label:\"Calculate Summary Stats\", node_type:\"process\", input:\"processed_data.csv\", output:\"summary_stats.json\"",
-  "",
-  "library(dplyr)",
-  "library(readr)",
-  "library(jsonlite)",
-  "",
-  "# Read processed data",
-  "data <- read_csv(\"processed_data.csv\")",
-  "",
-  "# Create summary statistics",
-  "summary_stats <- list(",
-  "  total_sales = sum(data$sales),",
-  "  avg_sales = mean(data$sales),",
-  "  sales_by_category = data %>%",
-  "    count(sales_category) %>%",
-  "    setNames(c(\"category\", \"count\"))",
-  ")",
-  "",
-  "# Save summary as JSON",
-  "write_json(summary_stats, \"summary_stats.json\", pretty = TRUE)",
-  "",
-  "# Generate HTML report (simplified)",
-  "report_html <- paste0(",
-  "  \"<html><body>\",",
-  "  \"<h1>Sales Report</h1>\",",
-  "  \"<p>Total Sales: \", summary_stats$total_sales, \"</p>\",",
-  "  \"<p>Average Sales: \", round(summary_stats$avg_sales, 2), \"</p>\",",
-  "  \"</body></html>\"",
-  ")",
-  "",
-  "writeLines(report_html, \"sales_report.html\")"
-)
-
-# Write example files
-writeLines(file1_lines, file.path(temp_dir, "01_collect_data.py"))
-writeLines(file2_lines, file.path(temp_dir, "02_process_data.R"))
-writeLines(file3_lines, file.path(temp_dir, "03_analyze_report.R"))
-
-cat("Created", length(list.files(temp_dir)), "example files\n")
-
-# ==============================================================================
-# EXTRACT WORKFLOW USING PUTIOR
-# ==============================================================================
-
-cat("\n=== Extracting workflow with putior::put() ===\n")
-workflow <- put(temp_dir)
-
-# Display results
-cat("\nWorkflow extraction results:\n")
-print(workflow)
-
-# ==============================================================================
-# ANALYZE WORKFLOW STRUCTURE
-# ==============================================================================
-
-if (nrow(workflow) > 0) {
-  
-  cat("\n=== Workflow Analysis ===\n")
-  
-  # Data lineage summary
-  cat("\nData Flow Summary:\n")
-  inputs <- unique(workflow$input[!is.na(workflow$input)])
-  outputs <- unique(workflow$output[!is.na(workflow$output)])
-  
-  cat("  External Inputs:", setdiff(inputs, outputs), "\n")
-  cat("  Intermediate Files:", intersect(inputs, outputs), "\n") 
-  cat("  Final Outputs:", setdiff(outputs, inputs), "\n")
-  
-  # Node types
-  cat("\nNode Types:\n")
-  node_types <- table(workflow$node_type)
-  for (i in seq_along(node_types)) {
-    cat("  ", names(node_types)[i], ":", node_types[i], "nodes\n")
-  }
-  
-  # File types
-  cat("\nFile Types:\n")
-  file_types <- table(workflow$file_type)
-  for (i in seq_along(file_types)) {
-    cat("  ", toupper(names(file_types)[i]), ":", file_types[i], "files\n")
-  }
-  
-  # Detailed workflow steps
-  cat("\nDetailed Workflow Steps:\n")
-  for (i in 1:nrow(workflow)) {
-    row <- workflow[i, ]
-    cat("  Step", i, ":", row$id, "\n")
-    cat("    File:", row$file_name, "(", row$file_type, ")\n")
-    cat("    Action:", row$label, "\n")
-    cat("    Type:", row$node_type, "\n")
-    if (!is.na(row$input)) cat("    Consumes:", row$input, "\n")
-    if (!is.na(row$output)) cat("    Produces:", row$output, "\n")
-    cat("\n")
-  }
-  
-} else {
-  cat("No workflow annotations found. Check PUT annotation syntax.\n")
-}
-
-# ==============================================================================
-# CLEANUP AND NEXT STEPS
-# ==============================================================================
-
-cat("=== Example Complete ===\n")
-cat("Example files location:", temp_dir, "\n")
-cat("\nTo explore further:\n")
-cat("1. Examine the generated files to see PUT annotation syntax\n")
-cat("2. Try modifying annotations and re-running put()\n")
-cat("3. Add your own workflow files with PUT annotations\n")
-
-# Optional: Clean up temporary files
-cat("\nClean up temporary files? (y/n): ")
-if (interactive()) {
-  response <- readline()
-  if (tolower(response) == "y") {
-    unlink(temp_dir, recursive = TRUE)
-    cat("Temporary files removed.\n")
-  } else {
-    cat("Temporary files preserved for inspection.\n")
-  }
-} else {
-  cat("(Running non-interactively - files preserved)\n")
+# Putior Package Example: Workflow Extraction
+# ==============================================================================
+# This example demonstrates putior's core functionality by creating a sample
+# multi-language data workflow and extracting its structure using PUT annotations.
+#
+# To run this example:
+#   source(system.file("examples", "reprex.R", package = "putior"))
+# ==============================================================================
+
+library(putior)
+
+# Create temporary directory for example files
+temp_dir <- file.path(tempdir(), "putior_workflow_example")
+dir.create(temp_dir, showWarnings = FALSE)
+
+cat("Creating example workflow in:", temp_dir, "\n")
+
+# ==============================================================================
+# CREATE SAMPLE WORKFLOW FILES
+# ==============================================================================
+
+# File 1: Data Collection (Python script)
+# Demonstrates: input node with output annotation
+file1_lines <- c(
+  "# Data Collection Script",
+  "# put id:\"collect_data\", label:\"Collect Raw Data\", node_type:\"input\", output:\"raw_data.csv\"",
+  "",
+  "import pandas as pd",
+  "import requests",
+  "",
+  "def collect_sales_data():",
+  "    \"\"\"Collect sales data from API\"\"\"",
+  "    # Simulate API call",
+  "    data = pd.DataFrame({",
+  "        \"date\": [\"2024-01-01\", \"2024-01-02\", \"2024-01-03\"],",
+  "        \"sales\": [100, 150, 120],",
+  "        \"region\": [\"North\", \"South\", \"East\"]",
+  "    })",
+  "    data.to_csv(\"raw_data.csv\", index=False)",
+  "    return data",
+  "",
+  "if __name__ == \"__main__\":",
+  "    collect_sales_data()"
+)
+
+# File 2: Data Processing (R script)
+# Demonstrates: process node with input and output annotations
+file2_lines <- c(
+  "# Data Processing Script",
+  "# put id:\"process_data\", label:\"Clean and Transform Data\", node_type:\"process\", input:\"raw_data.csv\", output:\"processed_data.csv\"",
+  "",
+  "library(dplyr)",
+  "library(readr)",
+  "",
+  "# Read raw data",
+  "raw_data <- read_csv(\"raw_data.csv\")",
+  "",
+  "# Clean and process data",
+  "processed_data <- raw_data %>%",
+  "  mutate(",
+  "    date = as.Date(date),",
+  "    sales_category = case_when(",
+  "      sales < 110 ~ \"Low\",",
+  "      sales < 140 ~ \"Medium\",",
+  "      TRUE ~ \"High\"",
+  "    )",
+  "  ) %>%",
+  "  arrange(date)",
+  "",
+  "# Save processed data",
+  "write_csv(processed_data, \"processed_data.csv\")"
+)
+
+# File 3: Analysis and Reporting (R script)
+# Demonstrates: multiple PUT annotations in one file
+file3_lines <- c(
+  "# Analysis and Reporting Script",
+  "# put id:\"create_report\", label:\"Generate Sales Report\", node_type:\"output\", input:\"processed_data.csv\", output:\"sales_report.html\"",
+  "# put id:\"create_summary\", label:\"Calculate Summary Stats\", node_type:\"process\", input:\"processed_data.csv\", output:\"summary_stats.json\"",
+  "",
+  "library(dplyr)",
+  "library(readr)",
+  "library(jsonlite)",
+  "",
+  "# Read processed data",
+  "data <- read_csv(\"processed_data.csv\")",
+  "",
+  "# Create summary statistics",
+  "summary_stats <- list(",
+  "  total_sales = sum(data$sales),",
+  "  avg_sales = mean(data$sales),",
+  "  sales_by_category = data %>%",
+  "    count(sales_category) %>%",
+  "    setNames(c(\"category\", \"count\"))",
+  ")",
+  "",
+  "# Save summary as JSON",
+  "write_json(summary_stats, \"summary_stats.json\", pretty = TRUE)",
+  "",
+  "# Generate HTML report (simplified)",
+  "report_html <- paste0(",
+  "  \"<html><body>\",",
+  "  \"<h1>Sales Report</h1>\",",
+  "  \"<p>Total Sales: \", summary_stats$total_sales, \"</p>\",",
+  "  \"<p>Average Sales: \", round(summary_stats$avg_sales, 2), \"</p>\",",
+  "  \"</body></html>\"",
+  ")",
+  "",
+  "writeLines(report_html, \"sales_report.html\")"
+)
+
+# Write example files
+writeLines(file1_lines, file.path(temp_dir, "01_collect_data.py"))
+writeLines(file2_lines, file.path(temp_dir, "02_process_data.R"))
+writeLines(file3_lines, file.path(temp_dir, "03_analyze_report.R"))
+
+cat("Created", length(list.files(temp_dir)), "example files\n")
+
+# ==============================================================================
+# EXTRACT WORKFLOW USING PUTIOR
+# ==============================================================================
+
+cat("\n=== Extracting workflow with putior::put() ===\n")
+workflow <- put(temp_dir)
+
+# Display results
+cat("\nWorkflow extraction results:\n")
+print(workflow)
+
+# ==============================================================================
+# ANALYZE WORKFLOW STRUCTURE
+# ==============================================================================
+
+if (nrow(workflow) > 0) {
+  
+  cat("\n=== Workflow Analysis ===\n")
+  
+  # Data lineage summary
+  cat("\nData Flow Summary:\n")
+  inputs <- unique(workflow$input[!is.na(workflow$input)])
+  outputs <- unique(workflow$output[!is.na(workflow$output)])
+  
+  cat("  External Inputs:", setdiff(inputs, outputs), "\n")
+  cat("  Intermediate Files:", intersect(inputs, outputs), "\n") 
+  cat("  Final Outputs:", setdiff(outputs, inputs), "\n")
+  
+  # Node types
+  cat("\nNode Types:\n")
+  node_types <- table(workflow$node_type)
+  for (i in seq_along(node_types)) {
+    cat("  ", names(node_types)[i], ":", node_types[i], "nodes\n")
+  }
+  
+  # File types
+  cat("\nFile Types:\n")
+  file_types <- table(workflow$file_type)
+  for (i in seq_along(file_types)) {
+    cat("  ", toupper(names(file_types)[i]), ":", file_types[i], "files\n")
+  }
+  
+  # Detailed workflow steps
+  cat("\nDetailed Workflow Steps:\n")
+  for (i in 1:nrow(workflow)) {
+    row <- workflow[i, ]
+    cat("  Step", i, ":", row$id, "\n")
+    cat("    File:", row$file_name, "(", row$file_type, ")\n")
+    cat("    Action:", row$label, "\n")
+    cat("    Type:", row$node_type, "\n")
+    if (!is.na(row$input)) cat("    Consumes:", row$input, "\n")
+    if (!is.na(row$output)) cat("    Produces:", row$output, "\n")
+    cat("\n")
+  }
+  
+} else {
+  cat("No workflow annotations found. Check PUT annotation syntax.\n")
+}
+
+# ==============================================================================
+# CLEANUP AND NEXT STEPS
+# ==============================================================================
+
+cat("=== Example Complete ===\n")
+cat("Example files location:", temp_dir, "\n")
+cat("\nTo explore further:\n")
+cat("1. Examine the generated files to see PUT annotation syntax\n")
+cat("2. Try modifying annotations and re-running put()\n")
+cat("3. Add your own workflow files with PUT annotations\n")
+
+# Optional: Clean up temporary files
+cat("\nClean up temporary files? (y/n): ")
+if (interactive()) {
+  response <- readline()
+  if (tolower(response) == "y") {
+    unlink(temp_dir, recursive = TRUE)
+    cat("Temporary files removed.\n")
+  } else {
+    cat("Temporary files preserved for inspection.\n")
+  }
+} else {
+  cat("(Running non-interactively - files preserved)\n")
 }
\ No newline at end of file
diff --git a/inst/examples/self-documentation.R b/inst/examples/self-documentation.R
index ff7c607..3aa0a69 100644
--- a/inst/examples/self-documentation.R
+++ b/inst/examples/self-documentation.R
@@ -1,46 +1,46 @@
-#!/usr/bin/env Rscript
-# Example: How putior documents its own workflow
-# This demonstrates how to add PUT annotations to your own R package
-
-library(putior)
-
-# Scan the putior package itself for PUT annotations
-cat("Scanning putior package for workflow annotations...\n\n")
-workflow <- put('./R/')
-
-# Show the extracted workflow data
-cat("Extracted workflow data:\n")
-print(workflow)
-
-cat("\n\n=== Simple Script-to-Script View ===\n")
-# Generate a simple diagram showing only script connections
-put_diagram(workflow, 
-            title = "Putior Package Workflow", 
-            show_workflow_boundaries = TRUE)
-
-cat("\n\n=== Complete Data Flow View ===\n")
-# Generate a complete diagram showing all data artifacts
-put_diagram(workflow, 
-            title = "Putior Data Flow with Artifacts",
-            show_artifacts = TRUE,
-            show_workflow_boundaries = TRUE)
-
-cat("\n\n=== GitHub-optimized Diagram ===\n")
-# Generate a GitHub-friendly diagram
-put_diagram(workflow,
-            title = "Putior Workflow (GitHub Theme)",
-            theme = "github",
-            show_workflow_boundaries = TRUE)
-
-# Explanation of the workflow
-cat("\n\nWorkflow Explanation:\n")
-cat("1. put() function (start) - Entry point that scans files for annotations\n")
-cat("2. process_file() - Processes each file to extract annotations\n")
-cat("3. parse_put_annotation() - Parses the PUT syntax into properties\n")
-cat("4. validate_annotation() - Validates annotation syntax and values\n")
-cat("5. convert_results_to_df() - Converts results to a data frame\n")
-cat("6. put_diagram() - Generates Mermaid diagram from workflow data\n")
-cat("7. generate_node_definitions() - Creates node definitions\n")
-cat("8. generate_connections() - Creates edges between nodes\n")
-cat("9. generate_node_styling() - Applies theme styling\n")
+#!/usr/bin/env Rscript
+# Example: How putior documents its own workflow
+# This demonstrates how to add PUT annotations to your own R package
+
+library(putior)
+
+# Scan the putior package itself for PUT annotations
+cat("Scanning putior package for workflow annotations...\n\n")
+workflow <- put('./R/')
+
+# Show the extracted workflow data
+cat("Extracted workflow data:\n")
+print(workflow)
+
+cat("\n\n=== Simple Script-to-Script View ===\n")
+# Generate a simple diagram showing only script connections
+put_diagram(workflow, 
+            title = "Putior Package Workflow", 
+            show_workflow_boundaries = TRUE)
+
+cat("\n\n=== Complete Data Flow View ===\n")
+# Generate a complete diagram showing all data artifacts
+put_diagram(workflow, 
+            title = "Putior Data Flow with Artifacts",
+            show_artifacts = TRUE,
+            show_workflow_boundaries = TRUE)
+
+cat("\n\n=== GitHub-optimized Diagram ===\n")
+# Generate a GitHub-friendly diagram
+put_diagram(workflow,
+            title = "Putior Workflow (GitHub Theme)",
+            theme = "github",
+            show_workflow_boundaries = TRUE)
+
+# Explanation of the workflow
+cat("\n\nWorkflow Explanation:\n")
+cat("1. put() function (start) - Entry point that scans files for annotations\n")
+cat("2. process_file() - Processes each file to extract annotations\n")
+cat("3. parse_put_annotation() - Parses the PUT syntax into properties\n")
+cat("4. validate_annotation() - Validates annotation syntax and values\n")
+cat("5. convert_results_to_df() - Converts results to a data frame\n")
+cat("6. put_diagram() - Generates Mermaid diagram from workflow data\n")
+cat("7. generate_node_definitions() - Creates node definitions\n")
+cat("8. generate_connections() - Creates edges between nodes\n")
+cat("9. generate_node_styling() - Applies theme styling\n")
 cat("10. handle_output() (end) - Outputs the final diagram\n")
\ No newline at end of file
diff --git a/inst/examples/source-tracking-example.R b/inst/examples/source-tracking-example.R
index fc5190d..bc42a80 100644
--- a/inst/examples/source-tracking-example.R
+++ b/inst/examples/source-tracking-example.R
@@ -1,133 +1,133 @@
-# Source Tracking Example: Demonstrating how to annotate source() relationships
-# ==============================================================================
-# This example shows how to properly annotate scripts that source other scripts
-# to track the source() relationships in putior workflows.
-#
-# To run this example:
-#   source(system.file("examples", "source-tracking-example.R", package = "putior"))
-# ==============================================================================
-
-library(putior)
-
-cat("📜 Source Tracking Example: Proper source() Annotation\n")
-cat(paste(rep("=", 55), collapse = ""), "\n\n")
-
-# Create example directory structure
-temp_dir <- file.path(tempdir(), "putior_source_example")
-dir.create(temp_dir, showWarnings = FALSE)
-
-cat("📁 Creating example workflow with source() relationships...\n")
-
-# Main orchestrator script
-main_script <- c(
-  "# Main workflow script that sources utility modules",
-  "# put label:\"Main Analysis Pipeline\", input:\"utils.R,analysis.R,plotting.R\", output:\"final_results.csv\"",
-  "",
-  "# Source utility modules (reading them INTO this script)",
-  "source(\"utils.R\")     # Reading utils.R into main.R",
-  "source(\"analysis.R\")  # Reading analysis.R into main.R", 
-  "source(\"plotting.R\")  # Reading plotting.R into main.R",
-  "",
-  "# Execute the pipeline",
-  "data <- load_and_clean(\"raw_data.csv\")",
-  "results <- perform_analysis(data)",
-  "create_plots(results)",
-  "write.csv(results, \"final_results.csv\")"
-)
-
-# Utility functions script 
-utils_script <- c(
-  "# Utility functions - sourced BY main.R",
-  "# put label:\"Data Utilities\", node_type:\"input\"",
-  "# output defaults to 'utils.R' - this script provides itself",
-  "",
-  "load_and_clean <- function(file) {",
-  "  # Load and clean data",
-  "  data <- read.csv(file)",
-  "  data[complete.cases(data), ]",
-  "}"
-)
-
-# Analysis functions script
-analysis_script <- c(
-  "# Analysis functions - sourced BY main.R, depends on utils.R",
-  "# put label:\"Statistical Analysis\", node_type:\"process\", input:\"utils.R\"",
-  "# input: utils.R because we depend on functions from utils.R",
-  "# output defaults to 'analysis.R'",
-  "",
-  "perform_analysis <- function(data) {",
-  "  # Perform statistical analysis",
-  "  # Uses load_and_clean() from utils.R",
-  "  summary(data)",
-  "}"
-)
-
-# Plotting functions script
-plotting_script <- c(
-  "# Plotting functions - sourced BY main.R, depends on analysis.R",
-  "# put label:\"Data Visualization\", node_type:\"output\", input:\"analysis.R\"",
-  "# input: analysis.R because we depend on analysis functions",
-  "# output defaults to 'plotting.R'",
-  "",
-  "create_plots <- function(results) {",
-  "  # Create visualizations",
-  "  # Uses perform_analysis() results",
-  "  plot(results)",
-  "}"
-)
-
-# Write all files
-writeLines(main_script, file.path(temp_dir, "main.R"))
-writeLines(utils_script, file.path(temp_dir, "utils.R"))
-writeLines(analysis_script, file.path(temp_dir, "analysis.R"))
-writeLines(plotting_script, file.path(temp_dir, "plotting.R"))
-
-cat("✅ Created source tracking example files\n\n")
-
-# Extract workflow
-cat("🔍 Extracting source() relationships...\n")
-workflow <- put(temp_dir)
-
-cat("\n📊 Source tracking results:\n")
-cat(paste(rep("-", 50), collapse = ""), "\n")
-
-# Display the relationships
-for (i in seq_len(nrow(workflow))) {
-  row <- workflow[i, ]
-  cat(sprintf("%-15s: %s\n", "File", row$file_name))
-  cat(sprintf("%-15s: %s\n", "Label", row$label))
-  cat(sprintf("%-15s: %s\n", "Node Type", ifelse(is.na(row$node_type), "process", row$node_type)))
-  cat(sprintf("%-15s: %s\n", "Input", ifelse(is.na(row$input), "none", row$input)))
-  cat(sprintf("%-15s: %s\n", "Output", row$output))
-  cat(paste(rep("-", 50), collapse = ""), "\n")
-}
-
-# Generate diagram
-cat("\n🎨 Source relationship diagram:\n")
-cat(paste(rep("-", 50), collapse = ""), "\n")
-put_diagram(workflow, 
-            theme = "github", 
-            show_files = TRUE,
-            title = "Source Tracking Example")
-
-cat("\n\n💡 Key Insights:\n")
-cat(paste(rep("=", 50), collapse = ""), "\n")
-cat("1. Scripts being sourced are INPUTS to the main script\n")
-cat("2. Flow direction: sourced scripts → main script\n") 
-cat("3. main.R reads utils.R, analysis.R, and plotting.R\n")
-cat("4. Dependencies: utils.R → analysis.R → plotting.R\n")
-cat("5. Arrows with file names show the source() relationships\n\n")
-
-cat("📝 Annotation Pattern Summary:\n")
-cat("• Main script: input=\"script1.R,script2.R,script3.R\"\n")
-cat("• Sourced scripts: output defaults to their filename\n")
-cat("• Dependencies: input=\"dependency_script.R\"\n\n")
-
-cat("🗂️ Example files created in:\n")
-cat("   ", temp_dir, "\n\n")
-
-cat("✅ Source tracking example complete!\n")
-
-# Clean up
-cat("🧹 Cleaning up...\n")
+# Source Tracking Example: Demonstrating how to annotate source() relationships
+# ==============================================================================
+# This example shows how to properly annotate scripts that source other scripts
+# to track the source() relationships in putior workflows.
+#
+# To run this example:
+#   source(system.file("examples", "source-tracking-example.R", package = "putior"))
+# ==============================================================================
+
+library(putior)
+
+cat("📜 Source Tracking Example: Proper source() Annotation\n")
+cat(paste(rep("=", 55), collapse = ""), "\n\n")
+
+# Create example directory structure
+temp_dir <- file.path(tempdir(), "putior_source_example")
+dir.create(temp_dir, showWarnings = FALSE)
+
+cat("📁 Creating example workflow with source() relationships...\n")
+
+# Main orchestrator script
+main_script <- c(
+  "# Main workflow script that sources utility modules",
+  "# put label:\"Main Analysis Pipeline\", input:\"utils.R,analysis.R,plotting.R\", output:\"final_results.csv\"",
+  "",
+  "# Source utility modules (reading them INTO this script)",
+  "source(\"utils.R\")     # Reading utils.R into main.R",
+  "source(\"analysis.R\")  # Reading analysis.R into main.R", 
+  "source(\"plotting.R\")  # Reading plotting.R into main.R",
+  "",
+  "# Execute the pipeline",
+  "data <- load_and_clean(\"raw_data.csv\")",
+  "results <- perform_analysis(data)",
+  "create_plots(results)",
+  "write.csv(results, \"final_results.csv\")"
+)
+
+# Utility functions script 
+utils_script <- c(
+  "# Utility functions - sourced BY main.R",
+  "# put label:\"Data Utilities\", node_type:\"input\"",
+  "# output defaults to 'utils.R' - this script provides itself",
+  "",
+  "load_and_clean <- function(file) {",
+  "  # Load and clean data",
+  "  data <- read.csv(file)",
+  "  data[complete.cases(data), ]",
+  "}"
+)
+
+# Analysis functions script
+analysis_script <- c(
+  "# Analysis functions - sourced BY main.R, depends on utils.R",
+  "# put label:\"Statistical Analysis\", node_type:\"process\", input:\"utils.R\"",
+  "# input: utils.R because we depend on functions from utils.R",
+  "# output defaults to 'analysis.R'",
+  "",
+  "perform_analysis <- function(data) {",
+  "  # Perform statistical analysis",
+  "  # Uses load_and_clean() from utils.R",
+  "  summary(data)",
+  "}"
+)
+
+# Plotting functions script
+plotting_script <- c(
+  "# Plotting functions - sourced BY main.R, depends on analysis.R",
+  "# put label:\"Data Visualization\", node_type:\"output\", input:\"analysis.R\"",
+  "# input: analysis.R because we depend on analysis functions",
+  "# output defaults to 'plotting.R'",
+  "",
+  "create_plots <- function(results) {",
+  "  # Create visualizations",
+  "  # Uses perform_analysis() results",
+  "  plot(results)",
+  "}"
+)
+
+# Write all files
+writeLines(main_script, file.path(temp_dir, "main.R"))
+writeLines(utils_script, file.path(temp_dir, "utils.R"))
+writeLines(analysis_script, file.path(temp_dir, "analysis.R"))
+writeLines(plotting_script, file.path(temp_dir, "plotting.R"))
+
+cat("✅ Created source tracking example files\n\n")
+
+# Extract workflow
+cat("🔍 Extracting source() relationships...\n")
+workflow <- put(temp_dir)
+
+cat("\n📊 Source tracking results:\n")
+cat(paste(rep("-", 50), collapse = ""), "\n")
+
+# Display the relationships
+for (i in seq_len(nrow(workflow))) {
+  row <- workflow[i, ]
+  cat(sprintf("%-15s: %s\n", "File", row$file_name))
+  cat(sprintf("%-15s: %s\n", "Label", row$label))
+  cat(sprintf("%-15s: %s\n", "Node Type", ifelse(is.na(row$node_type), "process", row$node_type)))
+  cat(sprintf("%-15s: %s\n", "Input", ifelse(is.na(row$input), "none", row$input)))
+  cat(sprintf("%-15s: %s\n", "Output", row$output))
+  cat(paste(rep("-", 50), collapse = ""), "\n")
+}
+
+# Generate diagram
+cat("\n🎨 Source relationship diagram:\n")
+cat(paste(rep("-", 50), collapse = ""), "\n")
+put_diagram(workflow, 
+            theme = "github", 
+            show_files = TRUE,
+            title = "Source Tracking Example")
+
+cat("\n\n💡 Key Insights:\n")
+cat(paste(rep("=", 50), collapse = ""), "\n")
+cat("1. Scripts being sourced are INPUTS to the main script\n")
+cat("2. Flow direction: sourced scripts → main script\n") 
+cat("3. main.R reads utils.R, analysis.R, and plotting.R\n")
+cat("4. Dependencies: utils.R → analysis.R → plotting.R\n")
+cat("5. Arrows with file names show the source() relationships\n\n")
+
+cat("📝 Annotation Pattern Summary:\n")
+cat("• Main script: input=\"script1.R,script2.R,script3.R\"\n")
+cat("• Sourced scripts: output defaults to their filename\n")
+cat("• Dependencies: input=\"dependency_script.R\"\n\n")
+
+cat("🗂️ Example files created in:\n")
+cat("   ", temp_dir, "\n\n")
+
+cat("✅ Source tracking example complete!\n")
+
+# Clean up
+cat("🧹 Cleaning up...\n")
 unlink(temp_dir, recursive = TRUE)
\ No newline at end of file
diff --git a/inst/examples/theme-examples.R b/inst/examples/theme-examples.R
index bdf0764..934f5ab 100644
--- a/inst/examples/theme-examples.R
+++ b/inst/examples/theme-examples.R
@@ -1,220 +1,220 @@
-# Putior Theme Examples: Standard and Colorblind-Safe Themes
-# ==============================================================================
-# This example demonstrates putior's 9 themes including colorblind-safe options.
-#
-# Standard themes: light, dark, auto, minimal, github
-# Colorblind-safe (viridis family): viridis, magma, plasma, cividis
-#
-# To run this example:
-#   source(system.file("examples", "theme-examples.R", package = "putior"))
-# ==============================================================================
-
-library(putior)
-
-cat("🎨 Putior Theme Examples\n")
-cat(paste(rep("=", 40), collapse = ""), "\n\n")
-
-# Create a sample workflow for theme demonstration
-temp_dir <- file.path(tempdir(), "putior_themes")
-dir.create(temp_dir, showWarnings = FALSE)
-
-cat("📁 Creating sample workflow...\n")
-
-# Simple but representative workflow
-workflow_files <- list(
-  "collect.py" = c(
-    "# put id:\"fetch_data\", label:\"Fetch API Data\", node_type:\"input\", output:\"raw_data.json\"",
-    "import requests",
-    "data = requests.get('/api/data').json()",
-    "with open('raw_data.json', 'w') as f:",
-    "    json.dump(data, f)"
-  ),
-  
-  "process.R" = c(
-    "# put id:\"clean_data\", label:\"Clean and Validate\", node_type:\"process\", input:\"raw_data.json\", output:\"clean_data.csv\"",
-    "library(jsonlite)",
-    "raw <- fromJSON('raw_data.json')",
-    "clean <- clean_dataset(raw)",
-    "write.csv(clean, 'clean_data.csv')"
-  ),
-  
-  "analyze.R" = c(
-    "# put id:\"statistical_analysis\", label:\"Statistical Analysis\", node_type:\"process\", input:\"clean_data.csv\", output:\"results.rds\"",
-    "# put id:\"quality_check\", label:\"Data Quality Check\", node_type:\"decision\", input:\"clean_data.csv\", output:\"quality_report.json\"",
-    "data <- read.csv('clean_data.csv')",
-    "results <- perform_analysis(data)",
-    "saveRDS(results, 'results.rds')"
-  ),
-  
-  "report.R" = c(
-    "# put id:\"generate_report\", label:\"Generate Final Report\", node_type:\"output\", input:\"results.rds\", output:\"final_report.html\"",
-    "results <- readRDS('results.rds')",
-    "rmarkdown::render('report_template.Rmd', output_file = 'final_report.html')"
-  )
-)
-
-# Write workflow files
-for (filename in names(workflow_files)) {
-  writeLines(workflow_files[[filename]], file.path(temp_dir, filename))
-}
-
-# Extract workflow
-workflow <- put(temp_dir)
-cat("✅ Found", nrow(workflow), "workflow nodes\n\n")
-
-# Show available themes
-cat("🎨 Available Themes:\n")
-themes <- get_diagram_themes()
-for (theme_name in names(themes)) {
-  cat("  ", theme_name, ":", themes[[theme_name]], "\n")
-}
-cat("\n")
-
-cat(paste(rep("=", 50), collapse = ""), "\n")
-cat("🌅 LIGHT THEME (Default)\n")
-cat("Perfect for: Documentation sites, light mode environments\n")
-cat(paste(rep("-", 50), collapse = ""), "\n")
-put_diagram(workflow, 
-            title = "Data Processing Pipeline - Light Theme",
-            theme = "light")
-
-cat("\n", paste(rep("=", 50), collapse = ""), "\n")
-cat("🌙 DARK THEME\n") 
-cat("Perfect for: Dark mode environments, terminal displays\n")
-cat(paste(rep("-", 50), collapse = ""), "\n")
-put_diagram(workflow,
-            title = "Data Processing Pipeline - Dark Theme", 
-            theme = "dark",
-            direction = "LR")
-
-cat("\n", paste(rep("=", 50), collapse = ""), "\n")
-cat("🔄 AUTO THEME (GitHub Adaptive)\n")
-cat("Perfect for: GitHub README files, automatically adapts to user's theme\n")
-cat(paste(rep("-", 50), collapse = ""), "\n")
-put_diagram(workflow,
-            title = "Data Processing Pipeline - Auto Theme",
-            theme = "auto",
-            show_files = TRUE)
-
-cat("\n", paste(rep("=", 50), collapse = ""), "\n")
-cat("⚪ MINIMAL THEME\n")
-cat("Perfect for: Professional documents, print-friendly diagrams\n")
-cat(paste(rep("-", 50), collapse = ""), "\n")
-put_diagram(workflow,
-            title = "Data Processing Pipeline - Minimal Theme",
-            theme = "minimal",
-            node_labels = "both")
-
-cat("\n", paste(rep("=", 50), collapse = ""), "\n")
-cat("🎯 VIRIDIS THEME (Colorblind-Safe)\n")
-cat("Perfect for: Accessibility, general use, perceptually uniform\n")
-cat(paste(rep("-", 50), collapse = ""), "\n")
-put_diagram(workflow,
-            title = "Data Processing Pipeline - Viridis Theme",
-            theme = "viridis")
-
-cat("\n", paste(rep("=", 50), collapse = ""), "\n")
-cat("🔥 MAGMA THEME (Colorblind-Safe, Warm)\n")
-cat("Perfect for: High contrast, print materials\n")
-cat(paste(rep("-", 50), collapse = ""), "\n")
-put_diagram(workflow,
-            title = "Data Processing Pipeline - Magma Theme",
-            theme = "magma")
-
-cat("\n", paste(rep("=", 50), collapse = ""), "\n")
-cat("🌈 PLASMA THEME (Colorblind-Safe, Vibrant)\n")
-cat("Perfect for: Presentations, digital displays\n")
-cat(paste(rep("-", 50), collapse = ""), "\n")
-put_diagram(workflow,
-            title = "Data Processing Pipeline - Plasma Theme",
-            theme = "plasma",
-            direction = "LR")
-
-cat("\n", paste(rep("=", 50), collapse = ""), "\n")
-cat("👁️ CIVIDIS THEME (Maximum Colorblind Accessibility)\n")
-cat("Perfect for: Red-green colorblindness (deuteranopia/protanopia)\n")
-cat(paste(rep("-", 50), collapse = ""), "\n")
-put_diagram(workflow,
-            title = "Data Processing Pipeline - Cividis Theme",
-            theme = "cividis")
-
-cat("\n", paste(rep("=", 50), collapse = ""), "\n")
-cat("💡 USAGE RECOMMENDATIONS\n")
-cat(paste(rep("=", 50), collapse = ""), "\n\n")
-
-cat("🌅 Light Theme:\n")
-cat("  • Default theme with bright, friendly colors\n")
-cat("  • Best for documentation websites and light backgrounds\n")
-cat("  • High contrast and readability\n\n")
-
-cat("🌙 Dark Theme:\n") 
-cat("  • Muted colors with light text\n")
-cat("  • Perfect for dark mode applications and terminals\n")
-cat("  • Easy on the eyes for extended viewing\n\n")
-
-cat("🔄 Auto Theme:\n")
-cat("  • Uses GitHub's adaptive color system\n")
-cat("  • Automatically looks good in both light and dark modes\n")
-cat("  • Recommended for GitHub README files\n\n")
-
-cat("⚪ Minimal Theme:\n")
-cat("  • Grayscale with subtle borders\n")
-cat("  • Professional appearance for business documents\n")
-cat("  • Print-friendly and accessible\n\n")
-
-cat("🎯 Viridis Theme (Colorblind-Safe):\n")
-cat("  • Purple → Blue → Green → Yellow palette\n")
-cat("  • Most widely tested colorblind-safe palette\n")
-cat("  • Perceptually uniform - equal steps appear equally different\n\n")
-
-cat("🔥 Magma Theme (Colorblind-Safe):\n")
-cat("  • Purple → Red → Yellow warm palette\n")
-cat("  • High contrast for print and presentations\n")
-cat("  • Works well in grayscale\n\n")
-
-cat("🌈 Plasma Theme (Colorblind-Safe):\n")
-cat("  • Purple → Pink → Orange → Yellow vibrant palette\n")
-cat("  • Bold colors ideal for digital displays\n")
-cat("  • Great for presentations\n\n")
-
-cat("👁️ Cividis Theme (Maximum Accessibility):\n")
-cat("  • Blue → Gray → Yellow palette\n")
-cat("  • Specifically optimized for deuteranopia and protanopia\n")
-cat("  • Avoids red-green entirely\n\n")
-
-cat("📋 Example Usage:\n")
-cat("  # For GitHub README (adapts to user's theme)\n")
-cat("  put_diagram(workflow, theme = 'auto')\n\n")
-cat("  # For dark documentation sites\n")
-cat("  put_diagram(workflow, theme = 'dark', direction = 'LR')\n\n")
-cat("  # For professional reports\n")
-cat("  put_diagram(workflow, theme = 'minimal', output = 'file')\n\n")
-cat("  # For colorblind-safe diagrams\n")
-cat("  put_diagram(workflow, theme = 'viridis')  # General accessibility\n")
-cat("  put_diagram(workflow, theme = 'cividis')  # Red-green colorblindness\n\n")
-
-# Save examples to files for comparison
-cat("💾 Saving theme examples to files...\n")
-
-themes_to_save <- c("light", "dark", "auto", "minimal", "github",
-                    "viridis", "magma", "plasma", "cividis")
-for (theme in themes_to_save) {
-  filename <- file.path(temp_dir, paste0("workflow_", theme, "_theme.md"))
-  put_diagram(workflow,
-              output = "file",
-              file = filename,
-              title = paste("Workflow -", stringr::str_to_title(theme), "Theme"),
-              theme = theme,
-              show_files = TRUE)
-}
-
-cat("✅ Saved theme examples:\n")
-for (theme in themes_to_save) {
-  filename <- paste0("workflow_", theme, "_theme.md")
-  cat("  •", filename, "\n")
-}
-
-cat("\n📂 All files saved to:", temp_dir, "\n")
-cat("💡 Try opening these files in different environments to see the themes!\n\n")
-
+# Putior Theme Examples: Standard and Colorblind-Safe Themes
+# ==============================================================================
+# This example demonstrates putior's 9 themes including colorblind-safe options.
+#
+# Standard themes: light, dark, auto, minimal, github
+# Colorblind-safe (viridis family): viridis, magma, plasma, cividis
+#
+# To run this example:
+#   source(system.file("examples", "theme-examples.R", package = "putior"))
+# ==============================================================================
+
+library(putior)
+
+cat("🎨 Putior Theme Examples\n")
+cat(paste(rep("=", 40), collapse = ""), "\n\n")
+
+# Create a sample workflow for theme demonstration
+temp_dir <- file.path(tempdir(), "putior_themes")
+dir.create(temp_dir, showWarnings = FALSE)
+
+cat("📁 Creating sample workflow...\n")
+
+# Simple but representative workflow
+workflow_files <- list(
+  "collect.py" = c(
+    "# put id:\"fetch_data\", label:\"Fetch API Data\", node_type:\"input\", output:\"raw_data.json\"",
+    "import requests",
+    "data = requests.get('/api/data').json()",
+    "with open('raw_data.json', 'w') as f:",
+    "    json.dump(data, f)"
+  ),
+  
+  "process.R" = c(
+    "# put id:\"clean_data\", label:\"Clean and Validate\", node_type:\"process\", input:\"raw_data.json\", output:\"clean_data.csv\"",
+    "library(jsonlite)",
+    "raw <- fromJSON('raw_data.json')",
+    "clean <- clean_dataset(raw)",
+    "write.csv(clean, 'clean_data.csv')"
+  ),
+  
+  "analyze.R" = c(
+    "# put id:\"statistical_analysis\", label:\"Statistical Analysis\", node_type:\"process\", input:\"clean_data.csv\", output:\"results.rds\"",
+    "# put id:\"quality_check\", label:\"Data Quality Check\", node_type:\"decision\", input:\"clean_data.csv\", output:\"quality_report.json\"",
+    "data <- read.csv('clean_data.csv')",
+    "results <- perform_analysis(data)",
+    "saveRDS(results, 'results.rds')"
+  ),
+  
+  "report.R" = c(
+    "# put id:\"generate_report\", label:\"Generate Final Report\", node_type:\"output\", input:\"results.rds\", output:\"final_report.html\"",
+    "results <- readRDS('results.rds')",
+    "rmarkdown::render('report_template.Rmd', output_file = 'final_report.html')"
+  )
+)
+
+# Write workflow files
+for (filename in names(workflow_files)) {
+  writeLines(workflow_files[[filename]], file.path(temp_dir, filename))
+}
+
+# Extract workflow
+workflow <- put(temp_dir)
+cat("✅ Found", nrow(workflow), "workflow nodes\n\n")
+
+# Show available themes
+cat("🎨 Available Themes:\n")
+themes <- get_diagram_themes()
+for (theme_name in names(themes)) {
+  cat("  ", theme_name, ":", themes[[theme_name]], "\n")
+}
+cat("\n")
+
+cat(paste(rep("=", 50), collapse = ""), "\n")
+cat("🌅 LIGHT THEME (Default)\n")
+cat("Perfect for: Documentation sites, light mode environments\n")
+cat(paste(rep("-", 50), collapse = ""), "\n")
+put_diagram(workflow, 
+            title = "Data Processing Pipeline - Light Theme",
+            theme = "light")
+
+cat("\n", paste(rep("=", 50), collapse = ""), "\n")
+cat("🌙 DARK THEME\n") 
+cat("Perfect for: Dark mode environments, terminal displays\n")
+cat(paste(rep("-", 50), collapse = ""), "\n")
+put_diagram(workflow,
+            title = "Data Processing Pipeline - Dark Theme", 
+            theme = "dark",
+            direction = "LR")
+
+cat("\n", paste(rep("=", 50), collapse = ""), "\n")
+cat("🔄 AUTO THEME (GitHub Adaptive)\n")
+cat("Perfect for: GitHub README files, automatically adapts to user's theme\n")
+cat(paste(rep("-", 50), collapse = ""), "\n")
+put_diagram(workflow,
+            title = "Data Processing Pipeline - Auto Theme",
+            theme = "auto",
+            show_files = TRUE)
+
+cat("\n", paste(rep("=", 50), collapse = ""), "\n")
+cat("⚪ MINIMAL THEME\n")
+cat("Perfect for: Professional documents, print-friendly diagrams\n")
+cat(paste(rep("-", 50), collapse = ""), "\n")
+put_diagram(workflow,
+            title = "Data Processing Pipeline - Minimal Theme",
+            theme = "minimal",
+            node_labels = "both")
+
+cat("\n", paste(rep("=", 50), collapse = ""), "\n")
+cat("🎯 VIRIDIS THEME (Colorblind-Safe)\n")
+cat("Perfect for: Accessibility, general use, perceptually uniform\n")
+cat(paste(rep("-", 50), collapse = ""), "\n")
+put_diagram(workflow,
+            title = "Data Processing Pipeline - Viridis Theme",
+            theme = "viridis")
+
+cat("\n", paste(rep("=", 50), collapse = ""), "\n")
+cat("🔥 MAGMA THEME (Colorblind-Safe, Warm)\n")
+cat("Perfect for: High contrast, print materials\n")
+cat(paste(rep("-", 50), collapse = ""), "\n")
+put_diagram(workflow,
+            title = "Data Processing Pipeline - Magma Theme",
+            theme = "magma")
+
+cat("\n", paste(rep("=", 50), collapse = ""), "\n")
+cat("🌈 PLASMA THEME (Colorblind-Safe, Vibrant)\n")
+cat("Perfect for: Presentations, digital displays\n")
+cat(paste(rep("-", 50), collapse = ""), "\n")
+put_diagram(workflow,
+            title = "Data Processing Pipeline - Plasma Theme",
+            theme = "plasma",
+            direction = "LR")
+
+cat("\n", paste(rep("=", 50), collapse = ""), "\n")
+cat("👁️ CIVIDIS THEME (Maximum Colorblind Accessibility)\n")
+cat("Perfect for: Red-green colorblindness (deuteranopia/protanopia)\n")
+cat(paste(rep("-", 50), collapse = ""), "\n")
+put_diagram(workflow,
+            title = "Data Processing Pipeline - Cividis Theme",
+            theme = "cividis")
+
+cat("\n", paste(rep("=", 50), collapse = ""), "\n")
+cat("💡 USAGE RECOMMENDATIONS\n")
+cat(paste(rep("=", 50), collapse = ""), "\n\n")
+
+cat("🌅 Light Theme:\n")
+cat("  • Default theme with bright, friendly colors\n")
+cat("  • Best for documentation websites and light backgrounds\n")
+cat("  • High contrast and readability\n\n")
+
+cat("🌙 Dark Theme:\n") 
+cat("  • Muted colors with light text\n")
+cat("  • Perfect for dark mode applications and terminals\n")
+cat("  • Easy on the eyes for extended viewing\n\n")
+
+cat("🔄 Auto Theme:\n")
+cat("  • Uses GitHub's adaptive color system\n")
+cat("  • Automatically looks good in both light and dark modes\n")
+cat("  • Recommended for GitHub README files\n\n")
+
+cat("⚪ Minimal Theme:\n")
+cat("  • Grayscale with subtle borders\n")
+cat("  • Professional appearance for business documents\n")
+cat("  • Print-friendly and accessible\n\n")
+
+cat("🎯 Viridis Theme (Colorblind-Safe):\n")
+cat("  • Purple → Blue → Green → Yellow palette\n")
+cat("  • Most widely tested colorblind-safe palette\n")
+cat("  • Perceptually uniform - equal steps appear equally different\n\n")
+
+cat("🔥 Magma Theme (Colorblind-Safe):\n")
+cat("  • Purple → Red → Yellow warm palette\n")
+cat("  • High contrast for print and presentations\n")
+cat("  • Works well in grayscale\n\n")
+
+cat("🌈 Plasma Theme (Colorblind-Safe):\n")
+cat("  • Purple → Pink → Orange → Yellow vibrant palette\n")
+cat("  • Bold colors ideal for digital displays\n")
+cat("  • Great for presentations\n\n")
+
+cat("👁️ Cividis Theme (Maximum Accessibility):\n")
+cat("  • Blue → Gray → Yellow palette\n")
+cat("  • Specifically optimized for deuteranopia and protanopia\n")
+cat("  • Avoids red-green entirely\n\n")
+
+cat("📋 Example Usage:\n")
+cat("  # For GitHub README (adapts to user's theme)\n")
+cat("  put_diagram(workflow, theme = 'auto')\n\n")
+cat("  # For dark documentation sites\n")
+cat("  put_diagram(workflow, theme = 'dark', direction = 'LR')\n\n")
+cat("  # For professional reports\n")
+cat("  put_diagram(workflow, theme = 'minimal', output = 'file')\n\n")
+cat("  # For colorblind-safe diagrams\n")
+cat("  put_diagram(workflow, theme = 'viridis')  # General accessibility\n")
+cat("  put_diagram(workflow, theme = 'cividis')  # Red-green colorblindness\n\n")
+
+# Save examples to files for comparison
+cat("💾 Saving theme examples to files...\n")
+
+themes_to_save <- c("light", "dark", "auto", "minimal", "github",
+                    "viridis", "magma", "plasma", "cividis")
+for (theme in themes_to_save) {
+  filename <- file.path(temp_dir, paste0("workflow_", theme, "_theme.md"))
+  put_diagram(workflow,
+              output = "file",
+              file = filename,
+              title = paste("Workflow -", stringr::str_to_title(theme), "Theme"),
+              theme = theme,
+              show_files = TRUE)
+}
+
+cat("✅ Saved theme examples:\n")
+for (theme in themes_to_save) {
+  filename <- paste0("workflow_", theme, "_theme.md")
+  cat("  •", filename, "\n")
+}
+
+cat("\n📂 All files saved to:", temp_dir, "\n")
+cat("💡 Try opening these files in different environments to see the themes!\n\n")
+
 cat("🎨 Happy theming with putior! 🚀\n")
\ No newline at end of file
diff --git a/inst/examples/uuid-example.R b/inst/examples/uuid-example.R
index 1299913..c728b73 100644
--- a/inst/examples/uuid-example.R
+++ b/inst/examples/uuid-example.R
@@ -1,124 +1,124 @@
-# Putior UUID Auto-Generation Example
-# ==============================================================================
-# This example demonstrates how putior automatically generates UUIDs for nodes
-# when the id field is omitted from annotations.
-#
-# To run this example:
-#   source(system.file("examples", "uuid-example.R", package = "putior"))
-# ==============================================================================
-
-library(putior)
-
-cat("🆔 Putior UUID Auto-Generation Example\n")
-cat(paste(rep("=", 50), collapse = ""), "\n\n")
-
-# Create a sample workflow demonstrating UUID generation
-temp_dir <- file.path(tempdir(), "putior_uuid_example")
-dir.create(temp_dir, showWarnings = FALSE)
-
-cat("📁 Creating example files with and without explicit IDs...\n\n")
-
-# File 1: Annotations without IDs (will get auto-generated UUIDs)
-no_ids_script <- c(
-  "# Script with annotations that omit the id field",
-  "# put label:\"Load Configuration\", node_type:\"input\", output:\"config.json\"",
-  "",
-  "config <- load_config()",
-  "save_json(config, 'config.json')",
-  "",
-  "# put label:\"Process Data\", node_type:\"process\", input:\"config.json\", output:\"processed.csv\"", 
-  "",
-  "data <- process_with_config('config.json')",
-  "write.csv(data, 'processed.csv')"
-)
-
-# File 2: Mix of explicit IDs and omitted IDs
-mixed_ids_script <- c(
-  "# Script with some explicit IDs and some omitted",
-  "# put id:\"fetch_data\", label:\"Fetch Raw Data\", node_type:\"input\", output:\"raw.csv\"",
-  "",
-  "raw_data <- fetch_from_api()",
-  "write.csv(raw_data, 'raw.csv')",
-  "",
-  "# This annotation omits the id - will get UUID",
-  "# put label:\"Validate Data\", node_type:\"process\", input:\"raw.csv\", output:\"validated.csv\"",
-  "",
-  "validated <- validate_data(read.csv('raw.csv'))",
-  "write.csv(validated, 'validated.csv')",
-  "",
-  "# put id:\"generate_report\", label:\"Generate Report\", node_type:\"output\", input:\"validated.csv\""
-)
-
-# File 3: Example with empty ID (will generate warning)
-empty_id_script <- c(
-  "# Script demonstrating empty id warning",
-  "# put id:\"\", label:\"This will warn\", node_type:\"process\"",
-  "",
-  "# Empty IDs generate validation warnings"
-)
-
-# Write files
-writeLines(no_ids_script, file.path(temp_dir, "01_no_ids.R"))
-writeLines(mixed_ids_script, file.path(temp_dir, "02_mixed_ids.R"))
-writeLines(empty_id_script, file.path(temp_dir, "03_empty_id.R"))
-
-cat("✅ Created example files\n\n")
-
-# Extract workflow with UUID auto-generation
-cat("🔍 Extracting workflow (UUIDs will be auto-generated)...\n")
-cat(paste(rep("-", 50), collapse = ""), "\n")
-
-# Capture the warning from empty ID
-workflow <- suppressWarnings(put(temp_dir))
-
-# Show results
-cat("\n📊 Extracted nodes:\n")
-cat(paste(rep("-", 50), collapse = ""), "\n")
-
-for (i in seq_len(nrow(workflow))) {
-  row <- workflow[i, ]
-  cat(sprintf("%-20s: %s\n", "File", row$file_name))
-  cat(sprintf("%-20s: %s\n", "ID", row$id))
-  cat(sprintf("%-20s: %s\n", "Label", row$label))
-  
-  # Check if ID looks like a UUID
-  is_uuid <- grepl("^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", 
-                   row$id, ignore.case = TRUE)
-  cat(sprintf("%-20s: %s\n", "Auto-generated?", ifelse(is_uuid, "Yes (UUID)", "No (explicit)")))
-  cat(paste(rep("-", 50), collapse = ""), "\n")
-}
-
-# Now extract with validation to see the warning
-cat("\n⚠️  Extracting with validation (to show empty ID warning):\n")
-cat(paste(rep("-", 50), collapse = ""), "\n")
-workflow_validated <- put(temp_dir, validate = TRUE)
-
-# Generate diagram
-cat("\n\n🎨 Generating diagram with auto-generated UUIDs:\n")
-cat(paste(rep("-", 50), collapse = ""), "\n")
-put_diagram(workflow[workflow$file_name != "03_empty_id.R", ],  # Exclude the empty ID example
-            title = "Workflow with Auto-Generated UUIDs",
-            node_labels = "label")  # Use labels since UUIDs are not human-friendly
-
-cat("\n\n💡 KEY POINTS:\n")
-cat(paste(rep("=", 50), collapse = ""), "\n")
-cat("1. When 'id' is omitted → UUID is auto-generated\n")
-cat("2. When 'id' is explicit → Your ID is used as-is\n")
-cat("3. When 'id' is empty (\"\") → Validation warning\n")
-cat("4. UUIDs ensure uniqueness across workflows\n")
-cat("5. Use 'label' for human-readable node names\n\n")
-
-cat("📝 BEST PRACTICES:\n")
-cat("• Omit 'id' for quick prototyping\n")
-cat("• Use explicit 'id' for stable references\n")
-cat("• Always provide descriptive 'label' values\n")
-cat("• Avoid empty 'id' values\n\n")
-
-cat("🗂️ Example files created in:\n")
-cat("   ", temp_dir, "\n\n")
-
-# Clean up
-cat("🧹 Cleaning up temporary files...\n")
-unlink(temp_dir, recursive = TRUE)
-
+# Putior UUID Auto-Generation Example
+# ==============================================================================
+# This example demonstrates how putior automatically generates UUIDs for nodes
+# when the id field is omitted from annotations.
+#
+# To run this example:
+#   source(system.file("examples", "uuid-example.R", package = "putior"))
+# ==============================================================================
+
+library(putior)
+
+cat("🆔 Putior UUID Auto-Generation Example\n")
+cat(paste(rep("=", 50), collapse = ""), "\n\n")
+
+# Create a sample workflow demonstrating UUID generation
+temp_dir <- file.path(tempdir(), "putior_uuid_example")
+dir.create(temp_dir, showWarnings = FALSE)
+
+cat("📁 Creating example files with and without explicit IDs...\n\n")
+
+# File 1: Annotations without IDs (will get auto-generated UUIDs)
+no_ids_script <- c(
+  "# Script with annotations that omit the id field",
+  "# put label:\"Load Configuration\", node_type:\"input\", output:\"config.json\"",
+  "",
+  "config <- load_config()",
+  "save_json(config, 'config.json')",
+  "",
+  "# put label:\"Process Data\", node_type:\"process\", input:\"config.json\", output:\"processed.csv\"", 
+  "",
+  "data <- process_with_config('config.json')",
+  "write.csv(data, 'processed.csv')"
+)
+
+# File 2: Mix of explicit IDs and omitted IDs
+mixed_ids_script <- c(
+  "# Script with some explicit IDs and some omitted",
+  "# put id:\"fetch_data\", label:\"Fetch Raw Data\", node_type:\"input\", output:\"raw.csv\"",
+  "",
+  "raw_data <- fetch_from_api()",
+  "write.csv(raw_data, 'raw.csv')",
+  "",
+  "# This annotation omits the id - will get UUID",
+  "# put label:\"Validate Data\", node_type:\"process\", input:\"raw.csv\", output:\"validated.csv\"",
+  "",
+  "validated <- validate_data(read.csv('raw.csv'))",
+  "write.csv(validated, 'validated.csv')",
+  "",
+  "# put id:\"generate_report\", label:\"Generate Report\", node_type:\"output\", input:\"validated.csv\""
+)
+
+# File 3: Example with empty ID (will generate warning)
+empty_id_script <- c(
+  "# Script demonstrating empty id warning",
+  "# put id:\"\", label:\"This will warn\", node_type:\"process\"",
+  "",
+  "# Empty IDs generate validation warnings"
+)
+
+# Write files
+writeLines(no_ids_script, file.path(temp_dir, "01_no_ids.R"))
+writeLines(mixed_ids_script, file.path(temp_dir, "02_mixed_ids.R"))
+writeLines(empty_id_script, file.path(temp_dir, "03_empty_id.R"))
+
+cat("✅ Created example files\n\n")
+
+# Extract workflow with UUID auto-generation
+cat("🔍 Extracting workflow (UUIDs will be auto-generated)...\n")
+cat(paste(rep("-", 50), collapse = ""), "\n")
+
+# Capture the warning from empty ID
+workflow <- suppressWarnings(put(temp_dir))
+
+# Show results
+cat("\n📊 Extracted nodes:\n")
+cat(paste(rep("-", 50), collapse = ""), "\n")
+
+for (i in seq_len(nrow(workflow))) {
+  row <- workflow[i, ]
+  cat(sprintf("%-20s: %s\n", "File", row$file_name))
+  cat(sprintf("%-20s: %s\n", "ID", row$id))
+  cat(sprintf("%-20s: %s\n", "Label", row$label))
+  
+  # Check if ID looks like a UUID
+  is_uuid <- grepl("^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", 
+                   row$id, ignore.case = TRUE)
+  cat(sprintf("%-20s: %s\n", "Auto-generated?", ifelse(is_uuid, "Yes (UUID)", "No (explicit)")))
+  cat(paste(rep("-", 50), collapse = ""), "\n")
+}
+
+# Now extract with validation to see the warning
+cat("\n⚠️  Extracting with validation (to show empty ID warning):\n")
+cat(paste(rep("-", 50), collapse = ""), "\n")
+workflow_validated <- put(temp_dir, validate = TRUE)
+
+# Generate diagram
+cat("\n\n🎨 Generating diagram with auto-generated UUIDs:\n")
+cat(paste(rep("-", 50), collapse = ""), "\n")
+put_diagram(workflow[workflow$file_name != "03_empty_id.R", ],  # Exclude the empty ID example
+            title = "Workflow with Auto-Generated UUIDs",
+            node_labels = "label")  # Use labels since UUIDs are not human-friendly
+
+cat("\n\n💡 KEY POINTS:\n")
+cat(paste(rep("=", 50), collapse = ""), "\n")
+cat("1. When 'id' is omitted → UUID is auto-generated\n")
+cat("2. When 'id' is explicit → Your ID is used as-is\n")
+cat("3. When 'id' is empty (\"\") → Validation warning\n")
+cat("4. UUIDs ensure uniqueness across workflows\n")
+cat("5. Use 'label' for human-readable node names\n\n")
+
+cat("📝 BEST PRACTICES:\n")
+cat("• Omit 'id' for quick prototyping\n")
+cat("• Use explicit 'id' for stable references\n")
+cat("• Always provide descriptive 'label' values\n")
+cat("• Avoid empty 'id' values\n\n")
+
+cat("🗂️ Example files created in:\n")
+cat("   ", temp_dir, "\n\n")
+
+# Clean up
+cat("🧹 Cleaning up temporary files...\n")
+unlink(temp_dir, recursive = TRUE)
+
 cat("\n✅ UUID auto-generation example complete!\n")
\ No newline at end of file
diff --git a/inst/examples/variable-reference-example.R b/inst/examples/variable-reference-example.R
index 3d547db..bb27193 100644
--- a/inst/examples/variable-reference-example.R
+++ b/inst/examples/variable-reference-example.R
@@ -1,269 +1,269 @@
-# Variable Reference Example for putior
-# ==============================================================================
-# This example demonstrates how to reference variables and objects within
-# putior workflow diagrams using the "internal" file extension pattern.
-# This technique allows tracking of non-persistent objects that exist only
-# during script execution.
-#
-# Problem: How to reference a variable created by a process as a label in
-# a put comment or track objects that don't persist to disk?
-#
-# Solution: Use the "internal" file extension to indicate non-persistent
-# outputs that represent variables, objects, or temporary results.
-#
-# Source: GitHub issue #2 - Response by @pjt222 (package maintainer)
-# To run this example:
-#   source(system.file("examples", "variable-reference-example.R", package = "putior"))
-# ==============================================================================
-
-library(putior)
-
-# Create temporary directory for example
-temp_dir <- file.path(tempdir(), "putior_variable_reference")
-dir.create(temp_dir, showWarnings = FALSE)
-
-cat("Creating variable reference example in:", temp_dir, "\n")
-
-# ==============================================================================
-# EXAMPLE 1: BASIC VARIABLE TRACKING
-# ==============================================================================
-
-# Script 1: Create a variable and save it
-script1_content <- c(
-  "# Variable Creation Script",
-  "# Demonstrates: Using 'internal' extension to track variables",
-  "# put id:'create_var', label:'Create Variable', node_type:'start', output:'var.internal, var.RData'",
-  "",
-  "# Create a variable (exists in memory)",
-  "var <- letters[1:5]",
-  "print(paste('Variable created:', paste(var, collapse=', ')))",
-  "",
-  "# Also save to disk for persistence (optional)",
-  "save(var, file = 'var.RData')",
-  "",
-  "# The .internal extension tells putior this represents a variable/object",
-  "# that exists during execution, while .RData is the persistent file"
-)
-
-# Script 2: Use the variable from Script 1
-script2_content <- c(
-  "# Variable Processing Script", 
-  "# Demonstrates: Loading persisted data and creating new variables",
-  "# put id:'process_var', label:'Process Variable', node_type:'process', input:'var.RData', output:'processed_var.internal, result.txt'",
-  "",
-  "# Load the variable if working with persistent version",
-  "load('var.RData')",
-  "",
-  "# Process the variable",
-  "processed_var <- toupper(var)",
-  "print(paste('Processed variable:', paste(processed_var, collapse=', ')))",
-  "",
-  "# Save result to file",
-  "writeLines(processed_var, 'result.txt')",
-  "",
-  "# processed_var.internal represents the new variable created in this script",
-  "# var.internal existed only in the previous script's memory"
-)
-
-# Write the scripts
-writeLines(script1_content, file.path(temp_dir, "01_create_variable.R"))
-writeLines(script2_content, file.path(temp_dir, "02_process_variable.R"))
-
-# ==============================================================================
-# EXAMPLE 2: EXTEND THE PIPELINE - BUILD ON PREVIOUS RESULTS
-# ==============================================================================
-
-# Script 3: Further processing using results from Script 2
-script3_content <- c(
-  "# Advanced Processing Script",
-  "# put id:'advanced_process', label:'Advanced Data Processing', node_type:'process', input:'result.txt', output:'enhanced_data.internal, enhanced_results.csv'",
-  "",
-  "# Read results from previous script",
-  "processed_text <- readLines('result.txt')",
-  "",
-  "# Create enhanced data based on previous results",
-  "enhanced_data <- data.frame(",
-  "  original = processed_text,",
-  "  length = nchar(processed_text),",
-  "  reversed = sapply(processed_text, function(x) paste(rev(strsplit(x, '')[[1]]), collapse = ''))",
-  ")",
-  "",
-  "# Save enhanced results",
-  "write.csv(enhanced_data, 'enhanced_results.csv', row.names = FALSE)",
-  "",
-  "print('Enhanced processing completed')"
-)
-
-# Script 4: Final analysis using all previous outputs
-script4_content <- c(
-  "# Final Analysis Script",
-  "# put id:'final_analysis', label:'Final Analysis & Report', node_type:'output', input:'var.RData, enhanced_results.csv', output:'final_report.internal, complete_analysis.txt'",
-  "",
-  "# Load original variable",
-  "load('var.RData')",
-  "",
-  "# Load enhanced results", 
-  "enhanced_data <- read.csv('enhanced_results.csv')",
-  "",
-  "# Create comprehensive final report (in-memory object)",
-  "final_report <- list(",
-  "  original_var_length = length(var),",
-  "  enhanced_data_rows = nrow(enhanced_data),",
-  "  processing_summary = paste('Processed', length(var), 'original items into', nrow(enhanced_data), 'enhanced records')",
-  ")",
-  "",
-  "# Save final analysis",
-  "writeLines(capture.output(str(final_report)), 'complete_analysis.txt')",
-  "",
-  "print('Final analysis completed')"
-)
-
-writeLines(script3_content, file.path(temp_dir, "03_advanced_process.R"))
-writeLines(script4_content, file.path(temp_dir, "04_final_analysis.R"))
-
-cat("Created", length(list.files(temp_dir, pattern = "*.R")), "example scripts\n")
-
-# ==============================================================================
-# EXTRACT WORKFLOW WITH PUTIOR
-# ==============================================================================
-
-cat("\n=== Extracting workflow with putior::put() ===\n")
-workflow <- put(temp_dir)
-
-# Display results
-cat("\nVariable Reference Workflow Results:\n")
-print(workflow)
-
-# ==============================================================================
-# ANALYZE VARIABLE TRACKING
-# ==============================================================================
-
-if (nrow(workflow) > 0) {
-  
-  cat("\n=== Variable Tracking Analysis ===\n")
-  
-  # Find .internal files (variables/objects)
-  all_outputs <- unlist(strsplit(workflow$output[!is.na(workflow$output)], ", "))
-  all_inputs <- unlist(strsplit(workflow$input[!is.na(workflow$input)], ", "))
-  
-  internal_outputs <- all_outputs[grepl("\\.internal$", all_outputs)]
-  internal_inputs <- all_inputs[grepl("\\.internal$", all_inputs)]
-  
-  cat("\nVariable/Object Tracking:\n")
-  cat("  Variables Created:", length(unique(internal_outputs)), "\n")
-  cat("  Variables Used:", length(unique(internal_inputs)), "\n")
-  
-  if (length(internal_outputs) > 0) {
-    cat("  \nVariables/Objects in Workflow:\n")
-    for (var in unique(internal_outputs)) {
-      var_name <- gsub("\\.internal$", "", var)
-      cat("    -", var_name, "\n")
-    }
-  }
-  
-  # Find persistent files  
-  persistent_outputs <- all_outputs[!grepl("\\.internal$", all_outputs)]
-  persistent_inputs <- all_inputs[!grepl("\\.internal$", all_inputs)]
-  
-  cat("\nPersistent Files:\n")
-  cat("  Files Created:", length(unique(persistent_outputs)), "\n")
-  cat("  Files Consumed:", length(unique(persistent_inputs)), "\n")
-  
-  if (length(persistent_outputs) > 0) {
-    cat("  \nPersistent Files in Workflow:\n")
-    for (file in unique(persistent_outputs)) {
-      cat("    -", file, "\n")
-    }
-  }
-  
-  # Show data flow
-  cat("\n=== Data Flow Summary ===\n")
-  for (i in 1:nrow(workflow)) {
-    row <- workflow[i, ]
-    cat("Step", i, ":", row$label, "\n")
-    
-    if (!is.na(row$input)) {
-      inputs <- unlist(strsplit(row$input, ", "))
-      var_inputs <- inputs[grepl("\\.internal$", inputs)]
-      file_inputs <- inputs[!grepl("\\.internal$", inputs)]
-      
-      if (length(var_inputs) > 0) {
-        cat("  Uses variables:", paste(gsub("\\.internal$", "", var_inputs), collapse = ", "), "\n")
-      }
-      if (length(file_inputs) > 0) {
-        cat("  Reads files:", paste(file_inputs, collapse = ", "), "\n")
-      }
-    }
-    
-    if (!is.na(row$output)) {
-      outputs <- unlist(strsplit(row$output, ", "))
-      var_outputs <- outputs[grepl("\\.internal$", outputs)]
-      file_outputs <- outputs[!grepl("\\.internal$", outputs)]
-      
-      if (length(var_outputs) > 0) {
-        cat("  Creates variables:", paste(gsub("\\.internal$", "", var_outputs), collapse = ", "), "\n")
-      }
-      if (length(file_outputs) > 0) {
-        cat("  Writes files:", paste(file_outputs, collapse = ", "), "\n")
-      }
-    }
-    cat("\n")
-  }
-  
-} else {
-  cat("No workflow annotations found. Check PUT annotation syntax.\n")
-}
-
-# ==============================================================================
-# KEY INSIGHTS AND BEST PRACTICES
-# ==============================================================================
-
-cat("=== Key Insights for Variable References ===\n")
-cat("\n1. Use '.internal' Extension for Variables:\n")
-cat("   - Append '.internal' to variable/object names\n") 
-cat("   - Example: 'my_variable.internal'\n")
-cat("   - This tells putior the item represents an in-memory object\n")
-
-cat("\n2. Combine with Persistent Files:\n")
-cat("   - Use both .internal and file outputs when appropriate\n")
-cat("   - Example: output:'data.internal, data.RData'\n")
-cat("   - .internal tracks the variable, .RData tracks the saved file\n")
-
-cat("\n3. .internal Variables Are Script-Local:\n")
-cat("   - .internal variables exist only during script execution\n")
-cat("   - They CANNOT be used as inputs to other scripts\n")
-cat("   - Use persistent files (RData, CSV, etc.) for inter-script data flow\n")
-
-cat("\n4. Multiple Variables in One Step:\n")
-cat("   - List multiple .internal items: 'var1.internal, var2.internal'\n")
-cat("   - Useful for scripts that create multiple objects\n")
-
-cat("\n5. Document Variable Purpose:\n")
-cat("   - Use descriptive names: 'cleaned_data.internal'\n")
-cat("   - The variable name (before .internal) shows what was created\n")
-cat("   - Helps document the computational steps within each script\n")
-
-# ==============================================================================
-# CLEANUP
-# ==============================================================================
-
-cat("\n=== Example Complete ===\n")
-cat("Example files location:", temp_dir, "\n")
-cat("\nTo explore further:\n")
-cat("1. Examine generated scripts to see .internal usage patterns\n")
-cat("2. Modify scripts to track your own variables\n") 
-cat("3. Try generating a diagram with put_diagram() to visualize\n")
-
-# Optional cleanup
-cat("\nClean up temporary files? (y/n): ")
-if (interactive()) {
-  response <- readline()
-  if (tolower(response) == "y") {
-    unlink(temp_dir, recursive = TRUE)
-    cat("Temporary files removed.\n")
-  } else {
-    cat("Temporary files preserved for inspection.\n")
-  }
-} else {
-  cat("(Running non-interactively - files preserved)\n")
+# Variable Reference Example for putior
+# ==============================================================================
+# This example demonstrates how to reference variables and objects within
+# putior workflow diagrams using the "internal" file extension pattern.
+# This technique allows tracking of non-persistent objects that exist only
+# during script execution.
+#
+# Problem: How to reference a variable created by a process as a label in
+# a put comment or track objects that don't persist to disk?
+#
+# Solution: Use the "internal" file extension to indicate non-persistent
+# outputs that represent variables, objects, or temporary results.
+#
+# Source: GitHub issue #2 - Response by @pjt222 (package maintainer)
+# To run this example:
+#   source(system.file("examples", "variable-reference-example.R", package = "putior"))
+# ==============================================================================
+
+library(putior)
+
+# Create temporary directory for example
+temp_dir <- file.path(tempdir(), "putior_variable_reference")
+dir.create(temp_dir, showWarnings = FALSE)
+
+cat("Creating variable reference example in:", temp_dir, "\n")
+
+# ==============================================================================
+# EXAMPLE 1: BASIC VARIABLE TRACKING
+# ==============================================================================
+
+# Script 1: Create a variable and save it
+script1_content <- c(
+  "# Variable Creation Script",
+  "# Demonstrates: Using 'internal' extension to track variables",
+  "# put id:'create_var', label:'Create Variable', node_type:'start', output:'var.internal, var.RData'",
+  "",
+  "# Create a variable (exists in memory)",
+  "var <- letters[1:5]",
+  "print(paste('Variable created:', paste(var, collapse=', ')))",
+  "",
+  "# Also save to disk for persistence (optional)",
+  "save(var, file = 'var.RData')",
+  "",
+  "# The .internal extension tells putior this represents a variable/object",
+  "# that exists during execution, while .RData is the persistent file"
+)
+
+# Script 2: Use the variable from Script 1
+script2_content <- c(
+  "# Variable Processing Script", 
+  "# Demonstrates: Loading persisted data and creating new variables",
+  "# put id:'process_var', label:'Process Variable', node_type:'process', input:'var.RData', output:'processed_var.internal, result.txt'",
+  "",
+  "# Load the variable if working with persistent version",
+  "load('var.RData')",
+  "",
+  "# Process the variable",
+  "processed_var <- toupper(var)",
+  "print(paste('Processed variable:', paste(processed_var, collapse=', ')))",
+  "",
+  "# Save result to file",
+  "writeLines(processed_var, 'result.txt')",
+  "",
+  "# processed_var.internal represents the new variable created in this script",
+  "# var.internal existed only in the previous script's memory"
+)
+
+# Write the scripts
+writeLines(script1_content, file.path(temp_dir, "01_create_variable.R"))
+writeLines(script2_content, file.path(temp_dir, "02_process_variable.R"))
+
+# ==============================================================================
+# EXAMPLE 2: EXTEND THE PIPELINE - BUILD ON PREVIOUS RESULTS
+# ==============================================================================
+
+# Script 3: Further processing using results from Script 2
+script3_content <- c(
+  "# Advanced Processing Script",
+  "# put id:'advanced_process', label:'Advanced Data Processing', node_type:'process', input:'result.txt', output:'enhanced_data.internal, enhanced_results.csv'",
+  "",
+  "# Read results from previous script",
+  "processed_text <- readLines('result.txt')",
+  "",
+  "# Create enhanced data based on previous results",
+  "enhanced_data <- data.frame(",
+  "  original = processed_text,",
+  "  length = nchar(processed_text),",
+  "  reversed = sapply(processed_text, function(x) paste(rev(strsplit(x, '')[[1]]), collapse = ''))",
+  ")",
+  "",
+  "# Save enhanced results",
+  "write.csv(enhanced_data, 'enhanced_results.csv', row.names = FALSE)",
+  "",
+  "print('Enhanced processing completed')"
+)
+
+# Script 4: Final analysis using all previous outputs
+script4_content <- c(
+  "# Final Analysis Script",
+  "# put id:'final_analysis', label:'Final Analysis & Report', node_type:'output', input:'var.RData, enhanced_results.csv', output:'final_report.internal, complete_analysis.txt'",
+  "",
+  "# Load original variable",
+  "load('var.RData')",
+  "",
+  "# Load enhanced results", 
+  "enhanced_data <- read.csv('enhanced_results.csv')",
+  "",
+  "# Create comprehensive final report (in-memory object)",
+  "final_report <- list(",
+  "  original_var_length = length(var),",
+  "  enhanced_data_rows = nrow(enhanced_data),",
+  "  processing_summary = paste('Processed', length(var), 'original items into', nrow(enhanced_data), 'enhanced records')",
+  ")",
+  "",
+  "# Save final analysis",
+  "writeLines(capture.output(str(final_report)), 'complete_analysis.txt')",
+  "",
+  "print('Final analysis completed')"
+)
+
+writeLines(script3_content, file.path(temp_dir, "03_advanced_process.R"))
+writeLines(script4_content, file.path(temp_dir, "04_final_analysis.R"))
+
+cat("Created", length(list.files(temp_dir, pattern = "*.R")), "example scripts\n")
+
+# ==============================================================================
+# EXTRACT WORKFLOW WITH PUTIOR
+# ==============================================================================
+
+cat("\n=== Extracting workflow with putior::put() ===\n")
+workflow <- put(temp_dir)
+
+# Display results
+cat("\nVariable Reference Workflow Results:\n")
+print(workflow)
+
+# ==============================================================================
+# ANALYZE VARIABLE TRACKING
+# ==============================================================================
+
+if (nrow(workflow) > 0) {
+  
+  cat("\n=== Variable Tracking Analysis ===\n")
+  
+  # Find .internal files (variables/objects)
+  all_outputs <- unlist(strsplit(workflow$output[!is.na(workflow$output)], ", "))
+  all_inputs <- unlist(strsplit(workflow$input[!is.na(workflow$input)], ", "))
+  
+  internal_outputs <- all_outputs[grepl("\\.internal$", all_outputs)]
+  internal_inputs <- all_inputs[grepl("\\.internal$", all_inputs)]
+  
+  cat("\nVariable/Object Tracking:\n")
+  cat("  Variables Created:", length(unique(internal_outputs)), "\n")
+  cat("  Variables Used:", length(unique(internal_inputs)), "\n")
+  
+  if (length(internal_outputs) > 0) {
+    cat("  \nVariables/Objects in Workflow:\n")
+    for (var in unique(internal_outputs)) {
+      var_name <- gsub("\\.internal$", "", var)
+      cat("    -", var_name, "\n")
+    }
+  }
+  
+  # Find persistent files  
+  persistent_outputs <- all_outputs[!grepl("\\.internal$", all_outputs)]
+  persistent_inputs <- all_inputs[!grepl("\\.internal$", all_inputs)]
+  
+  cat("\nPersistent Files:\n")
+  cat("  Files Created:", length(unique(persistent_outputs)), "\n")
+  cat("  Files Consumed:", length(unique(persistent_inputs)), "\n")
+  
+  if (length(persistent_outputs) > 0) {
+    cat("  \nPersistent Files in Workflow:\n")
+    for (file in unique(persistent_outputs)) {
+      cat("    -", file, "\n")
+    }
+  }
+  
+  # Show data flow
+  cat("\n=== Data Flow Summary ===\n")
+  for (i in 1:nrow(workflow)) {
+    row <- workflow[i, ]
+    cat("Step", i, ":", row$label, "\n")
+    
+    if (!is.na(row$input)) {
+      inputs <- unlist(strsplit(row$input, ", "))
+      var_inputs <- inputs[grepl("\\.internal$", inputs)]
+      file_inputs <- inputs[!grepl("\\.internal$", inputs)]
+      
+      if (length(var_inputs) > 0) {
+        cat("  Uses variables:", paste(gsub("\\.internal$", "", var_inputs), collapse = ", "), "\n")
+      }
+      if (length(file_inputs) > 0) {
+        cat("  Reads files:", paste(file_inputs, collapse = ", "), "\n")
+      }
+    }
+    
+    if (!is.na(row$output)) {
+      outputs <- unlist(strsplit(row$output, ", "))
+      var_outputs <- outputs[grepl("\\.internal$", outputs)]
+      file_outputs <- outputs[!grepl("\\.internal$", outputs)]
+      
+      if (length(var_outputs) > 0) {
+        cat("  Creates variables:", paste(gsub("\\.internal$", "", var_outputs), collapse = ", "), "\n")
+      }
+      if (length(file_outputs) > 0) {
+        cat("  Writes files:", paste(file_outputs, collapse = ", "), "\n")
+      }
+    }
+    cat("\n")
+  }
+  
+} else {
+  cat("No workflow annotations found. Check PUT annotation syntax.\n")
+}
+
+# ==============================================================================
+# KEY INSIGHTS AND BEST PRACTICES
+# ==============================================================================
+
+cat("=== Key Insights for Variable References ===\n")
+cat("\n1. Use '.internal' Extension for Variables:\n")
+cat("   - Append '.internal' to variable/object names\n") 
+cat("   - Example: 'my_variable.internal'\n")
+cat("   - This tells putior the item represents an in-memory object\n")
+
+cat("\n2. Combine with Persistent Files:\n")
+cat("   - Use both .internal and file outputs when appropriate\n")
+cat("   - Example: output:'data.internal, data.RData'\n")
+cat("   - .internal tracks the variable, .RData tracks the saved file\n")
+
+cat("\n3. .internal Variables Are Script-Local:\n")
+cat("   - .internal variables exist only during script execution\n")
+cat("   - They CANNOT be used as inputs to other scripts\n")
+cat("   - Use persistent files (RData, CSV, etc.) for inter-script data flow\n")
+
+cat("\n4. Multiple Variables in One Step:\n")
+cat("   - List multiple .internal items: 'var1.internal, var2.internal'\n")
+cat("   - Useful for scripts that create multiple objects\n")
+
+cat("\n5. Document Variable Purpose:\n")
+cat("   - Use descriptive names: 'cleaned_data.internal'\n")
+cat("   - The variable name (before .internal) shows what was created\n")
+cat("   - Helps document the computational steps within each script\n")
+
+# ==============================================================================
+# CLEANUP
+# ==============================================================================
+
+cat("\n=== Example Complete ===\n")
+cat("Example files location:", temp_dir, "\n")
+cat("\nTo explore further:\n")
+cat("1. Examine generated scripts to see .internal usage patterns\n")
+cat("2. Modify scripts to track your own variables\n") 
+cat("3. Try generating a diagram with put_diagram() to visualize\n")
+
+# Optional cleanup
+cat("\nClean up temporary files? (y/n): ")
+if (interactive()) {
+  response <- readline()
+  if (tolower(response) == "y") {
+    unlink(temp_dir, recursive = TRUE)
+    cat("Temporary files removed.\n")
+  } else {
+    cat("Temporary files preserved for inspection.\n")
+  }
+} else {
+  cat("(Running non-interactively - files preserved)\n")
 }
\ No newline at end of file
diff --git a/inst/hex-sticker/generated/create-hex.R b/inst/hex-sticker/generated/create-hex.R
index 443ed17..76c8033 100644
--- a/inst/hex-sticker/generated/create-hex.R
+++ b/inst/hex-sticker/generated/create-hex.R
@@ -1,260 +1,260 @@
-# Reproducible Hex Sticker Generation for putior
-# 
-# This script recreates the putior hex sticker design using pure ggplot2
-# for maximum reproducibility and maintainability.
-
-library(ggplot2)
-library(grid)
-
-#' Create the putior hex sticker
-#' 
-#' Generates the putior package hex sticker with all design elements:
-#' - Purple gradient background
-#' - Document icons with "# put" annotation
-#' - Network visualization with connected nodes
-#' - Package name typography
-#' 
-#' @param output_path Path where to save the hex sticker (PNG format)
-#' @param width Width in pixels (default: 400)
-#' @param height Height in pixels (default: 400) 
-#' @param dpi DPI for output (default: 300)
-#' @return Invisible ggplot object
-create_putior_hex <- function(output_path = "putior-hex.png", 
-                              width = 400, 
-                              height = 400, 
-                              dpi = 300) {
-  
-  # Hex sticker dimensions and positioning
-  hex_size <- 1.0
-  center_x <- 0
-  center_y <- 0
-  
-  # Create hexagon coordinates
-  create_hexagon <- function(center_x = 0, center_y = 0, size = 1) {
-    angles <- seq(0, 2*pi, length.out = 7)
-    data.frame(
-      x = center_x + size * cos(angles),
-      y = center_y + size * sin(angles)
-    )
-  }
-  
-  hex_coords <- create_hexagon(center_x, center_y, hex_size)
-  
-  # Color palette (from SVG: rgb(187, 173, 225) to rgb(0, 0, 0))
-  colors <- list(
-    bg_light = "#BBADE1",  # Light purple (top) - exact SVG color
-    bg_dark = "#6B5B95",   # Mid purple 
-    bg_black = "#000000",  # Black (bottom) - exact SVG color
-    border = "#000000",    # Black border (exact SVG)
-    white = "#FFFFFF",     # White for text and elements
-    gray = "#8C8C8C"       # Gray for "# put" text (exact SVG)
-  )
-  
-  # Create base plot
-  p <- ggplot() +
-    # Set coordinate system and limits
-    coord_fixed(ratio = 1) +
-    xlim(-1.3, 1.3) +
-    ylim(-1.3, 1.3) +
-    theme_void() +
-    theme(
-      plot.background = element_rect(fill = "transparent", color = NA),
-      panel.background = element_rect(fill = "transparent", color = NA),
-      plot.margin = margin(0, 0, 0, 0)
-    )
-  
-  # Add gradient background using multiple layers
-  gradient_layers <- 15
-  for (i in 1:gradient_layers) {
-    alpha_val <- 0.15
-    y_offset <- (i - gradient_layers/2) * 0.15
-    
-    # Interpolate color from light to dark based on position
-    color_mix <- i / gradient_layers
-    if (color_mix < 0.3) {
-      fill_color <- colors$bg_light
-    } else if (color_mix < 0.7) {
-      fill_color <- colors$bg_dark
-    } else {
-      fill_color <- colors$bg_black
-    }
-    
-    p <- p + 
-      geom_polygon(
-        data = hex_coords,
-        aes(x = x, y = y + y_offset * 0.1),
-        fill = fill_color,
-        alpha = alpha_val,
-        color = NA
-      )
-  }
-  
-  # Add main hexagon border
-  p <- p + 
-    geom_polygon(
-      data = hex_coords,
-      aes(x = x, y = y),
-      fill = NA,
-      color = colors$border,
-      linewidth = 2
-    )
-  
-  # Document stack coordinates (based on SVG: x="150" y="206" width="100" height="120")
-  # Converting SVG coordinates to our coordinate system
-  doc_base_x <- -0.55
-  doc_base_y <- -0.05
-  doc_width <- 0.32
-  doc_height <- 0.42
-  
-  # Create document icons (3 stacked papers with exact SVG positioning)
-  # SVG has documents at relative positions: (0,20), (10,10), (20,0)
-  docs_data <- data.frame(
-    xmin = c(doc_base_x, doc_base_x + 0.04, doc_base_x + 0.08),
-    xmax = c(doc_base_x + doc_width, doc_base_x + doc_width + 0.04, doc_base_x + doc_width + 0.08),
-    ymin = c(doc_base_y + 0.08, doc_base_y + 0.04, doc_base_y),
-    ymax = c(doc_base_y + doc_height + 0.08, doc_base_y + doc_height + 0.04, doc_base_y + doc_height),
-    layer = c(1, 2, 3)
-  )
-  
-  # Add document rectangles (back to front)
-  for (i in 3:1) {
-    doc <- docs_data[docs_data$layer == i, ]
-    alpha_val <- c(0.7, 0.8, 1.0)[i]
-    
-    p <- p + 
-      geom_rect(
-        data = doc,
-        aes(xmin = xmin, xmax = xmax, ymin = ymin, ymax = ymax),
-        fill = colors$white,
-        color = colors$border,
-        alpha = alpha_val,
-        linewidth = 0.5
-      )
-  }
-  
-  # Add "# put" text on the front document (SVG: x="10" y="70" within group)
-  p <- p + 
-    annotate("text", 
-             x = doc_base_x + 0.14, 
-             y = doc_base_y + 0.27,
-             label = "# put", 
-             size = 2.0, 
-             color = colors$gray,
-             family = "mono",
-             fontface = "bold")
-  
-  # Network visualization (right side - based on SVG group at x="196" y="136")
-  # Converting SVG node positions to our coordinate system
-  # Main large node at (0,10) 40x40, others positioned relative to this
-  nodes <- data.frame(
-    x = c(0.08, 0.28, 0.48, 0.43, 0.58, 0.35, 0.65, 0.5),
-    y = c(0.35, 0.42, 0.17, 0.3, 0.1, 0.1, 0.0, -0.07),
-    size = c(4.0, 2.0, 1.6, 3.0, 1.0, 1.8, 1.4, 2.2),
-    id = 1:8
-  )
-  
-  # Connection data for network edges (based on SVG edge definitions)
-  edges <- data.frame(
-    x1 = c(0.08, 0.08, 0.28, 0.48, 0.43, 0.43, 0.43),
-    y1 = c(0.35, 0.35, 0.42, 0.17, 0.3, 0.3, 0.3),
-    x2 = c(0.28, 0.35, 0.48, 0.35, 0.65, 0.58, 0.5),
-    y2 = c(0.42, 0.1, 0.17, 0.1, 0.0, 0.1, -0.07)
-  )
-  
-  # Add network edges
-  p <- p + 
-    geom_segment(
-      data = edges,
-      aes(x = x1, y = y1, xend = x2, yend = y2),
-      color = colors$white,
-      linewidth = 1.2,
-      alpha = 0.8
-    )
-  
-  # Add network nodes
-  p <- p + 
-    geom_point(
-      data = nodes,
-      aes(x = x, y = y, size = size),
-      color = colors$white,
-      fill = colors$white,
-      shape = 21,
-      stroke = 1.5,
-      alpha = 0.9
-    ) +
-    scale_size_identity()
-  
-  # Add package name "putior" (SVG: x="250" y="306" rotation=330)
-  p <- p + 
-    annotate("text", 
-             x = 0.15, 
-             y = -0.55,
-             label = "putior", 
-             size = 11, 
-             color = colors$white,
-             family = "sans",
-             fontface = "bold",
-             angle = 330)
-  
-  # Save the plot
-  ggsave(
-    filename = output_path,
-    plot = p,
-    width = width/dpi,
-    height = height/dpi,
-    dpi = dpi,
-    bg = "transparent"
-  )
-  
-  # Also save as SVG for comparison (same dimensions as your original)
-  svg_path <- sub("\\.png$", ".svg", output_path)
-  ggsave(
-    filename = svg_path,
-    plot = p,
-    width = 399/72,  # Convert pixels to inches (399px from your SVG)
-    height = 384/72, # Convert pixels to inches (384px from your SVG)
-    bg = "transparent",
-    device = "svg"
-  )
-  
-  cat("✨ Hex sticker saved to:", output_path, "\n")
-  
-  invisible(p)
-}
-
-#' Generate all hex sticker variants
-#' 
-#' Creates multiple versions of the hex sticker for different use cases
-generate_hex_variants <- function(base_dir = ".") {
-  
-  # High-res version for print/packaging
-  create_putior_hex(
-    output_path = file.path(base_dir, "putior-hex-large.png"),
-    width = 800,
-    height = 800,
-    dpi = 300
-  )
-  
-  # Standard web version
-  create_putior_hex(
-    output_path = file.path(base_dir, "putior-hex.png"),
-    width = 400,
-    height = 400,
-    dpi = 150
-  )
-  
-  # Small version for badges/icons
-  create_putior_hex(
-    output_path = file.path(base_dir, "putior-hex-small.png"),
-    width = 200,
-    height = 200,
-    dpi = 100
-  )
-  
-  cat("🎨 Generated all hex sticker variants!\n")
-}
-
-# If script is run directly, generate the hex stickers
-if (!interactive()) {
-  generate_hex_variants()
+# Reproducible Hex Sticker Generation for putior
+# 
+# This script recreates the putior hex sticker design using pure ggplot2
+# for maximum reproducibility and maintainability.
+
+library(ggplot2)
+library(grid)
+
+#' Create the putior hex sticker
+#' 
+#' Generates the putior package hex sticker with all design elements:
+#' - Purple gradient background
+#' - Document icons with "# put" annotation
+#' - Network visualization with connected nodes
+#' - Package name typography
+#' 
+#' @param output_path Path where to save the hex sticker (PNG format)
+#' @param width Width in pixels (default: 400)
+#' @param height Height in pixels (default: 400) 
+#' @param dpi DPI for output (default: 300)
+#' @return Invisible ggplot object
+create_putior_hex <- function(output_path = "putior-hex.png", 
+                              width = 400, 
+                              height = 400, 
+                              dpi = 300) {
+  
+  # Hex sticker dimensions and positioning
+  hex_size <- 1.0
+  center_x <- 0
+  center_y <- 0
+  
+  # Create hexagon coordinates
+  create_hexagon <- function(center_x = 0, center_y = 0, size = 1) {
+    angles <- seq(0, 2*pi, length.out = 7)
+    data.frame(
+      x = center_x + size * cos(angles),
+      y = center_y + size * sin(angles)
+    )
+  }
+  
+  hex_coords <- create_hexagon(center_x, center_y, hex_size)
+  
+  # Color palette (from SVG: rgb(187, 173, 225) to rgb(0, 0, 0))
+  colors <- list(
+    bg_light = "#BBADE1",  # Light purple (top) - exact SVG color
+    bg_dark = "#6B5B95",   # Mid purple 
+    bg_black = "#000000",  # Black (bottom) - exact SVG color
+    border = "#000000",    # Black border (exact SVG)
+    white = "#FFFFFF",     # White for text and elements
+    gray = "#8C8C8C"       # Gray for "# put" text (exact SVG)
+  )
+  
+  # Create base plot
+  p <- ggplot() +
+    # Set coordinate system and limits
+    coord_fixed(ratio = 1) +
+    xlim(-1.3, 1.3) +
+    ylim(-1.3, 1.3) +
+    theme_void() +
+    theme(
+      plot.background = element_rect(fill = "transparent", color = NA),
+      panel.background = element_rect(fill = "transparent", color = NA),
+      plot.margin = margin(0, 0, 0, 0)
+    )
+  
+  # Add gradient background using multiple layers
+  gradient_layers <- 15
+  for (i in 1:gradient_layers) {
+    alpha_val <- 0.15
+    y_offset <- (i - gradient_layers/2) * 0.15
+    
+    # Interpolate color from light to dark based on position
+    color_mix <- i / gradient_layers
+    if (color_mix < 0.3) {
+      fill_color <- colors$bg_light
+    } else if (color_mix < 0.7) {
+      fill_color <- colors$bg_dark
+    } else {
+      fill_color <- colors$bg_black
+    }
+    
+    p <- p + 
+      geom_polygon(
+        data = hex_coords,
+        aes(x = x, y = y + y_offset * 0.1),
+        fill = fill_color,
+        alpha = alpha_val,
+        color = NA
+      )
+  }
+  
+  # Add main hexagon border
+  p <- p + 
+    geom_polygon(
+      data = hex_coords,
+      aes(x = x, y = y),
+      fill = NA,
+      color = colors$border,
+      linewidth = 2
+    )
+  
+  # Document stack coordinates (based on SVG: x="150" y="206" width="100" height="120")
+  # Converting SVG coordinates to our coordinate system
+  doc_base_x <- -0.55
+  doc_base_y <- -0.05
+  doc_width <- 0.32
+  doc_height <- 0.42
+  
+  # Create document icons (3 stacked papers with exact SVG positioning)
+  # SVG has documents at relative positions: (0,20), (10,10), (20,0)
+  docs_data <- data.frame(
+    xmin = c(doc_base_x, doc_base_x + 0.04, doc_base_x + 0.08),
+    xmax = c(doc_base_x + doc_width, doc_base_x + doc_width + 0.04, doc_base_x + doc_width + 0.08),
+    ymin = c(doc_base_y + 0.08, doc_base_y + 0.04, doc_base_y),
+    ymax = c(doc_base_y + doc_height + 0.08, doc_base_y + doc_height + 0.04, doc_base_y + doc_height),
+    layer = c(1, 2, 3)
+  )
+  
+  # Add document rectangles (back to front)
+  for (i in 3:1) {
+    doc <- docs_data[docs_data$layer == i, ]
+    alpha_val <- c(0.7, 0.8, 1.0)[i]
+    
+    p <- p + 
+      geom_rect(
+        data = doc,
+        aes(xmin = xmin, xmax = xmax, ymin = ymin, ymax = ymax),
+        fill = colors$white,
+        color = colors$border,
+        alpha = alpha_val,
+        linewidth = 0.5
+      )
+  }
+  
+  # Add "# put" text on the front document (SVG: x="10" y="70" within group)
+  p <- p + 
+    annotate("text", 
+             x = doc_base_x + 0.14, 
+             y = doc_base_y + 0.27,
+             label = "# put", 
+             size = 2.0, 
+             color = colors$gray,
+             family = "mono",
+             fontface = "bold")
+  
+  # Network visualization (right side - based on SVG group at x="196" y="136")
+  # Converting SVG node positions to our coordinate system
+  # Main large node at (0,10) 40x40, others positioned relative to this
+  nodes <- data.frame(
+    x = c(0.08, 0.28, 0.48, 0.43, 0.58, 0.35, 0.65, 0.5),
+    y = c(0.35, 0.42, 0.17, 0.3, 0.1, 0.1, 0.0, -0.07),
+    size = c(4.0, 2.0, 1.6, 3.0, 1.0, 1.8, 1.4, 2.2),
+    id = 1:8
+  )
+  
+  # Connection data for network edges (based on SVG edge definitions)
+  edges <- data.frame(
+    x1 = c(0.08, 0.08, 0.28, 0.48, 0.43, 0.43, 0.43),
+    y1 = c(0.35, 0.35, 0.42, 0.17, 0.3, 0.3, 0.3),
+    x2 = c(0.28, 0.35, 0.48, 0.35, 0.65, 0.58, 0.5),
+    y2 = c(0.42, 0.1, 0.17, 0.1, 0.0, 0.1, -0.07)
+  )
+  
+  # Add network edges
+  p <- p + 
+    geom_segment(
+      data = edges,
+      aes(x = x1, y = y1, xend = x2, yend = y2),
+      color = colors$white,
+      linewidth = 1.2,
+      alpha = 0.8
+    )
+  
+  # Add network nodes
+  p <- p + 
+    geom_point(
+      data = nodes,
+      aes(x = x, y = y, size = size),
+      color = colors$white,
+      fill = colors$white,
+      shape = 21,
+      stroke = 1.5,
+      alpha = 0.9
+    ) +
+    scale_size_identity()
+  
+  # Add package name "putior" (SVG: x="250" y="306" rotation=330)
+  p <- p + 
+    annotate("text", 
+             x = 0.15, 
+             y = -0.55,
+             label = "putior", 
+             size = 11, 
+             color = colors$white,
+             family = "sans",
+             fontface = "bold",
+             angle = 330)
+  
+  # Save the plot
+  ggsave(
+    filename = output_path,
+    plot = p,
+    width = width/dpi,
+    height = height/dpi,
+    dpi = dpi,
+    bg = "transparent"
+  )
+  
+  # Also save as SVG for comparison (same dimensions as your original)
+  svg_path <- sub("\\.png$", ".svg", output_path)
+  ggsave(
+    filename = svg_path,
+    plot = p,
+    width = 399/72,  # Convert pixels to inches (399px from your SVG)
+    height = 384/72, # Convert pixels to inches (384px from your SVG)
+    bg = "transparent",
+    device = "svg"
+  )
+  
+  cat("✨ Hex sticker saved to:", output_path, "\n")
+  
+  invisible(p)
+}
+
+#' Generate all hex sticker variants
+#' 
+#' Creates multiple versions of the hex sticker for different use cases
+generate_hex_variants <- function(base_dir = ".") {
+  
+  # High-res version for print/packaging
+  create_putior_hex(
+    output_path = file.path(base_dir, "putior-hex-large.png"),
+    width = 800,
+    height = 800,
+    dpi = 300
+  )
+  
+  # Standard web version
+  create_putior_hex(
+    output_path = file.path(base_dir, "putior-hex.png"),
+    width = 400,
+    height = 400,
+    dpi = 150
+  )
+  
+  # Small version for badges/icons
+  create_putior_hex(
+    output_path = file.path(base_dir, "putior-hex-small.png"),
+    width = 200,
+    height = 200,
+    dpi = 100
+  )
+  
+  cat("🎨 Generated all hex sticker variants!\n")
+}
+
+# If script is run directly, generate the hex stickers
+if (!interactive()) {
+  generate_hex_variants()
 }
\ No newline at end of file
diff --git a/renv/activate.R b/renv/activate.R
index 256edab..90b251c 100644
--- a/renv/activate.R
+++ b/renv/activate.R
@@ -1,1334 +1,1334 @@
-
-local({
-
-  # the requested version of renv
-  version <- "1.1.4"
-  attr(version, "sha") <- NULL
-
-  # the project directory
-  project <- Sys.getenv("RENV_PROJECT")
-  if (!nzchar(project))
-    project <- getwd()
-
-  # use start-up diagnostics if enabled
-  diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
-  if (diagnostics) {
-    start <- Sys.time()
-    profile <- tempfile("renv-startup-", fileext = ".Rprof")
-    utils::Rprof(profile)
-    on.exit({
-      utils::Rprof(NULL)
-      elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L)
-      writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed)))
-      writeLines(sprintf("- Profile: %s", profile))
-      print(utils::summaryRprof(profile))
-    }, add = TRUE)
-  }
-
-  # figure out whether the autoloader is enabled
-  enabled <- local({
-
-    # first, check config option
-    override <- getOption("renv.config.autoloader.enabled")
-    if (!is.null(override))
-      return(override)
-
-    # if we're being run in a context where R_LIBS is already set,
-    # don't load -- presumably we're being run as a sub-process and
-    # the parent process has already set up library paths for us
-    rcmd <- Sys.getenv("R_CMD", unset = NA)
-    rlibs <- Sys.getenv("R_LIBS", unset = NA)
-    if (!is.na(rlibs) && !is.na(rcmd))
-      return(FALSE)
-
-    # next, check environment variables
-    # prefer using the configuration one in the future
-    envvars <- c(
-      "RENV_CONFIG_AUTOLOADER_ENABLED",
-      "RENV_AUTOLOADER_ENABLED",
-      "RENV_ACTIVATE_PROJECT"
-    )
-
-    for (envvar in envvars) {
-      envval <- Sys.getenv(envvar, unset = NA)
-      if (!is.na(envval))
-        return(tolower(envval) %in% c("true", "t", "1"))
-    }
-
-    # enable by default
-    TRUE
-
-  })
-
-  # bail if we're not enabled
-  if (!enabled) {
-
-    # if we're not enabled, we might still need to manually load
-    # the user profile here
-    profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
-    if (file.exists(profile)) {
-      cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
-      if (tolower(cfg) %in% c("true", "t", "1"))
-        sys.source(profile, envir = globalenv())
-    }
-
-    return(FALSE)
-
-  }
-
-  # avoid recursion
-  if (identical(getOption("renv.autoloader.running"), TRUE)) {
-    warning("ignoring recursive attempt to run renv autoloader")
-    return(invisible(TRUE))
-  }
-
-  # signal that we're loading renv during R startup
-  options(renv.autoloader.running = TRUE)
-  on.exit(options(renv.autoloader.running = NULL), add = TRUE)
-
-  # signal that we've consented to use renv
-  options(renv.consent = TRUE)
-
-  # load the 'utils' package eagerly -- this ensures that renv shims, which
-  # mask 'utils' packages, will come first on the search path
-  library(utils, lib.loc = .Library)
-
-  # unload renv if it's already been loaded
-  if ("renv" %in% loadedNamespaces())
-    unloadNamespace("renv")
-
-  # load bootstrap tools   
-  ansify <- function(text) {
-    if (renv_ansify_enabled())
-      renv_ansify_enhanced(text)
-    else
-      renv_ansify_default(text)
-  }
-  
-  renv_ansify_enabled <- function() {
-  
-    override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA)
-    if (!is.na(override))
-      return(as.logical(override))
-  
-    pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA)
-    if (identical(pane, "build"))
-      return(FALSE)
-  
-    testthat <- Sys.getenv("TESTTHAT", unset = "false")
-    if (tolower(testthat) %in% "true")
-      return(FALSE)
-  
-    iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false")
-    if (tolower(iderun) %in% "false")
-      return(FALSE)
-  
-    TRUE
-  
-  }
-  
-  renv_ansify_default <- function(text) {
-    text
-  }
-  
-  renv_ansify_enhanced <- function(text) {
-  
-    # R help links
-    pattern <- "`\\?(renv::(?:[^`])+)`"
-    replacement <- "`\033]8;;x-r-help:\\1\a?\\1\033]8;;\a`"
-    text <- gsub(pattern, replacement, text, perl = TRUE)
-  
-    # runnable code
-    pattern <- "`(renv::(?:[^`])+)`"
-    replacement <- "`\033]8;;x-r-run:\\1\a\\1\033]8;;\a`"
-    text <- gsub(pattern, replacement, text, perl = TRUE)
-  
-    # return ansified text
-    text
-  
-  }
-  
-  renv_ansify_init <- function() {
-  
-    envir <- renv_envir_self()
-    if (renv_ansify_enabled())
-      assign("ansify", renv_ansify_enhanced, envir = envir)
-    else
-      assign("ansify", renv_ansify_default, envir = envir)
-  
-  }
-  
-  `%||%` <- function(x, y) {
-    if (is.null(x)) y else x
-  }
-  
-  catf <- function(fmt, ..., appendLF = TRUE) {
-  
-    quiet <- getOption("renv.bootstrap.quiet", default = FALSE)
-    if (quiet)
-      return(invisible())
-  
-    msg <- sprintf(fmt, ...)
-    cat(msg, file = stdout(), sep = if (appendLF) "\n" else "")
-  
-    invisible(msg)
-  
-  }
-  
-  header <- function(label,
-                     ...,
-                     prefix = "#",
-                     suffix = "-",
-                     n = min(getOption("width"), 78))
-  {
-    label <- sprintf(label, ...)
-    n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L)
-    if (n <= 0)
-      return(paste(prefix, label))
-  
-    tail <- paste(rep.int(suffix, n), collapse = "")
-    paste0(prefix, " ", label, " ", tail)
-  
-  }
-  
-  heredoc <- function(text, leave = 0) {
-  
-    # remove leading, trailing whitespace
-    trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
-  
-    # split into lines
-    lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
-  
-    # compute common indent
-    indent <- regexpr("[^[:space:]]", lines)
-    common <- min(setdiff(indent, -1L)) - leave
-    text <- paste(substring(lines, common), collapse = "\n")
-  
-    # substitute in ANSI links for executable renv code
-    ansify(text)
-  
-  }
-  
-  bootstrap <- function(version, library) {
-  
-    friendly <- renv_bootstrap_version_friendly(version)
-    section <- header(sprintf("Bootstrapping renv %s", friendly))
-    catf(section)
-  
-    # attempt to download renv
-    catf("- Downloading renv ... ", appendLF = FALSE)
-    withCallingHandlers(
-      tarball <- renv_bootstrap_download(version),
-      error = function(err) {
-        catf("FAILED")
-        stop("failed to download:\n", conditionMessage(err))
-      }
-    )
-    catf("OK")
-    on.exit(unlink(tarball), add = TRUE)
-  
-    # now attempt to install
-    catf("- Installing renv  ... ", appendLF = FALSE)
-    withCallingHandlers(
-      status <- renv_bootstrap_install(version, tarball, library),
-      error = function(err) {
-        catf("FAILED")
-        stop("failed to install:\n", conditionMessage(err))
-      }
-    )
-    catf("OK")
-  
-    # add empty line to break up bootstrapping from normal output
-    catf("")
-  
-    return(invisible())
-  }
-  
-  renv_bootstrap_tests_running <- function() {
-    getOption("renv.tests.running", default = FALSE)
-  }
-  
-  renv_bootstrap_repos <- function() {
-  
-    # get CRAN repository
-    cran <- getOption("renv.repos.cran", "https://cloud.r-project.org")
-  
-    # check for repos override
-    repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
-    if (!is.na(repos)) {
-  
-      # check for RSPM; if set, use a fallback repository for renv
-      rspm <- Sys.getenv("RSPM", unset = NA)
-      if (identical(rspm, repos))
-        repos <- c(RSPM = rspm, CRAN = cran)
-  
-      return(repos)
-  
-    }
-  
-    # check for lockfile repositories
-    repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity)
-    if (!inherits(repos, "error") && length(repos))
-      return(repos)
-  
-    # retrieve current repos
-    repos <- getOption("repos")
-  
-    # ensure @CRAN@ entries are resolved
-    repos[repos == "@CRAN@"] <- cran
-  
-    # add in renv.bootstrap.repos if set
-    default <- c(FALLBACK = "https://cloud.r-project.org")
-    extra <- getOption("renv.bootstrap.repos", default = default)
-    repos <- c(repos, extra)
-  
-    # remove duplicates that might've snuck in
-    dupes <- duplicated(repos) | duplicated(names(repos))
-    repos[!dupes]
-  
-  }
-  
-  renv_bootstrap_repos_lockfile <- function() {
-  
-    lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock")
-    if (!file.exists(lockpath))
-      return(NULL)
-  
-    lockfile <- tryCatch(renv_json_read(lockpath), error = identity)
-    if (inherits(lockfile, "error")) {
-      warning(lockfile)
-      return(NULL)
-    }
-  
-    repos <- lockfile$R$Repositories
-    if (length(repos) == 0)
-      return(NULL)
-  
-    keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1))
-    vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1))
-    names(vals) <- keys
-  
-    return(vals)
-  
-  }
-  
-  renv_bootstrap_download <- function(version) {
-  
-    sha <- attr(version, "sha", exact = TRUE)
-  
-    methods <- if (!is.null(sha)) {
-  
-      # attempting to bootstrap a development version of renv
-      c(
-        function() renv_bootstrap_download_tarball(sha),
-        function() renv_bootstrap_download_github(sha)
-      )
-  
-    } else {
-  
-      # attempting to bootstrap a release version of renv
-      c(
-        function() renv_bootstrap_download_tarball(version),
-        function() renv_bootstrap_download_cran_latest(version),
-        function() renv_bootstrap_download_cran_archive(version)
-      )
-  
-    }
-  
-    for (method in methods) {
-      path <- tryCatch(method(), error = identity)
-      if (is.character(path) && file.exists(path))
-        return(path)
-    }
-  
-    stop("All download methods failed")
-  
-  }
-  
-  renv_bootstrap_download_impl <- function(url, destfile) {
-  
-    mode <- "wb"
-  
-    # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
-    fixup <-
-      Sys.info()[["sysname"]] == "Windows" &&
-      substring(url, 1L, 5L) == "file:"
-  
-    if (fixup)
-      mode <- "w+b"
-  
-    args <- list(
-      url      = url,
-      destfile = destfile,
-      mode     = mode,
-      quiet    = TRUE
-    )
-  
-    if ("headers" %in% names(formals(utils::download.file))) {
-      headers <- renv_bootstrap_download_custom_headers(url)
-      if (length(headers) && is.character(headers))
-        args$headers <- headers
-    }
-  
-    do.call(utils::download.file, args)
-  
-  }
-  
-  renv_bootstrap_download_custom_headers <- function(url) {
-  
-    headers <- getOption("renv.download.headers")
-    if (is.null(headers))
-      return(character())
-  
-    if (!is.function(headers))
-      stopf("'renv.download.headers' is not a function")
-  
-    headers <- headers(url)
-    if (length(headers) == 0L)
-      return(character())
-  
-    if (is.list(headers))
-      headers <- unlist(headers, recursive = FALSE, use.names = TRUE)
-  
-    ok <-
-      is.character(headers) &&
-      is.character(names(headers)) &&
-      all(nzchar(names(headers)))
-  
-    if (!ok)
-      stop("invocation of 'renv.download.headers' did not return a named character vector")
-  
-    headers
-  
-  }
-  
-  renv_bootstrap_download_cran_latest <- function(version) {
-  
-    spec <- renv_bootstrap_download_cran_latest_find(version)
-    type  <- spec$type
-    repos <- spec$repos
-  
-    baseurl <- utils::contrib.url(repos = repos, type = type)
-    ext <- if (identical(type, "source"))
-      ".tar.gz"
-    else if (Sys.info()[["sysname"]] == "Windows")
-      ".zip"
-    else
-      ".tgz"
-    name <- sprintf("renv_%s%s", version, ext)
-    url <- paste(baseurl, name, sep = "/")
-  
-    destfile <- file.path(tempdir(), name)
-    status <- tryCatch(
-      renv_bootstrap_download_impl(url, destfile),
-      condition = identity
-    )
-  
-    if (inherits(status, "condition"))
-      return(FALSE)
-  
-    # report success and return
-    destfile
-  
-  }
-  
-  renv_bootstrap_download_cran_latest_find <- function(version) {
-  
-    # check whether binaries are supported on this system
-    binary <-
-      getOption("renv.bootstrap.binary", default = TRUE) &&
-      !identical(.Platform$pkgType, "source") &&
-      !identical(getOption("pkgType"), "source") &&
-      Sys.info()[["sysname"]] %in% c("Darwin", "Windows")
-  
-    types <- c(if (binary) "binary", "source")
-  
-    # iterate over types + repositories
-    for (type in types) {
-      for (repos in renv_bootstrap_repos()) {
-  
-        # build arguments for utils::available.packages() call
-        args <- list(type = type, repos = repos)
-  
-        # add custom headers if available -- note that
-        # utils::available.packages() will pass this to download.file()
-        if ("headers" %in% names(formals(utils::download.file))) {
-          headers <- renv_bootstrap_download_custom_headers(repos)
-          if (length(headers) && is.character(headers))
-            args$headers <- headers
-        }
-  
-        # retrieve package database
-        db <- tryCatch(
-          as.data.frame(
-            do.call(utils::available.packages, args),
-            stringsAsFactors = FALSE
-          ),
-          error = identity
-        )
-  
-        if (inherits(db, "error"))
-          next
-  
-        # check for compatible entry
-        entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
-        if (nrow(entry) == 0)
-          next
-  
-        # found it; return spec to caller
-        spec <- list(entry = entry, type = type, repos = repos)
-        return(spec)
-  
-      }
-    }
-  
-    # if we got here, we failed to find renv
-    fmt <- "renv %s is not available from your declared package repositories"
-    stop(sprintf(fmt, version))
-  
-  }
-  
-  renv_bootstrap_download_cran_archive <- function(version) {
-  
-    name <- sprintf("renv_%s.tar.gz", version)
-    repos <- renv_bootstrap_repos()
-    urls <- file.path(repos, "src/contrib/Archive/renv", name)
-    destfile <- file.path(tempdir(), name)
-  
-    for (url in urls) {
-  
-      status <- tryCatch(
-        renv_bootstrap_download_impl(url, destfile),
-        condition = identity
-      )
-  
-      if (identical(status, 0L))
-        return(destfile)
-  
-    }
-  
-    return(FALSE)
-  
-  }
-  
-  renv_bootstrap_download_tarball <- function(version) {
-  
-    # if the user has provided the path to a tarball via
-    # an environment variable, then use it
-    tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA)
-    if (is.na(tarball))
-      return()
-  
-    # allow directories
-    if (dir.exists(tarball)) {
-      name <- sprintf("renv_%s.tar.gz", version)
-      tarball <- file.path(tarball, name)
-    }
-  
-    # bail if it doesn't exist
-    if (!file.exists(tarball)) {
-  
-      # let the user know we weren't able to honour their request
-      fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist."
-      msg <- sprintf(fmt, tarball)
-      warning(msg)
-  
-      # bail
-      return()
-  
-    }
-  
-    catf("- Using local tarball '%s'.", tarball)
-    tarball
-  
-  }
-  
-  renv_bootstrap_github_token <- function() {
-    for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) {
-      envval <- Sys.getenv(envvar, unset = NA)
-      if (!is.na(envval))
-        return(envval)
-    }
-  }
-  
-  renv_bootstrap_download_github <- function(version) {
-  
-    enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
-    if (!identical(enabled, "TRUE"))
-      return(FALSE)
-  
-    # prepare download options
-    token <- renv_bootstrap_github_token()
-    if (is.null(token))
-      token <- ""
-  
-    if (nzchar(Sys.which("curl")) && nzchar(token)) {
-      fmt <- "--location --fail --header \"Authorization: token %s\""
-      extra <- sprintf(fmt, token)
-      saved <- options("download.file.method", "download.file.extra")
-      options(download.file.method = "curl", download.file.extra = extra)
-      on.exit(do.call(base::options, saved), add = TRUE)
-    } else if (nzchar(Sys.which("wget")) && nzchar(token)) {
-      fmt <- "--header=\"Authorization: token %s\""
-      extra <- sprintf(fmt, token)
-      saved <- options("download.file.method", "download.file.extra")
-      options(download.file.method = "wget", download.file.extra = extra)
-      on.exit(do.call(base::options, saved), add = TRUE)
-    }
-  
-    url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version)
-    name <- sprintf("renv_%s.tar.gz", version)
-    destfile <- file.path(tempdir(), name)
-  
-    status <- tryCatch(
-      renv_bootstrap_download_impl(url, destfile),
-      condition = identity
-    )
-  
-    if (!identical(status, 0L))
-      return(FALSE)
-  
-    renv_bootstrap_download_augment(destfile)
-  
-    return(destfile)
-  
-  }
-  
-  # Add Sha to DESCRIPTION. This is stop gap until #890, after which we
-  # can use renv::install() to fully capture metadata.
-  renv_bootstrap_download_augment <- function(destfile) {
-    sha <- renv_bootstrap_git_extract_sha1_tar(destfile)
-    if (is.null(sha)) {
-      return()
-    }
-  
-    # Untar
-    tempdir <- tempfile("renv-github-")
-    on.exit(unlink(tempdir, recursive = TRUE), add = TRUE)
-    untar(destfile, exdir = tempdir)
-    pkgdir <- dir(tempdir, full.names = TRUE)[[1]]
-  
-    # Modify description
-    desc_path <- file.path(pkgdir, "DESCRIPTION")
-    desc_lines <- readLines(desc_path)
-    remotes_fields <- c(
-      "RemoteType: github",
-      "RemoteHost: api.github.com",
-      "RemoteRepo: renv",
-      "RemoteUsername: rstudio",
-      "RemotePkgRef: rstudio/renv",
-      paste("RemoteRef: ", sha),
-      paste("RemoteSha: ", sha)
-    )
-    writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path)
-  
-    # Re-tar
-    local({
-      old <- setwd(tempdir)
-      on.exit(setwd(old), add = TRUE)
-  
-      tar(destfile, compression = "gzip")
-    })
-    invisible()
-  }
-  
-  # Extract the commit hash from a git archive. Git archives include the SHA1
-  # hash as the comment field of the tarball pax extended header
-  # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html)
-  # For GitHub archives this should be the first header after the default one
-  # (512 byte) header.
-  renv_bootstrap_git_extract_sha1_tar <- function(bundle) {
-  
-    # open the bundle for reading
-    # We use gzcon for everything because (from ?gzcon)
-    # > Reading from a connection which does not supply a 'gzip' magic
-    # > header is equivalent to reading from the original connection
-    conn <- gzcon(file(bundle, open = "rb", raw = TRUE))
-    on.exit(close(conn))
-  
-    # The default pax header is 512 bytes long and the first pax extended header
-    # with the comment should be 51 bytes long
-    # `52 comment=` (11 chars) + 40 byte SHA1 hash
-    len <- 0x200 + 0x33
-    res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len])
-  
-    if (grepl("^52 comment=", res)) {
-      sub("52 comment=", "", res)
-    } else {
-      NULL
-    }
-  }
-  
-  renv_bootstrap_install <- function(version, tarball, library) {
-  
-    # attempt to install it into project library
-    dir.create(library, showWarnings = FALSE, recursive = TRUE)
-    output <- renv_bootstrap_install_impl(library, tarball)
-  
-    # check for successful install
-    status <- attr(output, "status")
-    if (is.null(status) || identical(status, 0L))
-      return(status)
-  
-    # an error occurred; report it
-    header <- "installation of renv failed"
-    lines <- paste(rep.int("=", nchar(header)), collapse = "")
-    text <- paste(c(header, lines, output), collapse = "\n")
-    stop(text)
-  
-  }
-  
-  renv_bootstrap_install_impl <- function(library, tarball) {
-  
-    # invoke using system2 so we can capture and report output
-    bin <- R.home("bin")
-    exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R"
-    R <- file.path(bin, exe)
-  
-    args <- c(
-      "--vanilla", "CMD", "INSTALL", "--no-multiarch",
-      "-l", shQuote(path.expand(library)),
-      shQuote(path.expand(tarball))
-    )
-  
-    system2(R, args, stdout = TRUE, stderr = TRUE)
-  
-  }
-  
-  renv_bootstrap_platform_prefix_default <- function() {
-  
-    # read version component
-    version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v")
-  
-    # expand placeholders
-    placeholders <- list(
-      list("%v", format(getRversion()[1, 1:2])),
-      list("%V", format(getRversion()[1, 1:3]))
-    )
-  
-    for (placeholder in placeholders)
-      version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE)
-  
-    # include SVN revision for development versions of R
-    # (to avoid sharing platform-specific artefacts with released versions of R)
-    devel <-
-      identical(R.version[["status"]],   "Under development (unstable)") ||
-      identical(R.version[["nickname"]], "Unsuffered Consequences")
-  
-    if (devel)
-      version <- paste(version, R.version[["svn rev"]], sep = "-r")
-  
-    version
-  
-  }
-  
-  renv_bootstrap_platform_prefix <- function() {
-  
-    # construct version prefix
-    version <- renv_bootstrap_platform_prefix_default()
-  
-    # build list of path components
-    components <- c(version, R.version$platform)
-  
-    # include prefix if provided by user
-    prefix <- renv_bootstrap_platform_prefix_impl()
-    if (!is.na(prefix) && nzchar(prefix))
-      components <- c(prefix, components)
-  
-    # build prefix
-    paste(components, collapse = "/")
-  
-  }
-  
-  renv_bootstrap_platform_prefix_impl <- function() {
-  
-    # if an explicit prefix has been supplied, use it
-    prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA)
-    if (!is.na(prefix))
-      return(prefix)
-  
-    # if the user has requested an automatic prefix, generate it
-    auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
-    if (is.na(auto) && getRversion() >= "4.4.0")
-      auto <- "TRUE"
-  
-    if (auto %in% c("TRUE", "True", "true", "1"))
-      return(renv_bootstrap_platform_prefix_auto())
-  
-    # empty string on failure
-    ""
-  
-  }
-  
-  renv_bootstrap_platform_prefix_auto <- function() {
-  
-    prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity)
-    if (inherits(prefix, "error") || prefix %in% "unknown") {
-  
-      msg <- paste(
-        "failed to infer current operating system",
-        "please file a bug report at https://github.com/rstudio/renv/issues",
-        sep = "; "
-      )
-  
-      warning(msg)
-  
-    }
-  
-    prefix
-  
-  }
-  
-  renv_bootstrap_platform_os <- function() {
-  
-    sysinfo <- Sys.info()
-    sysname <- sysinfo[["sysname"]]
-  
-    # handle Windows + macOS up front
-    if (sysname == "Windows")
-      return("windows")
-    else if (sysname == "Darwin")
-      return("macos")
-  
-    # check for os-release files
-    for (file in c("/etc/os-release", "/usr/lib/os-release"))
-      if (file.exists(file))
-        return(renv_bootstrap_platform_os_via_os_release(file, sysinfo))
-  
-    # check for redhat-release files
-    if (file.exists("/etc/redhat-release"))
-      return(renv_bootstrap_platform_os_via_redhat_release())
-  
-    "unknown"
-  
-  }
-  
-  renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) {
-  
-    # read /etc/os-release
-    release <- utils::read.table(
-      file             = file,
-      sep              = "=",
-      quote            = c("\"", "'"),
-      col.names        = c("Key", "Value"),
-      comment.char     = "#",
-      stringsAsFactors = FALSE
-    )
-  
-    vars <- as.list(release$Value)
-    names(vars) <- release$Key
-  
-    # get os name
-    os <- tolower(sysinfo[["sysname"]])
-  
-    # read id
-    id <- "unknown"
-    for (field in c("ID", "ID_LIKE")) {
-      if (field %in% names(vars) && nzchar(vars[[field]])) {
-        id <- vars[[field]]
-        break
-      }
-    }
-  
-    # read version
-    version <- "unknown"
-    for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) {
-      if (field %in% names(vars) && nzchar(vars[[field]])) {
-        version <- vars[[field]]
-        break
-      }
-    }
-  
-    # join together
-    paste(c(os, id, version), collapse = "-")
-  
-  }
-  
-  renv_bootstrap_platform_os_via_redhat_release <- function() {
-  
-    # read /etc/redhat-release
-    contents <- readLines("/etc/redhat-release", warn = FALSE)
-  
-    # infer id
-    id <- if (grepl("centos", contents, ignore.case = TRUE))
-      "centos"
-    else if (grepl("redhat", contents, ignore.case = TRUE))
-      "redhat"
-    else
-      "unknown"
-  
-    # try to find a version component (very hacky)
-    version <- "unknown"
-  
-    parts <- strsplit(contents, "[[:space:]]")[[1L]]
-    for (part in parts) {
-  
-      nv <- tryCatch(numeric_version(part), error = identity)
-      if (inherits(nv, "error"))
-        next
-  
-      version <- nv[1, 1]
-      break
-  
-    }
-  
-    paste(c("linux", id, version), collapse = "-")
-  
-  }
-  
-  renv_bootstrap_library_root_name <- function(project) {
-  
-    # use project name as-is if requested
-    asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE")
-    if (asis)
-      return(basename(project))
-  
-    # otherwise, disambiguate based on project's path
-    id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
-    paste(basename(project), id, sep = "-")
-  
-  }
-  
-  renv_bootstrap_library_root <- function(project) {
-  
-    prefix <- renv_bootstrap_profile_prefix()
-  
-    path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
-    if (!is.na(path))
-      return(paste(c(path, prefix), collapse = "/"))
-  
-    path <- renv_bootstrap_library_root_impl(project)
-    if (!is.null(path)) {
-      name <- renv_bootstrap_library_root_name(project)
-      return(paste(c(path, prefix, name), collapse = "/"))
-    }
-  
-    renv_bootstrap_paths_renv("library", project = project)
-  
-  }
-  
-  renv_bootstrap_library_root_impl <- function(project) {
-  
-    root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
-    if (!is.na(root))
-      return(root)
-  
-    type <- renv_bootstrap_project_type(project)
-    if (identical(type, "package")) {
-      userdir <- renv_bootstrap_user_dir()
-      return(file.path(userdir, "library"))
-    }
-  
-  }
-  
-  renv_bootstrap_validate_version <- function(version, description = NULL) {
-  
-    # resolve description file
-    #
-    # avoid passing lib.loc to `packageDescription()` below, since R will
-    # use the loaded version of the package by default anyhow. note that
-    # this function should only be called after 'renv' is loaded
-    # https://github.com/rstudio/renv/issues/1625
-    description <- description %||% packageDescription("renv")
-  
-    # check whether requested version 'version' matches loaded version of renv
-    sha <- attr(version, "sha", exact = TRUE)
-    valid <- if (!is.null(sha))
-      renv_bootstrap_validate_version_dev(sha, description)
-    else
-      renv_bootstrap_validate_version_release(version, description)
-  
-    if (valid)
-      return(TRUE)
-  
-    # the loaded version of renv doesn't match the requested version;
-    # give the user instructions on how to proceed
-    dev <- identical(description[["RemoteType"]], "github")
-    remote <- if (dev)
-      paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
-    else
-      paste("renv", description[["Version"]], sep = "@")
-  
-    # display both loaded version + sha if available
-    friendly <- renv_bootstrap_version_friendly(
-      version = description[["Version"]],
-      sha     = if (dev) description[["RemoteSha"]]
-    )
-  
-    fmt <- heredoc("
-      renv %1$s was loaded from project library, but this project is configured to use renv %2$s.
-      - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.
-      - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
-    ")
-    catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
-  
-    FALSE
-  
-  }
-  
-  renv_bootstrap_validate_version_dev <- function(version, description) {
-  
-    expected <- description[["RemoteSha"]]
-    if (!is.character(expected))
-      return(FALSE)
-  
-    pattern <- sprintf("^\\Q%s\\E", version)
-    grepl(pattern, expected, perl = TRUE)
-  
-  }
-  
-  renv_bootstrap_validate_version_release <- function(version, description) {
-    expected <- description[["Version"]]
-    is.character(expected) && identical(expected, version)
-  }
-  
-  renv_bootstrap_hash_text <- function(text) {
-  
-    hashfile <- tempfile("renv-hash-")
-    on.exit(unlink(hashfile), add = TRUE)
-  
-    writeLines(text, con = hashfile)
-    tools::md5sum(hashfile)
-  
-  }
-  
-  renv_bootstrap_load <- function(project, libpath, version) {
-  
-    # try to load renv from the project library
-    if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE))
-      return(FALSE)
-  
-    # warn if the version of renv loaded does not match
-    renv_bootstrap_validate_version(version)
-  
-    # execute renv load hooks, if any
-    hooks <- getHook("renv::autoload")
-    for (hook in hooks)
-      if (is.function(hook))
-        tryCatch(hook(), error = warnify)
-  
-    # load the project
-    renv::load(project)
-  
-    TRUE
-  
-  }
-  
-  renv_bootstrap_profile_load <- function(project) {
-  
-    # if RENV_PROFILE is already set, just use that
-    profile <- Sys.getenv("RENV_PROFILE", unset = NA)
-    if (!is.na(profile) && nzchar(profile))
-      return(profile)
-  
-    # check for a profile file (nothing to do if it doesn't exist)
-    path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project)
-    if (!file.exists(path))
-      return(NULL)
-  
-    # read the profile, and set it if it exists
-    contents <- readLines(path, warn = FALSE)
-    if (length(contents) == 0L)
-      return(NULL)
-  
-    # set RENV_PROFILE
-    profile <- contents[[1L]]
-    if (!profile %in% c("", "default"))
-      Sys.setenv(RENV_PROFILE = profile)
-  
-    profile
-  
-  }
-  
-  renv_bootstrap_profile_prefix <- function() {
-    profile <- renv_bootstrap_profile_get()
-    if (!is.null(profile))
-      return(file.path("profiles", profile, "renv"))
-  }
-  
-  renv_bootstrap_profile_get <- function() {
-    profile <- Sys.getenv("RENV_PROFILE", unset = "")
-    renv_bootstrap_profile_normalize(profile)
-  }
-  
-  renv_bootstrap_profile_set <- function(profile) {
-    profile <- renv_bootstrap_profile_normalize(profile)
-    if (is.null(profile))
-      Sys.unsetenv("RENV_PROFILE")
-    else
-      Sys.setenv(RENV_PROFILE = profile)
-  }
-  
-  renv_bootstrap_profile_normalize <- function(profile) {
-  
-    if (is.null(profile) || profile %in% c("", "default"))
-      return(NULL)
-  
-    profile
-  
-  }
-  
-  renv_bootstrap_path_absolute <- function(path) {
-  
-    substr(path, 1L, 1L) %in% c("~", "/", "\\") || (
-      substr(path, 1L, 1L) %in% c(letters, LETTERS) &&
-      substr(path, 2L, 3L) %in% c(":/", ":\\")
-    )
-  
-  }
-  
-  renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) {
-    renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv")
-    root <- if (renv_bootstrap_path_absolute(renv)) NULL else project
-    prefix <- if (profile) renv_bootstrap_profile_prefix()
-    components <- c(root, renv, prefix, ...)
-    paste(components, collapse = "/")
-  }
-  
-  renv_bootstrap_project_type <- function(path) {
-  
-    descpath <- file.path(path, "DESCRIPTION")
-    if (!file.exists(descpath))
-      return("unknown")
-  
-    desc <- tryCatch(
-      read.dcf(descpath, all = TRUE),
-      error = identity
-    )
-  
-    if (inherits(desc, "error"))
-      return("unknown")
-  
-    type <- desc$Type
-    if (!is.null(type))
-      return(tolower(type))
-  
-    package <- desc$Package
-    if (!is.null(package))
-      return("package")
-  
-    "unknown"
-  
-  }
-  
-  renv_bootstrap_user_dir <- function() {
-    dir <- renv_bootstrap_user_dir_impl()
-    path.expand(chartr("\\", "/", dir))
-  }
-  
-  renv_bootstrap_user_dir_impl <- function() {
-  
-    # use local override if set
-    override <- getOption("renv.userdir.override")
-    if (!is.null(override))
-      return(override)
-  
-    # use R_user_dir if available
-    tools <- asNamespace("tools")
-    if (is.function(tools$R_user_dir))
-      return(tools$R_user_dir("renv", "cache"))
-  
-    # try using our own backfill for older versions of R
-    envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME")
-    for (envvar in envvars) {
-      root <- Sys.getenv(envvar, unset = NA)
-      if (!is.na(root))
-        return(file.path(root, "R/renv"))
-    }
-  
-    # use platform-specific default fallbacks
-    if (Sys.info()[["sysname"]] == "Windows")
-      file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv")
-    else if (Sys.info()[["sysname"]] == "Darwin")
-      "~/Library/Caches/org.R-project.R/R/renv"
-    else
-      "~/.cache/R/renv"
-  
-  }
-  
-  renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) {
-    sha <- sha %||% attr(version, "sha", exact = TRUE)
-    parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L)))
-    paste(parts, collapse = "")
-  }
-  
-  renv_bootstrap_exec <- function(project, libpath, version) {
-    if (!renv_bootstrap_load(project, libpath, version))
-      renv_bootstrap_run(project, libpath, version)
-  }
-  
-  renv_bootstrap_run <- function(project, libpath, version) {
-  
-    # perform bootstrap
-    bootstrap(version, libpath)
-  
-    # exit early if we're just testing bootstrap
-    if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
-      return(TRUE)
-  
-    # try again to load
-    if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
-      return(renv::load(project = project))
-    }
-  
-    # failed to download or load renv; warn the user
-    msg <- c(
-      "Failed to find an renv installation: the project will not be loaded.",
-      "Use `renv::activate()` to re-initialize the project."
-    )
-  
-    warning(paste(msg, collapse = "\n"), call. = FALSE)
-  
-  }
-  
-  renv_json_read <- function(file = NULL, text = NULL) {
-  
-    jlerr <- NULL
-  
-    # if jsonlite is loaded, use that instead
-    if ("jsonlite" %in% loadedNamespaces()) {
-  
-      json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
-      if (!inherits(json, "error"))
-        return(json)
-  
-      jlerr <- json
-  
-    }
-  
-    # otherwise, fall back to the default JSON reader
-    json <- tryCatch(renv_json_read_default(file, text), error = identity)
-    if (!inherits(json, "error"))
-      return(json)
-  
-    # report an error
-    if (!is.null(jlerr))
-      stop(jlerr)
-    else
-      stop(json)
-  
-  }
-  
-  renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
-    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
-    jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
-  }
-  
-  renv_json_read_patterns <- function() {
-  
-    list(
-  
-      # objects
-      list("{", "\t\n\tobject(\t\n\t", TRUE),
-      list("}", "\t\n\t)\t\n\t",       TRUE),
-  
-      # arrays
-      list("[", "\t\n\tarray(\t\n\t", TRUE),
-      list("]", "\n\t\n)\n\t\n",      TRUE),
-  
-      # maps
-      list(":", "\t\n\t=\t\n\t", TRUE),
-  
-      # newlines
-      list("\\u000a", "\n", FALSE)
-  
-    )
-  
-  }
-  
-  renv_json_read_envir <- function() {
-  
-    envir <- new.env(parent = emptyenv())
-  
-    envir[["+"]] <- `+`
-    envir[["-"]] <- `-`
-  
-    envir[["object"]] <- function(...) {
-      result <- list(...)
-      names(result) <- as.character(names(result))
-      result
-    }
-  
-    envir[["array"]] <- list
-  
-    envir[["true"]]  <- TRUE
-    envir[["false"]] <- FALSE
-    envir[["null"]]  <- NULL
-  
-    envir
-  
-  }
-  
-  renv_json_read_remap <- function(object, patterns) {
-  
-    # repair names if necessary
-    if (!is.null(names(object))) {
-  
-      nms <- names(object)
-      for (pattern in patterns)
-        nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE)
-      names(object) <- nms
-  
-    }
-  
-    # repair strings if necessary
-    if (is.character(object)) {
-      for (pattern in patterns)
-        object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE)
-    }
-  
-    # recurse for other objects
-    if (is.recursive(object))
-      for (i in seq_along(object))
-        object[i] <- list(renv_json_read_remap(object[[i]], patterns))
-  
-    # return remapped object
-    object
-  
-  }
-  
-  renv_json_read_default <- function(file = NULL, text = NULL) {
-  
-    # read json text
-    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
-  
-    # convert into something the R parser will understand
-    patterns <- renv_json_read_patterns()
-    transformed <- text
-    for (pattern in patterns)
-      transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE)
-  
-    # parse it
-    rfile <- tempfile("renv-json-", fileext = ".R")
-    on.exit(unlink(rfile), add = TRUE)
-    writeLines(transformed, con = rfile)
-    json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]]
-  
-    # evaluate in safe environment
-    result <- eval(json, envir = renv_json_read_envir())
-  
-    # fix up strings if necessary -- do so only with reversible patterns
-    patterns <- Filter(function(pattern) pattern[[3L]], patterns)
-    renv_json_read_remap(result, patterns)
-  
-  }
-  
-
-  # load the renv profile, if any
-  renv_bootstrap_profile_load(project)
-
-  # construct path to library root
-  root <- renv_bootstrap_library_root(project)
-
-  # construct library prefix for platform
-  prefix <- renv_bootstrap_platform_prefix()
-
-  # construct full libpath
-  libpath <- file.path(root, prefix)
-
-  # run bootstrap code
-  renv_bootstrap_exec(project, libpath, version)
-
-  invisible()
-
-})
+
+local({
+
+  # the requested version of renv
+  version <- "1.1.4"
+  attr(version, "sha") <- NULL
+
+  # the project directory
+  project <- Sys.getenv("RENV_PROJECT")
+  if (!nzchar(project))
+    project <- getwd()
+
+  # use start-up diagnostics if enabled
+  diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
+  if (diagnostics) {
+    start <- Sys.time()
+    profile <- tempfile("renv-startup-", fileext = ".Rprof")
+    utils::Rprof(profile)
+    on.exit({
+      utils::Rprof(NULL)
+      elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L)
+      writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed)))
+      writeLines(sprintf("- Profile: %s", profile))
+      print(utils::summaryRprof(profile))
+    }, add = TRUE)
+  }
+
+  # figure out whether the autoloader is enabled
+  enabled <- local({
+
+    # first, check config option
+    override <- getOption("renv.config.autoloader.enabled")
+    if (!is.null(override))
+      return(override)
+
+    # if we're being run in a context where R_LIBS is already set,
+    # don't load -- presumably we're being run as a sub-process and
+    # the parent process has already set up library paths for us
+    rcmd <- Sys.getenv("R_CMD", unset = NA)
+    rlibs <- Sys.getenv("R_LIBS", unset = NA)
+    if (!is.na(rlibs) && !is.na(rcmd))
+      return(FALSE)
+
+    # next, check environment variables
+    # prefer using the configuration one in the future
+    envvars <- c(
+      "RENV_CONFIG_AUTOLOADER_ENABLED",
+      "RENV_AUTOLOADER_ENABLED",
+      "RENV_ACTIVATE_PROJECT"
+    )
+
+    for (envvar in envvars) {
+      envval <- Sys.getenv(envvar, unset = NA)
+      if (!is.na(envval))
+        return(tolower(envval) %in% c("true", "t", "1"))
+    }
+
+    # enable by default
+    TRUE
+
+  })
+
+  # bail if we're not enabled
+  if (!enabled) {
+
+    # if we're not enabled, we might still need to manually load
+    # the user profile here
+    profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
+    if (file.exists(profile)) {
+      cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
+      if (tolower(cfg) %in% c("true", "t", "1"))
+        sys.source(profile, envir = globalenv())
+    }
+
+    return(FALSE)
+
+  }
+
+  # avoid recursion
+  if (identical(getOption("renv.autoloader.running"), TRUE)) {
+    warning("ignoring recursive attempt to run renv autoloader")
+    return(invisible(TRUE))
+  }
+
+  # signal that we're loading renv during R startup
+  options(renv.autoloader.running = TRUE)
+  on.exit(options(renv.autoloader.running = NULL), add = TRUE)
+
+  # signal that we've consented to use renv
+  options(renv.consent = TRUE)
+
+  # load the 'utils' package eagerly -- this ensures that renv shims, which
+  # mask 'utils' packages, will come first on the search path
+  library(utils, lib.loc = .Library)
+
+  # unload renv if it's already been loaded
+  if ("renv" %in% loadedNamespaces())
+    unloadNamespace("renv")
+
+  # load bootstrap tools   
+  ansify <- function(text) {
+    if (renv_ansify_enabled())
+      renv_ansify_enhanced(text)
+    else
+      renv_ansify_default(text)
+  }
+  
+  renv_ansify_enabled <- function() {
+  
+    override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA)
+    if (!is.na(override))
+      return(as.logical(override))
+  
+    pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA)
+    if (identical(pane, "build"))
+      return(FALSE)
+  
+    testthat <- Sys.getenv("TESTTHAT", unset = "false")
+    if (tolower(testthat) %in% "true")
+      return(FALSE)
+  
+    iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false")
+    if (tolower(iderun) %in% "false")
+      return(FALSE)
+  
+    TRUE
+  
+  }
+  
+  renv_ansify_default <- function(text) {
+    text
+  }
+  
+  renv_ansify_enhanced <- function(text) {
+  
+    # R help links
+    pattern <- "`\\?(renv::(?:[^`])+)`"
+    replacement <- "`\033]8;;x-r-help:\\1\a?\\1\033]8;;\a`"
+    text <- gsub(pattern, replacement, text, perl = TRUE)
+  
+    # runnable code
+    pattern <- "`(renv::(?:[^`])+)`"
+    replacement <- "`\033]8;;x-r-run:\\1\a\\1\033]8;;\a`"
+    text <- gsub(pattern, replacement, text, perl = TRUE)
+  
+    # return ansified text
+    text
+  
+  }
+  
+  renv_ansify_init <- function() {
+  
+    envir <- renv_envir_self()
+    if (renv_ansify_enabled())
+      assign("ansify", renv_ansify_enhanced, envir = envir)
+    else
+      assign("ansify", renv_ansify_default, envir = envir)
+  
+  }
+  
+  `%||%` <- function(x, y) {
+    if (is.null(x)) y else x
+  }
+  
+  catf <- function(fmt, ..., appendLF = TRUE) {
+  
+    quiet <- getOption("renv.bootstrap.quiet", default = FALSE)
+    if (quiet)
+      return(invisible())
+  
+    msg <- sprintf(fmt, ...)
+    cat(msg, file = stdout(), sep = if (appendLF) "\n" else "")
+  
+    invisible(msg)
+  
+  }
+  
+  header <- function(label,
+                     ...,
+                     prefix = "#",
+                     suffix = "-",
+                     n = min(getOption("width"), 78))
+  {
+    label <- sprintf(label, ...)
+    n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L)
+    if (n <= 0)
+      return(paste(prefix, label))
+  
+    tail <- paste(rep.int(suffix, n), collapse = "")
+    paste0(prefix, " ", label, " ", tail)
+  
+  }
+  
+  heredoc <- function(text, leave = 0) {
+  
+    # remove leading, trailing whitespace
+    trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
+  
+    # split into lines
+    lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
+  
+    # compute common indent
+    indent <- regexpr("[^[:space:]]", lines)
+    common <- min(setdiff(indent, -1L)) - leave
+    text <- paste(substring(lines, common), collapse = "\n")
+  
+    # substitute in ANSI links for executable renv code
+    ansify(text)
+  
+  }
+  
+  bootstrap <- function(version, library) {
+  
+    friendly <- renv_bootstrap_version_friendly(version)
+    section <- header(sprintf("Bootstrapping renv %s", friendly))
+    catf(section)
+  
+    # attempt to download renv
+    catf("- Downloading renv ... ", appendLF = FALSE)
+    withCallingHandlers(
+      tarball <- renv_bootstrap_download(version),
+      error = function(err) {
+        catf("FAILED")
+        stop("failed to download:\n", conditionMessage(err))
+      }
+    )
+    catf("OK")
+    on.exit(unlink(tarball), add = TRUE)
+  
+    # now attempt to install
+    catf("- Installing renv  ... ", appendLF = FALSE)
+    withCallingHandlers(
+      status <- renv_bootstrap_install(version, tarball, library),
+      error = function(err) {
+        catf("FAILED")
+        stop("failed to install:\n", conditionMessage(err))
+      }
+    )
+    catf("OK")
+  
+    # add empty line to break up bootstrapping from normal output
+    catf("")
+  
+    return(invisible())
+  }
+  
+  renv_bootstrap_tests_running <- function() {
+    getOption("renv.tests.running", default = FALSE)
+  }
+  
+  renv_bootstrap_repos <- function() {
+  
+    # get CRAN repository
+    cran <- getOption("renv.repos.cran", "https://cloud.r-project.org")
+  
+    # check for repos override
+    repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
+    if (!is.na(repos)) {
+  
+      # check for RSPM; if set, use a fallback repository for renv
+      rspm <- Sys.getenv("RSPM", unset = NA)
+      if (identical(rspm, repos))
+        repos <- c(RSPM = rspm, CRAN = cran)
+  
+      return(repos)
+  
+    }
+  
+    # check for lockfile repositories
+    repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity)
+    if (!inherits(repos, "error") && length(repos))
+      return(repos)
+  
+    # retrieve current repos
+    repos <- getOption("repos")
+  
+    # ensure @CRAN@ entries are resolved
+    repos[repos == "@CRAN@"] <- cran
+  
+    # add in renv.bootstrap.repos if set
+    default <- c(FALLBACK = "https://cloud.r-project.org")
+    extra <- getOption("renv.bootstrap.repos", default = default)
+    repos <- c(repos, extra)
+  
+    # remove duplicates that might've snuck in
+    dupes <- duplicated(repos) | duplicated(names(repos))
+    repos[!dupes]
+  
+  }
+  
+  renv_bootstrap_repos_lockfile <- function() {
+  
+    lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock")
+    if (!file.exists(lockpath))
+      return(NULL)
+  
+    lockfile <- tryCatch(renv_json_read(lockpath), error = identity)
+    if (inherits(lockfile, "error")) {
+      warning(lockfile)
+      return(NULL)
+    }
+  
+    repos <- lockfile$R$Repositories
+    if (length(repos) == 0)
+      return(NULL)
+  
+    keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1))
+    vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1))
+    names(vals) <- keys
+  
+    return(vals)
+  
+  }
+  
+  renv_bootstrap_download <- function(version) {
+  
+    sha <- attr(version, "sha", exact = TRUE)
+  
+    methods <- if (!is.null(sha)) {
+  
+      # attempting to bootstrap a development version of renv
+      c(
+        function() renv_bootstrap_download_tarball(sha),
+        function() renv_bootstrap_download_github(sha)
+      )
+  
+    } else {
+  
+      # attempting to bootstrap a release version of renv
+      c(
+        function() renv_bootstrap_download_tarball(version),
+        function() renv_bootstrap_download_cran_latest(version),
+        function() renv_bootstrap_download_cran_archive(version)
+      )
+  
+    }
+  
+    for (method in methods) {
+      path <- tryCatch(method(), error = identity)
+      if (is.character(path) && file.exists(path))
+        return(path)
+    }
+  
+    stop("All download methods failed")
+  
+  }
+  
+  renv_bootstrap_download_impl <- function(url, destfile) {
+  
+    mode <- "wb"
+  
+    # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
+    fixup <-
+      Sys.info()[["sysname"]] == "Windows" &&
+      substring(url, 1L, 5L) == "file:"
+  
+    if (fixup)
+      mode <- "w+b"
+  
+    args <- list(
+      url      = url,
+      destfile = destfile,
+      mode     = mode,
+      quiet    = TRUE
+    )
+  
+    if ("headers" %in% names(formals(utils::download.file))) {
+      headers <- renv_bootstrap_download_custom_headers(url)
+      if (length(headers) && is.character(headers))
+        args$headers <- headers
+    }
+  
+    do.call(utils::download.file, args)
+  
+  }
+  
+  renv_bootstrap_download_custom_headers <- function(url) {
+  
+    headers <- getOption("renv.download.headers")
+    if (is.null(headers))
+      return(character())
+  
+    if (!is.function(headers))
+      stopf("'renv.download.headers' is not a function")
+  
+    headers <- headers(url)
+    if (length(headers) == 0L)
+      return(character())
+  
+    if (is.list(headers))
+      headers <- unlist(headers, recursive = FALSE, use.names = TRUE)
+  
+    ok <-
+      is.character(headers) &&
+      is.character(names(headers)) &&
+      all(nzchar(names(headers)))
+  
+    if (!ok)
+      stop("invocation of 'renv.download.headers' did not return a named character vector")
+  
+    headers
+  
+  }
+  
+  renv_bootstrap_download_cran_latest <- function(version) {
+  
+    spec <- renv_bootstrap_download_cran_latest_find(version)
+    type  <- spec$type
+    repos <- spec$repos
+  
+    baseurl <- utils::contrib.url(repos = repos, type = type)
+    ext <- if (identical(type, "source"))
+      ".tar.gz"
+    else if (Sys.info()[["sysname"]] == "Windows")
+      ".zip"
+    else
+      ".tgz"
+    name <- sprintf("renv_%s%s", version, ext)
+    url <- paste(baseurl, name, sep = "/")
+  
+    destfile <- file.path(tempdir(), name)
+    status <- tryCatch(
+      renv_bootstrap_download_impl(url, destfile),
+      condition = identity
+    )
+  
+    if (inherits(status, "condition"))
+      return(FALSE)
+  
+    # report success and return
+    destfile
+  
+  }
+  
+  renv_bootstrap_download_cran_latest_find <- function(version) {
+  
+    # check whether binaries are supported on this system
+    binary <-
+      getOption("renv.bootstrap.binary", default = TRUE) &&
+      !identical(.Platform$pkgType, "source") &&
+      !identical(getOption("pkgType"), "source") &&
+      Sys.info()[["sysname"]] %in% c("Darwin", "Windows")
+  
+    types <- c(if (binary) "binary", "source")
+  
+    # iterate over types + repositories
+    for (type in types) {
+      for (repos in renv_bootstrap_repos()) {
+  
+        # build arguments for utils::available.packages() call
+        args <- list(type = type, repos = repos)
+  
+        # add custom headers if available -- note that
+        # utils::available.packages() will pass this to download.file()
+        if ("headers" %in% names(formals(utils::download.file))) {
+          headers <- renv_bootstrap_download_custom_headers(repos)
+          if (length(headers) && is.character(headers))
+            args$headers <- headers
+        }
+  
+        # retrieve package database
+        db <- tryCatch(
+          as.data.frame(
+            do.call(utils::available.packages, args),
+            stringsAsFactors = FALSE
+          ),
+          error = identity
+        )
+  
+        if (inherits(db, "error"))
+          next
+  
+        # check for compatible entry
+        entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
+        if (nrow(entry) == 0)
+          next
+  
+        # found it; return spec to caller
+        spec <- list(entry = entry, type = type, repos = repos)
+        return(spec)
+  
+      }
+    }
+  
+    # if we got here, we failed to find renv
+    fmt <- "renv %s is not available from your declared package repositories"
+    stop(sprintf(fmt, version))
+  
+  }
+  
+  renv_bootstrap_download_cran_archive <- function(version) {
+  
+    name <- sprintf("renv_%s.tar.gz", version)
+    repos <- renv_bootstrap_repos()
+    urls <- file.path(repos, "src/contrib/Archive/renv", name)
+    destfile <- file.path(tempdir(), name)
+  
+    for (url in urls) {
+  
+      status <- tryCatch(
+        renv_bootstrap_download_impl(url, destfile),
+        condition = identity
+      )
+  
+      if (identical(status, 0L))
+        return(destfile)
+  
+    }
+  
+    return(FALSE)
+  
+  }
+  
+  renv_bootstrap_download_tarball <- function(version) {
+  
+    # if the user has provided the path to a tarball via
+    # an environment variable, then use it
+    tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA)
+    if (is.na(tarball))
+      return()
+  
+    # allow directories
+    if (dir.exists(tarball)) {
+      name <- sprintf("renv_%s.tar.gz", version)
+      tarball <- file.path(tarball, name)
+    }
+  
+    # bail if it doesn't exist
+    if (!file.exists(tarball)) {
+  
+      # let the user know we weren't able to honour their request
+      fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist."
+      msg <- sprintf(fmt, tarball)
+      warning(msg)
+  
+      # bail
+      return()
+  
+    }
+  
+    catf("- Using local tarball '%s'.", tarball)
+    tarball
+  
+  }
+  
+  renv_bootstrap_github_token <- function() {
+    for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) {
+      envval <- Sys.getenv(envvar, unset = NA)
+      if (!is.na(envval))
+        return(envval)
+    }
+  }
+  
+  renv_bootstrap_download_github <- function(version) {
+  
+    enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
+    if (!identical(enabled, "TRUE"))
+      return(FALSE)
+  
+    # prepare download options
+    token <- renv_bootstrap_github_token()
+    if (is.null(token))
+      token <- ""
+  
+    if (nzchar(Sys.which("curl")) && nzchar(token)) {
+      fmt <- "--location --fail --header \"Authorization: token %s\""
+      extra <- sprintf(fmt, token)
+      saved <- options("download.file.method", "download.file.extra")
+      options(download.file.method = "curl", download.file.extra = extra)
+      on.exit(do.call(base::options, saved), add = TRUE)
+    } else if (nzchar(Sys.which("wget")) && nzchar(token)) {
+      fmt <- "--header=\"Authorization: token %s\""
+      extra <- sprintf(fmt, token)
+      saved <- options("download.file.method", "download.file.extra")
+      options(download.file.method = "wget", download.file.extra = extra)
+      on.exit(do.call(base::options, saved), add = TRUE)
+    }
+  
+    url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version)
+    name <- sprintf("renv_%s.tar.gz", version)
+    destfile <- file.path(tempdir(), name)
+  
+    status <- tryCatch(
+      renv_bootstrap_download_impl(url, destfile),
+      condition = identity
+    )
+  
+    if (!identical(status, 0L))
+      return(FALSE)
+  
+    renv_bootstrap_download_augment(destfile)
+  
+    return(destfile)
+  
+  }
+  
+  # Add Sha to DESCRIPTION. This is stop gap until #890, after which we
+  # can use renv::install() to fully capture metadata.
+  renv_bootstrap_download_augment <- function(destfile) {
+    sha <- renv_bootstrap_git_extract_sha1_tar(destfile)
+    if (is.null(sha)) {
+      return()
+    }
+  
+    # Untar
+    tempdir <- tempfile("renv-github-")
+    on.exit(unlink(tempdir, recursive = TRUE), add = TRUE)
+    untar(destfile, exdir = tempdir)
+    pkgdir <- dir(tempdir, full.names = TRUE)[[1]]
+  
+    # Modify description
+    desc_path <- file.path(pkgdir, "DESCRIPTION")
+    desc_lines <- readLines(desc_path)
+    remotes_fields <- c(
+      "RemoteType: github",
+      "RemoteHost: api.github.com",
+      "RemoteRepo: renv",
+      "RemoteUsername: rstudio",
+      "RemotePkgRef: rstudio/renv",
+      paste("RemoteRef: ", sha),
+      paste("RemoteSha: ", sha)
+    )
+    writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path)
+  
+    # Re-tar
+    local({
+      old <- setwd(tempdir)
+      on.exit(setwd(old), add = TRUE)
+  
+      tar(destfile, compression = "gzip")
+    })
+    invisible()
+  }
+  
+  # Extract the commit hash from a git archive. Git archives include the SHA1
+  # hash as the comment field of the tarball pax extended header
+  # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html)
+  # For GitHub archives this should be the first header after the default one
+  # (512 byte) header.
+  renv_bootstrap_git_extract_sha1_tar <- function(bundle) {
+  
+    # open the bundle for reading
+    # We use gzcon for everything because (from ?gzcon)
+    # > Reading from a connection which does not supply a 'gzip' magic
+    # > header is equivalent to reading from the original connection
+    conn <- gzcon(file(bundle, open = "rb", raw = TRUE))
+    on.exit(close(conn))
+  
+    # The default pax header is 512 bytes long and the first pax extended header
+    # with the comment should be 51 bytes long
+    # `52 comment=` (11 chars) + 40 byte SHA1 hash
+    len <- 0x200 + 0x33
+    res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len])
+  
+    if (grepl("^52 comment=", res)) {
+      sub("52 comment=", "", res)
+    } else {
+      NULL
+    }
+  }
+  
+  renv_bootstrap_install <- function(version, tarball, library) {
+  
+    # attempt to install it into project library
+    dir.create(library, showWarnings = FALSE, recursive = TRUE)
+    output <- renv_bootstrap_install_impl(library, tarball)
+  
+    # check for successful install
+    status <- attr(output, "status")
+    if (is.null(status) || identical(status, 0L))
+      return(status)
+  
+    # an error occurred; report it
+    header <- "installation of renv failed"
+    lines <- paste(rep.int("=", nchar(header)), collapse = "")
+    text <- paste(c(header, lines, output), collapse = "\n")
+    stop(text)
+  
+  }
+  
+  renv_bootstrap_install_impl <- function(library, tarball) {
+  
+    # invoke using system2 so we can capture and report output
+    bin <- R.home("bin")
+    exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R"
+    R <- file.path(bin, exe)
+  
+    args <- c(
+      "--vanilla", "CMD", "INSTALL", "--no-multiarch",
+      "-l", shQuote(path.expand(library)),
+      shQuote(path.expand(tarball))
+    )
+  
+    system2(R, args, stdout = TRUE, stderr = TRUE)
+  
+  }
+  
+  renv_bootstrap_platform_prefix_default <- function() {
+  
+    # read version component
+    version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v")
+  
+    # expand placeholders
+    placeholders <- list(
+      list("%v", format(getRversion()[1, 1:2])),
+      list("%V", format(getRversion()[1, 1:3]))
+    )
+  
+    for (placeholder in placeholders)
+      version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE)
+  
+    # include SVN revision for development versions of R
+    # (to avoid sharing platform-specific artefacts with released versions of R)
+    devel <-
+      identical(R.version[["status"]],   "Under development (unstable)") ||
+      identical(R.version[["nickname"]], "Unsuffered Consequences")
+  
+    if (devel)
+      version <- paste(version, R.version[["svn rev"]], sep = "-r")
+  
+    version
+  
+  }
+  
+  renv_bootstrap_platform_prefix <- function() {
+  
+    # construct version prefix
+    version <- renv_bootstrap_platform_prefix_default()
+  
+    # build list of path components
+    components <- c(version, R.version$platform)
+  
+    # include prefix if provided by user
+    prefix <- renv_bootstrap_platform_prefix_impl()
+    if (!is.na(prefix) && nzchar(prefix))
+      components <- c(prefix, components)
+  
+    # build prefix
+    paste(components, collapse = "/")
+  
+  }
+  
+  renv_bootstrap_platform_prefix_impl <- function() {
+  
+    # if an explicit prefix has been supplied, use it
+    prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA)
+    if (!is.na(prefix))
+      return(prefix)
+  
+    # if the user has requested an automatic prefix, generate it
+    auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
+    if (is.na(auto) && getRversion() >= "4.4.0")
+      auto <- "TRUE"
+  
+    if (auto %in% c("TRUE", "True", "true", "1"))
+      return(renv_bootstrap_platform_prefix_auto())
+  
+    # empty string on failure
+    ""
+  
+  }
+  
+  renv_bootstrap_platform_prefix_auto <- function() {
+  
+    prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity)
+    if (inherits(prefix, "error") || prefix %in% "unknown") {
+  
+      msg <- paste(
+        "failed to infer current operating system",
+        "please file a bug report at https://github.com/rstudio/renv/issues",
+        sep = "; "
+      )
+  
+      warning(msg)
+  
+    }
+  
+    prefix
+  
+  }
+  
+  renv_bootstrap_platform_os <- function() {
+  
+    sysinfo <- Sys.info()
+    sysname <- sysinfo[["sysname"]]
+  
+    # handle Windows + macOS up front
+    if (sysname == "Windows")
+      return("windows")
+    else if (sysname == "Darwin")
+      return("macos")
+  
+    # check for os-release files
+    for (file in c("/etc/os-release", "/usr/lib/os-release"))
+      if (file.exists(file))
+        return(renv_bootstrap_platform_os_via_os_release(file, sysinfo))
+  
+    # check for redhat-release files
+    if (file.exists("/etc/redhat-release"))
+      return(renv_bootstrap_platform_os_via_redhat_release())
+  
+    "unknown"
+  
+  }
+  
+  renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) {
+  
+    # read /etc/os-release
+    release <- utils::read.table(
+      file             = file,
+      sep              = "=",
+      quote            = c("\"", "'"),
+      col.names        = c("Key", "Value"),
+      comment.char     = "#",
+      stringsAsFactors = FALSE
+    )
+  
+    vars <- as.list(release$Value)
+    names(vars) <- release$Key
+  
+    # get os name
+    os <- tolower(sysinfo[["sysname"]])
+  
+    # read id
+    id <- "unknown"
+    for (field in c("ID", "ID_LIKE")) {
+      if (field %in% names(vars) && nzchar(vars[[field]])) {
+        id <- vars[[field]]
+        break
+      }
+    }
+  
+    # read version
+    version <- "unknown"
+    for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) {
+      if (field %in% names(vars) && nzchar(vars[[field]])) {
+        version <- vars[[field]]
+        break
+      }
+    }
+  
+    # join together
+    paste(c(os, id, version), collapse = "-")
+  
+  }
+  
+  renv_bootstrap_platform_os_via_redhat_release <- function() {
+  
+    # read /etc/redhat-release
+    contents <- readLines("/etc/redhat-release", warn = FALSE)
+  
+    # infer id
+    id <- if (grepl("centos", contents, ignore.case = TRUE))
+      "centos"
+    else if (grepl("redhat", contents, ignore.case = TRUE))
+      "redhat"
+    else
+      "unknown"
+  
+    # try to find a version component (very hacky)
+    version <- "unknown"
+  
+    parts <- strsplit(contents, "[[:space:]]")[[1L]]
+    for (part in parts) {
+  
+      nv <- tryCatch(numeric_version(part), error = identity)
+      if (inherits(nv, "error"))
+        next
+  
+      version <- nv[1, 1]
+      break
+  
+    }
+  
+    paste(c("linux", id, version), collapse = "-")
+  
+  }
+  
+  renv_bootstrap_library_root_name <- function(project) {
+  
+    # use project name as-is if requested
+    asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE")
+    if (asis)
+      return(basename(project))
+  
+    # otherwise, disambiguate based on project's path
+    id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
+    paste(basename(project), id, sep = "-")
+  
+  }
+  
+  renv_bootstrap_library_root <- function(project) {
+  
+    prefix <- renv_bootstrap_profile_prefix()
+  
+    path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
+    if (!is.na(path))
+      return(paste(c(path, prefix), collapse = "/"))
+  
+    path <- renv_bootstrap_library_root_impl(project)
+    if (!is.null(path)) {
+      name <- renv_bootstrap_library_root_name(project)
+      return(paste(c(path, prefix, name), collapse = "/"))
+    }
+  
+    renv_bootstrap_paths_renv("library", project = project)
+  
+  }
+  
+  renv_bootstrap_library_root_impl <- function(project) {
+  
+    root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
+    if (!is.na(root))
+      return(root)
+  
+    type <- renv_bootstrap_project_type(project)
+    if (identical(type, "package")) {
+      userdir <- renv_bootstrap_user_dir()
+      return(file.path(userdir, "library"))
+    }
+  
+  }
+  
+  renv_bootstrap_validate_version <- function(version, description = NULL) {
+  
+    # resolve description file
+    #
+    # avoid passing lib.loc to `packageDescription()` below, since R will
+    # use the loaded version of the package by default anyhow. note that
+    # this function should only be called after 'renv' is loaded
+    # https://github.com/rstudio/renv/issues/1625
+    description <- description %||% packageDescription("renv")
+  
+    # check whether requested version 'version' matches loaded version of renv
+    sha <- attr(version, "sha", exact = TRUE)
+    valid <- if (!is.null(sha))
+      renv_bootstrap_validate_version_dev(sha, description)
+    else
+      renv_bootstrap_validate_version_release(version, description)
+  
+    if (valid)
+      return(TRUE)
+  
+    # the loaded version of renv doesn't match the requested version;
+    # give the user instructions on how to proceed
+    dev <- identical(description[["RemoteType"]], "github")
+    remote <- if (dev)
+      paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
+    else
+      paste("renv", description[["Version"]], sep = "@")
+  
+    # display both loaded version + sha if available
+    friendly <- renv_bootstrap_version_friendly(
+      version = description[["Version"]],
+      sha     = if (dev) description[["RemoteSha"]]
+    )
+  
+    fmt <- heredoc("
+      renv %1$s was loaded from project library, but this project is configured to use renv %2$s.
+      - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.
+      - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
+    ")
+    catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
+  
+    FALSE
+  
+  }
+  
+  renv_bootstrap_validate_version_dev <- function(version, description) {
+  
+    expected <- description[["RemoteSha"]]
+    if (!is.character(expected))
+      return(FALSE)
+  
+    pattern <- sprintf("^\\Q%s\\E", version)
+    grepl(pattern, expected, perl = TRUE)
+  
+  }
+  
+  renv_bootstrap_validate_version_release <- function(version, description) {
+    expected <- description[["Version"]]
+    is.character(expected) && identical(expected, version)
+  }
+  
+  renv_bootstrap_hash_text <- function(text) {
+  
+    hashfile <- tempfile("renv-hash-")
+    on.exit(unlink(hashfile), add = TRUE)
+  
+    writeLines(text, con = hashfile)
+    tools::md5sum(hashfile)
+  
+  }
+  
+  renv_bootstrap_load <- function(project, libpath, version) {
+  
+    # try to load renv from the project library
+    if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE))
+      return(FALSE)
+  
+    # warn if the version of renv loaded does not match
+    renv_bootstrap_validate_version(version)
+  
+    # execute renv load hooks, if any
+    hooks <- getHook("renv::autoload")
+    for (hook in hooks)
+      if (is.function(hook))
+        tryCatch(hook(), error = warnify)
+  
+    # load the project
+    renv::load(project)
+  
+    TRUE
+  
+  }
+  
+  renv_bootstrap_profile_load <- function(project) {
+  
+    # if RENV_PROFILE is already set, just use that
+    profile <- Sys.getenv("RENV_PROFILE", unset = NA)
+    if (!is.na(profile) && nzchar(profile))
+      return(profile)
+  
+    # check for a profile file (nothing to do if it doesn't exist)
+    path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project)
+    if (!file.exists(path))
+      return(NULL)
+  
+    # read the profile, and set it if it exists
+    contents <- readLines(path, warn = FALSE)
+    if (length(contents) == 0L)
+      return(NULL)
+  
+    # set RENV_PROFILE
+    profile <- contents[[1L]]
+    if (!profile %in% c("", "default"))
+      Sys.setenv(RENV_PROFILE = profile)
+  
+    profile
+  
+  }
+  
+  renv_bootstrap_profile_prefix <- function() {
+    profile <- renv_bootstrap_profile_get()
+    if (!is.null(profile))
+      return(file.path("profiles", profile, "renv"))
+  }
+  
+  renv_bootstrap_profile_get <- function() {
+    profile <- Sys.getenv("RENV_PROFILE", unset = "")
+    renv_bootstrap_profile_normalize(profile)
+  }
+  
+  renv_bootstrap_profile_set <- function(profile) {
+    profile <- renv_bootstrap_profile_normalize(profile)
+    if (is.null(profile))
+      Sys.unsetenv("RENV_PROFILE")
+    else
+      Sys.setenv(RENV_PROFILE = profile)
+  }
+  
+  renv_bootstrap_profile_normalize <- function(profile) {
+  
+    if (is.null(profile) || profile %in% c("", "default"))
+      return(NULL)
+  
+    profile
+  
+  }
+  
+  renv_bootstrap_path_absolute <- function(path) {
+  
+    substr(path, 1L, 1L) %in% c("~", "/", "\\") || (
+      substr(path, 1L, 1L) %in% c(letters, LETTERS) &&
+      substr(path, 2L, 3L) %in% c(":/", ":\\")
+    )
+  
+  }
+  
+  renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) {
+    renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv")
+    root <- if (renv_bootstrap_path_absolute(renv)) NULL else project
+    prefix <- if (profile) renv_bootstrap_profile_prefix()
+    components <- c(root, renv, prefix, ...)
+    paste(components, collapse = "/")
+  }
+  
+  renv_bootstrap_project_type <- function(path) {
+  
+    descpath <- file.path(path, "DESCRIPTION")
+    if (!file.exists(descpath))
+      return("unknown")
+  
+    desc <- tryCatch(
+      read.dcf(descpath, all = TRUE),
+      error = identity
+    )
+  
+    if (inherits(desc, "error"))
+      return("unknown")
+  
+    type <- desc$Type
+    if (!is.null(type))
+      return(tolower(type))
+  
+    package <- desc$Package
+    if (!is.null(package))
+      return("package")
+  
+    "unknown"
+  
+  }
+  
+  renv_bootstrap_user_dir <- function() {
+    dir <- renv_bootstrap_user_dir_impl()
+    path.expand(chartr("\\", "/", dir))
+  }
+  
+  renv_bootstrap_user_dir_impl <- function() {
+  
+    # use local override if set
+    override <- getOption("renv.userdir.override")
+    if (!is.null(override))
+      return(override)
+  
+    # use R_user_dir if available
+    tools <- asNamespace("tools")
+    if (is.function(tools$R_user_dir))
+      return(tools$R_user_dir("renv", "cache"))
+  
+    # try using our own backfill for older versions of R
+    envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME")
+    for (envvar in envvars) {
+      root <- Sys.getenv(envvar, unset = NA)
+      if (!is.na(root))
+        return(file.path(root, "R/renv"))
+    }
+  
+    # use platform-specific default fallbacks
+    if (Sys.info()[["sysname"]] == "Windows")
+      file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv")
+    else if (Sys.info()[["sysname"]] == "Darwin")
+      "~/Library/Caches/org.R-project.R/R/renv"
+    else
+      "~/.cache/R/renv"
+  
+  }
+  
+  renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) {
+    sha <- sha %||% attr(version, "sha", exact = TRUE)
+    parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L)))
+    paste(parts, collapse = "")
+  }
+  
+  renv_bootstrap_exec <- function(project, libpath, version) {
+    if (!renv_bootstrap_load(project, libpath, version))
+      renv_bootstrap_run(project, libpath, version)
+  }
+  
+  renv_bootstrap_run <- function(project, libpath, version) {
+  
+    # perform bootstrap
+    bootstrap(version, libpath)
+  
+    # exit early if we're just testing bootstrap
+    if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
+      return(TRUE)
+  
+    # try again to load
+    if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
+      return(renv::load(project = project))
+    }
+  
+    # failed to download or load renv; warn the user
+    msg <- c(
+      "Failed to find an renv installation: the project will not be loaded.",
+      "Use `renv::activate()` to re-initialize the project."
+    )
+  
+    warning(paste(msg, collapse = "\n"), call. = FALSE)
+  
+  }
+  
+  renv_json_read <- function(file = NULL, text = NULL) {
+  
+    jlerr <- NULL
+  
+    # if jsonlite is loaded, use that instead
+    if ("jsonlite" %in% loadedNamespaces()) {
+  
+      json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
+      if (!inherits(json, "error"))
+        return(json)
+  
+      jlerr <- json
+  
+    }
+  
+    # otherwise, fall back to the default JSON reader
+    json <- tryCatch(renv_json_read_default(file, text), error = identity)
+    if (!inherits(json, "error"))
+      return(json)
+  
+    # report an error
+    if (!is.null(jlerr))
+      stop(jlerr)
+    else
+      stop(json)
+  
+  }
+  
+  renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
+    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
+    jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
+  }
+  
+  renv_json_read_patterns <- function() {
+  
+    list(
+  
+      # objects
+      list("{", "\t\n\tobject(\t\n\t", TRUE),
+      list("}", "\t\n\t)\t\n\t",       TRUE),
+  
+      # arrays
+      list("[", "\t\n\tarray(\t\n\t", TRUE),
+      list("]", "\n\t\n)\n\t\n",      TRUE),
+  
+      # maps
+      list(":", "\t\n\t=\t\n\t", TRUE),
+  
+      # newlines
+      list("\\u000a", "\n", FALSE)
+  
+    )
+  
+  }
+  
+  renv_json_read_envir <- function() {
+  
+    envir <- new.env(parent = emptyenv())
+  
+    envir[["+"]] <- `+`
+    envir[["-"]] <- `-`
+  
+    envir[["object"]] <- function(...) {
+      result <- list(...)
+      names(result) <- as.character(names(result))
+      result
+    }
+  
+    envir[["array"]] <- list
+  
+    envir[["true"]]  <- TRUE
+    envir[["false"]] <- FALSE
+    envir[["null"]]  <- NULL
+  
+    envir
+  
+  }
+  
+  renv_json_read_remap <- function(object, patterns) {
+  
+    # repair names if necessary
+    if (!is.null(names(object))) {
+  
+      nms <- names(object)
+      for (pattern in patterns)
+        nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE)
+      names(object) <- nms
+  
+    }
+  
+    # repair strings if necessary
+    if (is.character(object)) {
+      for (pattern in patterns)
+        object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE)
+    }
+  
+    # recurse for other objects
+    if (is.recursive(object))
+      for (i in seq_along(object))
+        object[i] <- list(renv_json_read_remap(object[[i]], patterns))
+  
+    # return remapped object
+    object
+  
+  }
+  
+  renv_json_read_default <- function(file = NULL, text = NULL) {
+  
+    # read json text
+    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
+  
+    # convert into something the R parser will understand
+    patterns <- renv_json_read_patterns()
+    transformed <- text
+    for (pattern in patterns)
+      transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE)
+  
+    # parse it
+    rfile <- tempfile("renv-json-", fileext = ".R")
+    on.exit(unlink(rfile), add = TRUE)
+    writeLines(transformed, con = rfile)
+    json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]]
+  
+    # evaluate in safe environment
+    result <- eval(json, envir = renv_json_read_envir())
+  
+    # fix up strings if necessary -- do so only with reversible patterns
+    patterns <- Filter(function(pattern) pattern[[3L]], patterns)
+    renv_json_read_remap(result, patterns)
+  
+  }
+  
+
+  # load the renv profile, if any
+  renv_bootstrap_profile_load(project)
+
+  # construct path to library root
+  root <- renv_bootstrap_library_root(project)
+
+  # construct library prefix for platform
+  prefix <- renv_bootstrap_platform_prefix()
+
+  # construct full libpath
+  libpath <- file.path(root, prefix)
+
+  # run bootstrap code
+  renv_bootstrap_exec(project, libpath, version)
+
+  invisible()
+
+})
diff --git a/tests/testthat/test-parse.R b/tests/testthat/test-parse.R
index 43f3390..5fab9b5 100644
--- a/tests/testthat/test-parse.R
+++ b/tests/testthat/test-parse.R
@@ -1,360 +1,360 @@
-# Test suite for parsing functionality
-# Tests for parse_put_annotation(), parse_comma_separated_pairs(), and related functions
-
-library(testthat)
-
-# Test basic PUT annotation parsing
-test_that("parse_put_annotation() handles basic formats correctly", {
-  # Standard format
-  result1 <- parse_put_annotation('#put id:"test", label:"Test Label"')
-  expect_equal(result1$id, "test")
-  expect_equal(result1$label, "Test Label")
-  expect_equal(length(result1), 2)
-
-  # With spaces after #
-  result2 <- parse_put_annotation('# put id:"test2", node_type:"process"')
-  expect_equal(result2$id, "test2")
-  expect_equal(result2$node_type, "process")
-
-  # With pipe separator
-  result3 <- parse_put_annotation('#put| id:"test3", input:"data.csv"')
-  expect_equal(result3$id, "test3")
-  expect_equal(result3$input, "data.csv")
-
-  # With colon separator
-  result4 <- parse_put_annotation('#put: id:"test4", output:"result.txt"')
-  expect_equal(result4$id, "test4")
-  expect_equal(result4$output, "result.txt")
-})
-
-test_that("parse_put_annotation() handles different quote styles", {
-  # Single quotes
-  result1 <- parse_put_annotation("#put id:'test1', label:'Single Quotes'")
-  expect_equal(result1$id, "test1")
-  expect_equal(result1$label, "Single Quotes")
-
-  # Mixed quotes
-  result2 <- parse_put_annotation('#put id:"test2", label:\'Mixed Quotes\'')
-  expect_equal(result2$id, "test2")
-  expect_equal(result2$label, "Mixed Quotes")
-
-  # Double quotes (standard)
-  result3 <- parse_put_annotation('#put id:"test3", label:"Double Quotes"')
-  expect_equal(result3$id, "test3")
-  expect_equal(result3$label, "Double Quotes")
-})
-
-test_that("parse_put_annotation() handles whitespace correctly", {
-  # Extra spaces around properties
-  result1 <- parse_put_annotation('#put  id : "test" , label : "Test Label"  ')
-  expect_equal(result1$id, "test")
-  expect_equal(result1$label, "Test Label")
-
-  # Tabs and mixed whitespace
-  result2 <- parse_put_annotation("#put\tid:\t\"test\",\t\tlabel:\t\"Test\"")
-  expect_equal(result2$id, "test")
-  expect_equal(result2$label, "Test")
-
-  # Leading and trailing whitespace in values should be preserved
-  result3 <- parse_put_annotation('#put id:" test ", label:" Test Label "')
-  expect_equal(result3$id, " test ") # Preserve internal whitespace
-  expect_equal(result3$label, " Test Label ")
-})
-
-test_that("parse_put_annotation() handles empty and invalid inputs", {
-  # Empty PUT annotation
-  expect_null(parse_put_annotation("#put"))
-  expect_null(parse_put_annotation("# put "))
-  expect_null(parse_put_annotation("#put|"))
-  expect_null(parse_put_annotation("#put:"))
-
-  # Only whitespace after PUT
-  expect_null(parse_put_annotation("#put   "))
-  expect_null(parse_put_annotation("# put \t\n"))
-
-  # Invalid syntax - no quotes
-  expect_null(parse_put_annotation("#put id:test"))
-  expect_null(parse_put_annotation("#put id:test, label:label"))
-
-  # Invalid syntax - malformed
-  expect_null(parse_put_annotation("#put invalid"))
-  expect_null(parse_put_annotation("#put id"))
-  expect_null(parse_put_annotation("#put :"))
-
-  # Not a PUT annotation
-  expect_null(parse_put_annotation("# Regular comment"))
-  expect_null(parse_put_annotation("puts name:test"))
-  expect_null(parse_put_annotation("put name:test"))
-})
-
-test_that("parse_put_annotation() handles complex property values", {
-  # Commas inside quotes should be preserved
-  result1 <- parse_put_annotation('#put id:"test", label:"Label with, commas, inside"')
-  expect_equal(result1$id, "test")
-  expect_equal(result1$label, "Label with, commas, inside")
-
-  # Multiple commas and complex descriptions
-  result2 <- parse_put_annotation('#put id:"complex", description:"Process A, B, and C data", files:"file1.csv,file2.csv"')
-  expect_equal(result2$description, "Process A, B, and C data")
-  expect_equal(result2$files, "file1.csv,file2.csv")
-
-  # Special characters in values
-  result3 <- parse_put_annotation('#put name:"special", path:"/path/to/file.csv", regex:"\\\\d+\\.csv$"')
-  expect_equal(result3$path, "/path/to/file.csv")
-  expect_equal(result3$regex, "\\\\d+\\.csv$")
-
-  # URLs and complex strings
-  result4 <- parse_put_annotation('#put name:"url_test", endpoint:"https://api.example.com/data?param=value&other=123"')
-  expect_equal(result4$endpoint, "https://api.example.com/data?param=value&other=123")
-})
-
-test_that("parse_put_annotation() handles empty values", {
-  # Empty string values
-  result1 <- parse_put_annotation('#put name:"", label:"Not Empty"')
-  expect_equal(result1$name, "")
-  expect_equal(result1$label, "Not Empty")
-
-  # Multiple empty values
-  result2 <- parse_put_annotation('#put name:"test", input:"", output:"", label:"Test"')
-  expect_equal(result2$name, "test")
-  expect_equal(result2$input, "")
-  expect_equal(result2$output, "")
-  expect_equal(result2$label, "Test")
-})
-
-test_that("parse_put_annotation() auto-generates UUID when id is missing", {
-  skip_if_not_installed("uuid", minimum_version = NULL)
-  
-  # Missing id should get auto-generated UUID
-  result1 <- parse_put_annotation('#put label:"Test Node", node_type:"process"')
-  expect_false(is.null(result1$id))
-  expect_true(nchar(result1$id) > 0)
-  # Check it looks like a UUID (basic check)
-  expect_true(grepl("^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", result1$id, ignore.case = TRUE))
-  
-  # Empty id should NOT get auto-generated
-  result2 <- parse_put_annotation('#put id:"", label:"Test Node"')
-  expect_equal(result2$id, "")
-  
-  # Explicit id should be preserved
-  result3 <- parse_put_annotation('#put id:"my_custom_id", label:"Test Node"')
-  expect_equal(result3$id, "my_custom_id")
-})
-
-test_that("parse_put_annotation() preserves property order", {
-  # Properties should be returned in the order they appear
-  result <- parse_put_annotation('#put zebra:"z", alpha:"a", name:"test", beta:"b", id:"explicit_id"')
-
-  # Check that all properties are present
-  expect_equal(result$zebra, "z")
-  expect_equal(result$alpha, "a")
-  expect_equal(result$name, "test")
-  expect_equal(result$beta, "b")
-  expect_equal(result$id, "explicit_id")
-  expect_equal(length(result), 5)
-})
-
-# Test the comma-separated parsing function
-test_that("parse_comma_separated_pairs() handles basic cases", {
-  # Basic case
-  result1 <- parse_comma_separated_pairs('name:"test", label:"Test Label"')
-  expect_equal(length(result1), 2)
-  expect_true(any(grepl('name:"test"', result1)))
-  expect_true(any(grepl('label:"Test Label"', result1)))
-
-  # Single pair
-  result2 <- parse_comma_separated_pairs('name:"single"')
-  expect_equal(length(result2), 1)
-  expect_equal(trimws(result2[1]), 'name:"single"')
-
-  # No pairs (empty string)
-  result3 <- parse_comma_separated_pairs("")
-  expect_equal(length(result3), 0)
-})
-
-test_that("parse_comma_separated_pairs() respects quotes", {
-  # Commas inside quotes should not split
-  result1 <- parse_comma_separated_pairs('name:"test", desc:"A, B, and C", type:"complex"')
-  expect_equal(length(result1), 3)
-  expect_true(any(grepl("A, B, and C", result1)))
-
-  # Mixed quote types
-  result2 <- parse_comma_separated_pairs('name:"test", label:\'Single quotes\', desc:"Double quotes"')
-  expect_equal(length(result2), 3)
-  expect_true(any(grepl("Single quotes", result2)))
-  expect_true(any(grepl("Double quotes", result2)))
-
-  # Nested-like scenarios (but no actual nesting)
-  result3 <- parse_comma_separated_pairs('code:"if (x > 0) { print(\\"positive\\") }", desc:"Complex code"')
-  expect_equal(length(result3), 2)
-  expect_true(any(grepl("positive", result3)))
-})
-
-test_that("parse_comma_separated_pairs() handles edge cases", {
-  # Extra commas and whitespace
-  result1 <- parse_comma_separated_pairs('name:"test",,, label:"Test",  ')
-  expect_equal(length(result1), 2) # Empty parts should be filtered out
-
-  # Only commas
-  result2 <- parse_comma_separated_pairs(",,,")
-  expect_equal(length(result2), 0)
-
-  # Unmatched quotes (should still try to parse)
-  result3 <- parse_comma_separated_pairs('name:"test", broken:"unmatched')
-  expect_equal(length(result3), 2)
-  expect_true(any(grepl("test", result3)))
-  expect_true(any(grepl("unmatched", result3)))
-})
-
-# Test validation functionality
-test_that("validate_annotation() handles id validation correctly", {
-  # Missing id property should NOT generate issues (auto-generated)
-  props1 <- list(label = "Test", node_type = "process")
-  issues1 <- validate_annotation(props1, "test line")
-  expect_false(any(grepl("id", issues1)))
-
-  # Empty id property should generate issue
-  props2 <- list(id = "", label = "Test", node_type = "process")
-  issues2 <- validate_annotation(props2, "test line")
-  expect_true(any(grepl("Empty.*id", issues2)))
-
-  # Valid id property
-  props3 <- list(id = "valid_id", label = "Test")
-  issues3 <- validate_annotation(props3, "test line")
-  expect_false(any(grepl("id", issues3)))
-})
-
-test_that("validate_annotation() checks node_type values", {
-  # Invalid node type
-  props1 <- list(name = "test", node_type = "invalid_type")
-  issues1 <- validate_annotation(props1, "test line")
-  expect_true(any(grepl("Unusual node_type", issues1)))
-
-  # Valid node types
-  valid_types <- c("input", "process", "output", "decision", "start", "end")
-  for (type in valid_types) {
-    props <- list(name = "test", node_type = type)
-    issues <- validate_annotation(props, "test line")
-    expect_false(any(grepl("Unusual node_type", issues)),
-      info = paste("Type", type, "should be valid")
-    )
-  }
-
-  # Missing node_type (should not generate warning)
-  props2 <- list(name = "test", label = "Test")
-  issues2 <- validate_annotation(props2, "test line")
-  expect_false(any(grepl("node_type", issues2)))
-})
-
-test_that("validate_annotation() checks file extensions", {
-  # File without extension
-  props1 <- list(name = "test", input = "noextension")
-  issues1 <- validate_annotation(props1, "test line")
-  expect_true(any(grepl("missing extension", issues1)))
-
-  # Multiple files, some without extensions
-  props2 <- list(name = "test", input = "file1.csv", output = "noextension")
-  issues2 <- validate_annotation(props2, "test line")
-  expect_true(any(grepl("missing extension", issues2)))
-
-  # All files with extensions (should pass)
-  props3 <- list(name = "test", input = "input.csv", output = "output.json")
-  issues3 <- validate_annotation(props3, "test line")
-  expect_false(any(grepl("missing extension", issues3)))
-
-  # No file references (should pass)
-  props4 <- list(name = "test", label = "Test")
-  issues4 <- validate_annotation(props4, "test line")
-  expect_false(any(grepl("missing extension", issues4)))
-})
-
-test_that("validate_annotation() handles multiple issues", {
-  # Multiple validation problems
-  props <- list(
-    # id missing (but that's ok - auto-generated)
-    id = "",  # empty id - this is an issue
-    node_type = "invalid_type", # invalid node type
-    input = "noextension" # missing file extension
-  )
-
-  issues <- validate_annotation(props, "test line")
-
-  # Should catch the three issues (empty id, invalid node_type, missing extension)
-  expect_true(any(grepl("Empty.*id", issues)))
-  expect_true(any(grepl("Unusual node_type", issues)))
-  expect_true(any(grepl("missing extension", issues)))
-  expect_equal(length(issues), 3)
-})
-
-# Test the exported validation function
-test_that("is_valid_put_annotation() correctly identifies valid annotations", {
-  # Valid annotations
-  expect_true(is_valid_put_annotation('#put name:"test", label:"Test"'))
-  expect_true(is_valid_put_annotation('# put name:"test"'))
-  expect_true(is_valid_put_annotation('#put| name:"test", type:"process"'))
-  expect_true(is_valid_put_annotation("#put name:'test', label:'Test'"))
-
-  # Valid with complex values
-  expect_true(is_valid_put_annotation('#put name:"test", desc:"Complex, description", path:"/path/to/file"'))
-
-  # Invalid annotations
-  expect_false(is_valid_put_annotation("#put"))
-  expect_false(is_valid_put_annotation("#put invalid"))
-  expect_false(is_valid_put_annotation("#put name:noQuotes"))
-  expect_false(is_valid_put_annotation("not a put annotation"))
-  expect_false(is_valid_put_annotation(""))
-  expect_false(is_valid_put_annotation("#comment"))
-})
-
-# Test error handling in parsing
-test_that("parse_put_annotation() handles malformed input gracefully", {
-  # Should not throw errors, just return NULL
-  expect_silent(expect_null(parse_put_annotation(NULL)))
-  expect_silent(expect_null(parse_put_annotation("")))
-  expect_silent(expect_null(parse_put_annotation("malformed")))
-
-  # Very long strings should still work
-  long_value <- paste(rep("a", 1000), collapse = "")
-  long_annotation <- paste0('#put name:"test", long_value:"', long_value, '"')
-  result <- parse_put_annotation(long_annotation)
-  expect_equal(result$name, "test")
-  expect_equal(nchar(result$long_value), 1000)
-})
-
-# Test consistency between parsing and validation
-test_that("Parsing and validation work together correctly", {
-  # Valid annotation should parse and validate
-  valid_annotation <- '#put id:"test_node", label:"Test Node", node_type:"process"'
-  parsed <- parse_put_annotation(valid_annotation)
-  expect_false(is.null(parsed))
-  expect_true(is_valid_put_annotation(valid_annotation))
-
-  issues <- validate_annotation(parsed, valid_annotation)
-  expect_equal(length(issues), 0)
-
-  # Invalid annotation should not parse
-  invalid_annotation <- "#put invalid syntax"
-  parsed_invalid <- parse_put_annotation(invalid_annotation)
-  expect_null(parsed_invalid)
-  expect_false(is_valid_put_annotation(invalid_annotation))
-})
-
-# Performance tests for parsing
-test_that("Parsing performs well with many properties", {
-  # Create annotation with many properties (including id to prevent auto-generation)
-  many_props <- paste(paste0("prop", 1:50, ':"value', 1:50, '"'), collapse = ", ")
-  annotation <- paste0("#put id:\"test\", ", many_props)
-
-  # Should parse without issues
-  start_time <- Sys.time()
-  result <- parse_put_annotation(annotation)
-  end_time <- Sys.time()
-
-  expect_equal(length(result), 51)  # 50 props + id
-  expect_lt(as.numeric(end_time - start_time), 1) # Should take less than 1 second
-
-  # Verify some properties
-  expect_equal(result$id, "test")
-  expect_equal(result$prop1, "value1")
-  expect_equal(result$prop50, "value50")
-})
+# Test suite for parsing functionality
+# Tests for parse_put_annotation(), parse_comma_separated_pairs(), and related functions
+
+library(testthat)
+
+# Test basic PUT annotation parsing
+test_that("parse_put_annotation() handles basic formats correctly", {
+  # Standard format
+  result1 <- parse_put_annotation('#put id:"test", label:"Test Label"')
+  expect_equal(result1$id, "test")
+  expect_equal(result1$label, "Test Label")
+  expect_equal(length(result1), 2)
+
+  # With spaces after #
+  result2 <- parse_put_annotation('# put id:"test2", node_type:"process"')
+  expect_equal(result2$id, "test2")
+  expect_equal(result2$node_type, "process")
+
+  # With pipe separator
+  result3 <- parse_put_annotation('#put| id:"test3", input:"data.csv"')
+  expect_equal(result3$id, "test3")
+  expect_equal(result3$input, "data.csv")
+
+  # With colon separator
+  result4 <- parse_put_annotation('#put: id:"test4", output:"result.txt"')
+  expect_equal(result4$id, "test4")
+  expect_equal(result4$output, "result.txt")
+})
+
+test_that("parse_put_annotation() handles different quote styles", {
+  # Single quotes
+  result1 <- parse_put_annotation("#put id:'test1', label:'Single Quotes'")
+  expect_equal(result1$id, "test1")
+  expect_equal(result1$label, "Single Quotes")
+
+  # Mixed quotes
+  result2 <- parse_put_annotation('#put id:"test2", label:\'Mixed Quotes\'')
+  expect_equal(result2$id, "test2")
+  expect_equal(result2$label, "Mixed Quotes")
+
+  # Double quotes (standard)
+  result3 <- parse_put_annotation('#put id:"test3", label:"Double Quotes"')
+  expect_equal(result3$id, "test3")
+  expect_equal(result3$label, "Double Quotes")
+})
+
+test_that("parse_put_annotation() handles whitespace correctly", {
+  # Extra spaces around properties
+  result1 <- parse_put_annotation('#put  id : "test" , label : "Test Label"  ')
+  expect_equal(result1$id, "test")
+  expect_equal(result1$label, "Test Label")
+
+  # Tabs and mixed whitespace
+  result2 <- parse_put_annotation("#put\tid:\t\"test\",\t\tlabel:\t\"Test\"")
+  expect_equal(result2$id, "test")
+  expect_equal(result2$label, "Test")
+
+  # Leading and trailing whitespace in values should be preserved
+  result3 <- parse_put_annotation('#put id:" test ", label:" Test Label "')
+  expect_equal(result3$id, " test ") # Preserve internal whitespace
+  expect_equal(result3$label, " Test Label ")
+})
+
+test_that("parse_put_annotation() handles empty and invalid inputs", {
+  # Empty PUT annotation
+  expect_null(parse_put_annotation("#put"))
+  expect_null(parse_put_annotation("# put "))
+  expect_null(parse_put_annotation("#put|"))
+  expect_null(parse_put_annotation("#put:"))
+
+  # Only whitespace after PUT
+  expect_null(parse_put_annotation("#put   "))
+  expect_null(parse_put_annotation("# put \t\n"))
+
+  # Invalid syntax - no quotes
+  expect_null(parse_put_annotation("#put id:test"))
+  expect_null(parse_put_annotation("#put id:test, label:label"))
+
+  # Invalid syntax - malformed
+  expect_null(parse_put_annotation("#put invalid"))
+  expect_null(parse_put_annotation("#put id"))
+  expect_null(parse_put_annotation("#put :"))
+
+  # Not a PUT annotation
+  expect_null(parse_put_annotation("# Regular comment"))
+  expect_null(parse_put_annotation("puts name:test"))
+  expect_null(parse_put_annotation("put name:test"))
+})
+
+test_that("parse_put_annotation() handles complex property values", {
+  # Commas inside quotes should be preserved
+  result1 <- parse_put_annotation('#put id:"test", label:"Label with, commas, inside"')
+  expect_equal(result1$id, "test")
+  expect_equal(result1$label, "Label with, commas, inside")
+
+  # Multiple commas and complex descriptions
+  result2 <- parse_put_annotation('#put id:"complex", description:"Process A, B, and C data", files:"file1.csv,file2.csv"')
+  expect_equal(result2$description, "Process A, B, and C data")
+  expect_equal(result2$files, "file1.csv,file2.csv")
+
+  # Special characters in values
+  result3 <- parse_put_annotation('#put name:"special", path:"/path/to/file.csv", regex:"\\\\d+\\.csv$"')
+  expect_equal(result3$path, "/path/to/file.csv")
+  expect_equal(result3$regex, "\\\\d+\\.csv$")
+
+  # URLs and complex strings
+  result4 <- parse_put_annotation('#put name:"url_test", endpoint:"https://api.example.com/data?param=value&other=123"')
+  expect_equal(result4$endpoint, "https://api.example.com/data?param=value&other=123")
+})
+
+test_that("parse_put_annotation() handles empty values", {
+  # Empty string values
+  result1 <- parse_put_annotation('#put name:"", label:"Not Empty"')
+  expect_equal(result1$name, "")
+  expect_equal(result1$label, "Not Empty")
+
+  # Multiple empty values
+  result2 <- parse_put_annotation('#put name:"test", input:"", output:"", label:"Test"')
+  expect_equal(result2$name, "test")
+  expect_equal(result2$input, "")
+  expect_equal(result2$output, "")
+  expect_equal(result2$label, "Test")
+})
+
+test_that("parse_put_annotation() auto-generates UUID when id is missing", {
+  skip_if_not_installed("uuid", minimum_version = NULL)
+  
+  # Missing id should get auto-generated UUID
+  result1 <- parse_put_annotation('#put label:"Test Node", node_type:"process"')
+  expect_false(is.null(result1$id))
+  expect_true(nchar(result1$id) > 0)
+  # Check it looks like a UUID (basic check)
+  expect_true(grepl("^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", result1$id, ignore.case = TRUE))
+  
+  # Empty id should NOT get auto-generated
+  result2 <- parse_put_annotation('#put id:"", label:"Test Node"')
+  expect_equal(result2$id, "")
+  
+  # Explicit id should be preserved
+  result3 <- parse_put_annotation('#put id:"my_custom_id", label:"Test Node"')
+  expect_equal(result3$id, "my_custom_id")
+})
+
+test_that("parse_put_annotation() preserves property order", {
+  # Properties should be returned in the order they appear
+  result <- parse_put_annotation('#put zebra:"z", alpha:"a", name:"test", beta:"b", id:"explicit_id"')
+
+  # Check that all properties are present
+  expect_equal(result$zebra, "z")
+  expect_equal(result$alpha, "a")
+  expect_equal(result$name, "test")
+  expect_equal(result$beta, "b")
+  expect_equal(result$id, "explicit_id")
+  expect_equal(length(result), 5)
+})
+
+# Test the comma-separated parsing function
+test_that("parse_comma_separated_pairs() handles basic cases", {
+  # Basic case
+  result1 <- parse_comma_separated_pairs('name:"test", label:"Test Label"')
+  expect_equal(length(result1), 2)
+  expect_true(any(grepl('name:"test"', result1)))
+  expect_true(any(grepl('label:"Test Label"', result1)))
+
+  # Single pair
+  result2 <- parse_comma_separated_pairs('name:"single"')
+  expect_equal(length(result2), 1)
+  expect_equal(trimws(result2[1]), 'name:"single"')
+
+  # No pairs (empty string)
+  result3 <- parse_comma_separated_pairs("")
+  expect_equal(length(result3), 0)
+})
+
+test_that("parse_comma_separated_pairs() respects quotes", {
+  # Commas inside quotes should not split
+  result1 <- parse_comma_separated_pairs('name:"test", desc:"A, B, and C", type:"complex"')
+  expect_equal(length(result1), 3)
+  expect_true(any(grepl("A, B, and C", result1)))
+
+  # Mixed quote types
+  result2 <- parse_comma_separated_pairs('name:"test", label:\'Single quotes\', desc:"Double quotes"')
+  expect_equal(length(result2), 3)
+  expect_true(any(grepl("Single quotes", result2)))
+  expect_true(any(grepl("Double quotes", result2)))
+
+  # Nested-like scenarios (but no actual nesting)
+  result3 <- parse_comma_separated_pairs('code:"if (x > 0) { print(\\"positive\\") }", desc:"Complex code"')
+  expect_equal(length(result3), 2)
+  expect_true(any(grepl("positive", result3)))
+})
+
+test_that("parse_comma_separated_pairs() handles edge cases", {
+  # Extra commas and whitespace
+  result1 <- parse_comma_separated_pairs('name:"test",,, label:"Test",  ')
+  expect_equal(length(result1), 2) # Empty parts should be filtered out
+
+  # Only commas
+  result2 <- parse_comma_separated_pairs(",,,")
+  expect_equal(length(result2), 0)
+
+  # Unmatched quotes (should still try to parse)
+  result3 <- parse_comma_separated_pairs('name:"test", broken:"unmatched')
+  expect_equal(length(result3), 2)
+  expect_true(any(grepl("test", result3)))
+  expect_true(any(grepl("unmatched", result3)))
+})
+
+# Test validation functionality
+test_that("validate_annotation() handles id validation correctly", {
+  # Missing id property should NOT generate issues (auto-generated)
+  props1 <- list(label = "Test", node_type = "process")
+  issues1 <- validate_annotation(props1, "test line")
+  expect_false(any(grepl("id", issues1)))
+
+  # Empty id property should generate issue
+  props2 <- list(id = "", label = "Test", node_type = "process")
+  issues2 <- validate_annotation(props2, "test line")
+  expect_true(any(grepl("Empty.*id", issues2)))
+
+  # Valid id property
+  props3 <- list(id = "valid_id", label = "Test")
+  issues3 <- validate_annotation(props3, "test line")
+  expect_false(any(grepl("id", issues3)))
+})
+
+test_that("validate_annotation() checks node_type values", {
+  # Invalid node type
+  props1 <- list(name = "test", node_type = "invalid_type")
+  issues1 <- validate_annotation(props1, "test line")
+  expect_true(any(grepl("Unusual node_type", issues1)))
+
+  # Valid node types
+  valid_types <- c("input", "process", "output", "decision", "start", "end")
+  for (type in valid_types) {
+    props <- list(name = "test", node_type = type)
+    issues <- validate_annotation(props, "test line")
+    expect_false(any(grepl("Unusual node_type", issues)),
+      info = paste("Type", type, "should be valid")
+    )
+  }
+
+  # Missing node_type (should not generate warning)
+  props2 <- list(name = "test", label = "Test")
+  issues2 <- validate_annotation(props2, "test line")
+  expect_false(any(grepl("node_type", issues2)))
+})
+
+test_that("validate_annotation() checks file extensions", {
+  # File without extension
+  props1 <- list(name = "test", input = "noextension")
+  issues1 <- validate_annotation(props1, "test line")
+  expect_true(any(grepl("missing extension", issues1)))
+
+  # Multiple files, some without extensions
+  props2 <- list(name = "test", input = "file1.csv", output = "noextension")
+  issues2 <- validate_annotation(props2, "test line")
+  expect_true(any(grepl("missing extension", issues2)))
+
+  # All files with extensions (should pass)
+  props3 <- list(name = "test", input = "input.csv", output = "output.json")
+  issues3 <- validate_annotation(props3, "test line")
+  expect_false(any(grepl("missing extension", issues3)))
+
+  # No file references (should pass)
+  props4 <- list(name = "test", label = "Test")
+  issues4 <- validate_annotation(props4, "test line")
+  expect_false(any(grepl("missing extension", issues4)))
+})
+
+test_that("validate_annotation() handles multiple issues", {
+  # Multiple validation problems
+  props <- list(
+    # id missing (but that's ok - auto-generated)
+    id = "",  # empty id - this is an issue
+    node_type = "invalid_type", # invalid node type
+    input = "noextension" # missing file extension
+  )
+
+  issues <- validate_annotation(props, "test line")
+
+  # Should catch the three issues (empty id, invalid node_type, missing extension)
+  expect_true(any(grepl("Empty.*id", issues)))
+  expect_true(any(grepl("Unusual node_type", issues)))
+  expect_true(any(grepl("missing extension", issues)))
+  expect_equal(length(issues), 3)
+})
+
+# Test the exported validation function
+test_that("is_valid_put_annotation() correctly identifies valid annotations", {
+  # Valid annotations
+  expect_true(is_valid_put_annotation('#put name:"test", label:"Test"'))
+  expect_true(is_valid_put_annotation('# put name:"test"'))
+  expect_true(is_valid_put_annotation('#put| name:"test", type:"process"'))
+  expect_true(is_valid_put_annotation("#put name:'test', label:'Test'"))
+
+  # Valid with complex values
+  expect_true(is_valid_put_annotation('#put name:"test", desc:"Complex, description", path:"/path/to/file"'))
+
+  # Invalid annotations
+  expect_false(is_valid_put_annotation("#put"))
+  expect_false(is_valid_put_annotation("#put invalid"))
+  expect_false(is_valid_put_annotation("#put name:noQuotes"))
+  expect_false(is_valid_put_annotation("not a put annotation"))
+  expect_false(is_valid_put_annotation(""))
+  expect_false(is_valid_put_annotation("#comment"))
+})
+
+# Test error handling in parsing
+test_that("parse_put_annotation() handles malformed input gracefully", {
+  # Should not throw errors, just return NULL
+  expect_silent(expect_null(parse_put_annotation(NULL)))
+  expect_silent(expect_null(parse_put_annotation("")))
+  expect_silent(expect_null(parse_put_annotation("malformed")))
+
+  # Very long strings should still work
+  long_value <- paste(rep("a", 1000), collapse = "")
+  long_annotation <- paste0('#put name:"test", long_value:"', long_value, '"')
+  result <- parse_put_annotation(long_annotation)
+  expect_equal(result$name, "test")
+  expect_equal(nchar(result$long_value), 1000)
+})
+
+# Test consistency between parsing and validation
+test_that("Parsing and validation work together correctly", {
+  # Valid annotation should parse and validate
+  valid_annotation <- '#put id:"test_node", label:"Test Node", node_type:"process"'
+  parsed <- parse_put_annotation(valid_annotation)
+  expect_false(is.null(parsed))
+  expect_true(is_valid_put_annotation(valid_annotation))
+
+  issues <- validate_annotation(parsed, valid_annotation)
+  expect_equal(length(issues), 0)
+
+  # Invalid annotation should not parse
+  invalid_annotation <- "#put invalid syntax"
+  parsed_invalid <- parse_put_annotation(invalid_annotation)
+  expect_null(parsed_invalid)
+  expect_false(is_valid_put_annotation(invalid_annotation))
+})
+
+# Performance tests for parsing
+test_that("Parsing performs well with many properties", {
+  # Create annotation with many properties (including id to prevent auto-generation)
+  many_props <- paste(paste0("prop", 1:50, ':"value', 1:50, '"'), collapse = ", ")
+  annotation <- paste0("#put id:\"test\", ", many_props)
+
+  # Should parse without issues
+  start_time <- Sys.time()
+  result <- parse_put_annotation(annotation)
+  end_time <- Sys.time()
+
+  expect_equal(length(result), 51)  # 50 props + id
+  expect_lt(as.numeric(end_time - start_time), 1) # Should take less than 1 second
+
+  # Verify some properties
+  expect_equal(result$id, "test")
+  expect_equal(result$prop1, "value1")
+  expect_equal(result$prop50, "value50")
+})
diff --git a/tests/testthat/test-put.R b/tests/testthat/test-put.R
index 0da7f7f..4eabf86 100644
--- a/tests/testthat/test-put.R
+++ b/tests/testthat/test-put.R
@@ -1,681 +1,681 @@
-# Test suite for putior package
-library(testthat)
-library(putior)
-
-# Test basic functionality
-test_that("put() handles basic directory scanning", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_basic")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  # Create test files
-  r_content <- c(
-    "# Test R file",
-    "#put id:\"test_r\", label:\"Test R Node\", node_type:\"process\"",
-    "x <- 1"
-  )
-
-  py_content <- c(
-    "# Test Python file",
-    "#put id:\"test_py\", label:\"Test Python Node\", node_type:\"input\"",
-    "x = 1"
-  )
-
-  create_test_file(r_content, "test.R", test_dir)
-  create_test_file(py_content, "test.py", test_dir)
-
-  # Test the function
-  result <- put(test_dir)
-
-  expect_s3_class(result, "data.frame")
-  expect_equal(nrow(result), 2)
-  expect_true(all(c("file_name", "file_type", "id", "label", "node_type") %in% names(result)))
-  expect_equal(sort(result$id), c("test_py", "test_r"))
-  expect_equal(sort(result$file_type), c("py", "r"))
-})
-
-test_that("put() handles single file processing", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_single")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  content <- c(
-    "# Single file test",
-    "#put id:\"single\", label:\"Single Node\", output:\"result.csv\"",
-    "write.csv(data, 'result.csv')"
-  )
-
-  filepath <- create_test_file(content, "single.R", test_dir)
-
-  # Test single file processing
-  result <- put(filepath)
-
-  expect_s3_class(result, "data.frame")
-  expect_equal(nrow(result), 1)
-  expect_equal(result$id, "single")
-  expect_equal(result$output, "result.csv")
-})
-
-test_that("put() handles recursive directory scanning", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_recursive")
-  subdir <- file.path(test_dir, "subdir")
-  dir.create(test_dir, showWarnings = FALSE)
-  dir.create(subdir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  # Create files in main directory
-  create_test_file(c("#put id:\"main\", label:\"Main\""), "main.R", test_dir)
-
-  # Create files in subdirectory
-  create_test_file(c("#put id:\"sub\", label:\"Sub\""), "sub.py", subdir)
-
-  # Test non-recursive (should find 1)
-  result_non_recursive <- put(test_dir, recursive = FALSE)
-  expect_equal(nrow(result_non_recursive), 1)
-
-  # Test recursive (should find 2)
-  result_recursive <- put(test_dir, recursive = TRUE)
-  expect_equal(nrow(result_recursive), 2)
-  expect_true(all(c("main", "sub") %in% result_recursive$id))
-})
-
-test_that("put() defaults to recursive scanning", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_default_recursive")
-  subdir <- file.path(test_dir, "subdir")
-  dir.create(subdir, recursive = TRUE, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  create_test_file(c("#put id:\"top\", label:\"Top\""), "top.R", test_dir)
-  create_test_file(c("#put id:\"nested\", label:\"Nested\""), "nested.R", subdir)
-
-  # Default (no explicit recursive arg) should find both files
-  result <- put(test_dir)
-  expect_equal(nrow(result), 2)
-  expect_true(all(c("top", "nested") %in% result$id))
-})
-
-test_that("put() includes line numbers when requested", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_lines")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  content <- c(
-    "# Line 1",
-    "#put id:\"first\", label:\"First\"", # Line 2
-    "# Line 3",
-    "#put id:\"second\", label:\"Second\"" # Line 4
-  )
-
-  create_test_file(content, "test.R", test_dir)
-
-  # Without line numbers
-  result_no_lines <- put(test_dir, include_line_numbers = FALSE)
-  expect_false("line_number" %in% names(result_no_lines))
-
-  # With line numbers
-  result_with_lines <- put(test_dir, include_line_numbers = TRUE)
-  expect_true("line_number" %in% names(result_with_lines))
-  expect_equal(result_with_lines$line_number, c(2, 4))
-})
-
-# Test annotation parsing
-test_that("parse_put_annotation() handles various formats", {
-  # Basic format
-  result1 <- parse_put_annotation('#put id:"test", label:"Test Label"')
-  expect_equal(result1$id, "test")
-  expect_equal(result1$label, "Test Label")
-
-  # With spaces
-  result2 <- parse_put_annotation('# put id:"test2", node_type:"process"')
-  expect_equal(result2$id, "test2")
-  expect_equal(result2$node_type, "process")
-
-  # With pipe separator
-  result3 <- parse_put_annotation('#put| id:"test3", input:"data.csv"')
-  expect_equal(result3$id, "test3")
-  expect_equal(result3$input, "data.csv")
-
-  # Single quotes
-  result4 <- parse_put_annotation("#put id:'test4', label:'Single Quotes'")
-  expect_equal(result4$id, "test4")
-  expect_equal(result4$label, "Single Quotes")
-
-  # Mixed quotes
-  result5 <- parse_put_annotation('#put id:"test5", label:\'Mixed Quotes\'')
-  expect_equal(result5$id, "test5")
-  expect_equal(result5$label, "Mixed Quotes")
-})
-
-test_that("parse_put_annotation() handles edge cases", {
-  # Empty annotation
-  expect_null(parse_put_annotation("#put"))
-  expect_null(parse_put_annotation("# put "))
-
-  # Invalid syntax
-  expect_null(parse_put_annotation("#put invalid"))
-  expect_null(parse_put_annotation("#put no quotes"))
-
-  # Not a PUT annotation
-  expect_null(parse_put_annotation("# Regular comment"))
-  expect_null(parse_put_annotation("puts something"))
-})
-
-test_that("put() handles files with no annotations", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_no_annotations")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  # Create file without PUT annotations
-  content <- c(
-    "# Regular R file",
-    "x <- 1:10",
-    "mean(x)"
-  )
-
-  create_test_file(content, "no_annotations.R", test_dir)
-
-  result <- put(test_dir)
-  expect_s3_class(result, "data.frame")
-  expect_equal(nrow(result), 0)
-})
-
-test_that("put() validation works correctly", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_validation")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  # Create file with validation issues
-  content_with_issues <- c(
-    "#put label:\"No ID\"", # Missing id
-    "#put id:\"test\", node_type:\"invalid_type\"", # Invalid node type
-    "#put id:\"test2\", input:\"noextension\"", # File without extension
-    "#put id:\"good\", label:\"Good Annotation\", node_type:\"process\"" # Valid
-  )
-
-  create_test_file(content_with_issues, "test.R", test_dir)
-
-  # Test with validation enabled (should give warnings)
-  expect_warning({
-    result_with_validation <- put(test_dir, validate = TRUE)
-  })
-
-  # Should still return results for valid annotations
-  expect_gte(nrow(result_with_validation), 1)
-
-  # Test with validation disabled (should not give warnings)
-  expect_silent({
-    result_no_validation <- put(test_dir, validate = FALSE)
-  })
-})
-
-test_that("is_valid_put_annotation() correctly identifies valid annotations", {
-  # Valid annotations
-  expect_true(is_valid_put_annotation('#put id:"test", label:"Test"'))
-  expect_true(is_valid_put_annotation('# put id:"test"'))
-  expect_true(is_valid_put_annotation('#put| id:"test", type:"process"'))
-
-  # Invalid annotations
-  expect_false(is_valid_put_annotation("#put"))
-  expect_false(is_valid_put_annotation("#put invalid"))
-  expect_false(is_valid_put_annotation("#put id:noQuotes"))
-  expect_false(is_valid_put_annotation("not a put annotation"))
-})
-
-# Test error handling
-test_that("put() handles errors gracefully", {
-  # Non-existent directory
-  expect_error(put("/path/that/does/not/exist"), "Path does not exist")
-
-  # Invalid path type
-  expect_error(put(123), "'path' must be a single character string")
-  expect_error(put(c("path1", "path2")), "'path' must be a single character string")
-
-  # Empty directory
-  temp_dir <- tempdir()
-  empty_dir <- file.path(temp_dir, "empty_test_dir")
-  dir.create(empty_dir, showWarnings = FALSE)
-  on.exit(unlink(empty_dir, recursive = TRUE))
-
-  expect_warning(
-    {
-      result <- put(empty_dir)
-    },
-    "No files matching pattern"
-  )
-
-  expect_s3_class(result, "data.frame")
-  expect_equal(nrow(result), 0)
-})
-
-test_that("put() handles different file extensions", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_extensions")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  # Create files with different extensions
-  # Note: The default pattern is "\\.(R|r|py|sql|sh|jl)$"
-  # Each file type needs its appropriate comment prefix
-  extensions <- c("R", "py", "sql", "sh", "jl") # Removed lowercase "r" to avoid duplicates
-
-  for (ext in extensions) {
-    # Use the appropriate comment prefix for each file type
-    prefix <- get_comment_prefix(ext)
-    content <- paste0(prefix, "put id:\"test_", ext, "\", label:\"Test ", ext, "\"")
-    create_test_file(content, paste0("test.", ext), test_dir)
-  }
-
-  result <- put(test_dir)
-  expect_equal(nrow(result), length(extensions))
-  expect_true(all(tolower(extensions) %in% result$file_type))
-})
-
-test_that("put() preserves custom properties", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_custom")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  content <- c(
-    '#put id:"custom", label:"Custom Node", color:"blue", priority:"high", duration:"5min"'
-  )
-
-  create_test_file(content, "custom.R", test_dir)
-
-  result <- put(test_dir)
-  expect_equal(result$color, "blue")
-  expect_equal(result$priority, "high")
-  expect_equal(result$duration, "5min")
-})
-
-# Performance and stress tests
-test_that("put() handles multiple annotations efficiently", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_many")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  # Create file with many annotations
-  many_annotations <- character()
-  for (i in 1:50) {
-    many_annotations <- c(
-      many_annotations,
-      paste0('#put id:"node', i, '", label:"Node ', i, '", step:', i)
-    )
-  }
-
-  create_test_file(many_annotations, "many.R", test_dir)
-
-  # Should complete reasonably quickly
-  start_time <- Sys.time()
-  result <- put(test_dir)
-  end_time <- Sys.time()
-
-  expect_equal(nrow(result), 50)
-  expect_lt(as.numeric(end_time - start_time), 5) # Should take less than 5 seconds
-})
-
-test_that("put() column ordering is consistent", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_columns")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  content <- c(
-    '#put zebra:"z", alpha:"a", id:"test", beta:"b"'
-  )
-
-  create_test_file(content, "test.R", test_dir)
-
-  result <- put(test_dir)
-
-  # Standard columns should come first
-  expect_true(which(names(result) == "file_name") < which(names(result) == "alpha"))
-  expect_true(which(names(result) == "file_type") < which(names(result) == "alpha"))
-
-  # Custom columns should be alphabetically ordered
-  custom_cols <- names(result)[!names(result) %in% c("file_name", "file_path", "file_type")]
-  expect_equal(custom_cols, sort(custom_cols))
-})
-
-test_that("put() detects duplicate IDs", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_duplicates")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  content <- c(
-    '#put id:"test_dup", label:"First Duplicate"',
-    '#put id:"test_dup", label:"Second Duplicate"',
-    '#put id:"unique_node", label:"Unique Node"'
-  )
-
-  create_test_file(content, "test.R", test_dir)
-
-  # Should warn about duplicate IDs
-  expect_warning({
-    result <- put(test_dir, validate = TRUE)
-  }, "Duplicate node IDs found: test_dup")
-
-  # Should still return all nodes
-  expect_equal(nrow(result), 3)
-})
-
-test_that("put() defaults output to file_name when missing", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_output_default")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  # Create file where output is not specified
-  content <- c(
-    '#put label:"Process Step", node_type:"process", input:"data.csv"',
-    '# No output specified - should default to file name'
-  )
-
-  create_test_file(content, "process_script.R", test_dir)
-  
-  result <- put(test_dir)
-  
-  # Check that output was defaulted to the file name
-  expect_equal(nrow(result), 1)
-  expect_equal(result$output, "process_script.R")
-  expect_equal(result$file_name, "process_script.R")
-})
-
-# Tests for multiline annotations
-test_that("put() handles multiline annotations correctly", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_multiline")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-  
-  # Test file with multiline annotations
-  multiline_content <- c(
-    "#put id:\"multi1\", label:\"Multiline Test\", \\",
-    "#    input:\"file1.csv,file2.csv,file3.csv\", \\",
-    "#    output:\"result.csv\"",
-    "",
-    "# Some R code here",
-    "",
-    "#put id:\"multi2\", \\",
-    "#    label:\"Complex Process\", \\",
-    "#    node_type:\"process\", \\",
-    "#    input:\"data1.csv,data2.csv,data3.csv,data4.csv,data5.csv\", \\",
-    "#    output:\"processed_data.csv\"",
-    "",
-    "# More code",
-    "",
-    "# Single line annotation for comparison",
-    "#put id:\"single\", label:\"Single Line\", input:\"test.csv\""
-  )
-  
-  test_file <- create_test_file(multiline_content, "multiline_test.R", test_dir)
-  
-  # Extract annotations
-  result <- put(test_dir)
-  
-  # Should find 3 annotations
-  expect_equal(nrow(result), 3)
-  
-  # Check first multiline annotation
-  multi1 <- result[result$id == "multi1", ]
-  expect_equal(multi1$label, "Multiline Test")
-  expect_equal(multi1$input, "file1.csv,file2.csv,file3.csv")
-  expect_equal(multi1$output, "result.csv")
-  
-  # Check second multiline annotation
-  multi2 <- result[result$id == "multi2", ]
-  expect_equal(multi2$label, "Complex Process")
-  expect_equal(multi2$node_type, "process")
-  expect_equal(multi2$input, "data1.csv,data2.csv,data3.csv,data4.csv,data5.csv")
-  expect_equal(multi2$output, "processed_data.csv")
-  
-  # Check single line annotation still works
-  single <- result[result$id == "single", ]
-  expect_equal(single$label, "Single Line")
-  expect_equal(single$input, "test.csv")
-})
-
-test_that("put() handles edge cases in multiline annotations", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_multiline_edge")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-  
-  # Test edge cases
-  edge_case_content <- c(
-    "# Multiline with trailing backslash but no continuation",
-    "#put id:\"edge1\", label:\"Edge Case 1\" \\",
-    "",
-    "# Next annotation immediately after multiline",
-    "#put id:\"edge2\", label:\"Edge Case 2\" \\",
-    "#put id:\"edge3\", label:\"This is separate\"",
-    "",
-    "# Multiline with empty continuation lines",
-    "#put id:\"edge4\", label:\"With Empty Lines\", \\",
-    "#",
-    "#    input:\"test.csv\"",
-    "",
-    "# Backslash at end of file",
-    "#put id:\"edge5\", label:\"End of File\" \\"
-  )
-  
-  test_file <- create_test_file(edge_case_content, "edge_cases.R", test_dir)
-  
-  # Extract annotations
-  result <- put(test_dir)
-  
-  # Should find all annotations (at least 4)
-  expect_gte(nrow(result), 4)
-  
-  # Check that edge cases are handled
-  edge1 <- result[result$id == "edge1", ]
-  expect_equal(edge1$label, "Edge Case 1")
-  
-  edge3 <- result[result$id == "edge3", ]
-  expect_equal(edge3$label, "This is separate")
-  
-  edge4 <- result[result$id == "edge4", ]
-  expect_equal(edge4$label, "With Empty Lines")
-  expect_equal(edge4$input, "test.csv")
-})
-
-test_that("put() preserves line numbers with multiline annotations", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_multiline_lines")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-  
-  content <- c(
-    "# Line 1",
-    "#put id:\"first\", label:\"First\" \\",  # Line 2
-    "#    input:\"test.csv\"",              # Line 3
-    "",
-    "# Line 5",
-    "#put id:\"second\", label:\"Second\""   # Line 6
-  )
-  
-  test_file <- create_test_file(content, "line_test.R", test_dir)
-  
-  # Extract with line numbers
-  result <- put(test_dir, include_line_numbers = TRUE)
-  
-  # Check line numbers point to start of annotation
-  first <- result[result$id == "first", ]
-  expect_equal(first$line_number, 2)
-  
-  second <- result[result$id == "second", ]
-  expect_equal(second$line_number, 6)
-})
-
-test_that("put() handles different multiline syntax variations", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_multiline_syntax")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-  
-  # Test different syntax variations
-  syntax_content <- c(
-    "# Standard multiline with spaces",
-    "#put id:\"style1\", label:\"Style 1\" \\",
-    "#    input:\"file1.csv\"",
-    "",
-    "# Multiline with pipe separator",
-    "#put| id:\"style2\", label:\"Style 2\" \\",
-    "#     input:\"file2.csv\"",
-    "",
-    "# Multiline with colon separator",
-    "#put: id:\"style3\", label:\"Style 3\" \\",
-    "#     input:\"file3.csv\"",
-    "",
-    "# Backslash with trailing spaces",
-    "#put id:\"style4\", label:\"Style 4\"  \\   ",
-    "#    input:\"file4.csv\""
-  )
-  
-  test_file <- create_test_file(syntax_content, "syntax_test.R", test_dir)
-  
-  # Extract annotations
-  result <- put(test_dir)
-  
-  # Should find 4 annotations
-  expect_equal(nrow(result), 4)
-  
-  # Verify all styles work
-  for (i in 1:4) {
-    style <- result[result$id == paste0("style", i), ]
-    expect_equal(style$label, paste("Style", i))
-    expect_equal(style$input, paste0("file", i, ".csv"))
-  }
-})
-
-# =============================================================================
-# S3 Class Tests (putior_workflow)
-# =============================================================================
-
-test_that("put() returns a putior_workflow object", {
-  test_dir <- tempfile("putior_s3_test_")
-  dir.create(test_dir)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  create_test_file(c('# put label:"Step 1", output:"data.csv"'), "test.R", test_dir)
-  result <- put(test_dir)
-
-  expect_s3_class(result, "putior_workflow")
-  expect_s3_class(result, "data.frame")
-})
-
-test_that("print.putior_workflow shows header with counts", {
-  test_dir <- tempfile("putior_print_test_")
-  dir.create(test_dir)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  create_test_file(c(
-    '# put label:"Load", node_type:"input", output:"data.csv"',
-    '# put label:"Process", node_type:"process", input:"data.csv"'
-  ), "test.R", test_dir)
-  result <- put(test_dir)
-
-  output <- capture.output(print(result))
-  expect_true(any(grepl("putior workflow:", output)))
-  expect_true(any(grepl("2 node", output)))
-  expect_true(any(grepl("1 file", output)))
-  expect_true(any(grepl("Node types:", output)))
-})
-
-test_that("print.putior_workflow handles empty workflow", {
-  empty_wf <- putior:::as_putior_workflow(putior:::empty_result_df())
-  output <- capture.output(print(empty_wf))
-  expect_true(any(grepl("0 nodes", output)))
-})
-
-test_that("summary.putior_workflow returns structured list", {
-  test_dir <- tempfile("putior_summary_test_")
-  dir.create(test_dir)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  create_test_file(c(
-    '# put label:"Load", node_type:"input", output:"data.csv"',
-    '# put label:"Save", node_type:"output", input:"data.csv"'
-  ), "test.R", test_dir)
-  result <- put(test_dir)
-
-  output <- capture.output(summ <- summary(result))
-  expect_true(any(grepl("putior workflow summary", output)))
-  expect_true(any(grepl("Nodes: 2", output)))
-  expect_equal(summ$n_nodes, 2)
-  expect_equal(summ$n_files, 1)
-  expect_true(!is.null(summ$node_types))
-})
-
-# Tests for sanitize_mermaid_label
-test_that("sanitize_mermaid_label wraps labels in quotes", {
-  result <- putior:::sanitize_mermaid_label("Simple Label")
-  expect_equal(result, '"Simple Label"')
-})
-
-test_that("sanitize_mermaid_label escapes internal quotes", {
-  result <- putior:::sanitize_mermaid_label('Say "hello"')
-  expect_equal(result, '"Say #quot;hello#quot;"')
-})
-
-test_that("sanitize_mermaid_label handles empty/NA/NULL", {
-  expect_equal(putior:::sanitize_mermaid_label(""), "")
-  expect_true(is.na(putior:::sanitize_mermaid_label(NA)))
-  expect_null(putior:::sanitize_mermaid_label(NULL))
-})
-
-test_that("sanitize_mermaid_label handles special Mermaid characters", {
-  # Brackets, braces, parens are safe inside quotes
-  result <- putior:::sanitize_mermaid_label("data [v2] (final)")
-  expect_equal(result, '"data [v2] (final)"')
-})
-
-test_that("sanitize_mermaid_label escapes pipe characters", {
-  result <- putior:::sanitize_mermaid_label("Input | Output")
-  expect_equal(result, '"Input #124; Output"')
-  expect_false(grepl("\\|", result))
-})
-
-test_that("sanitize_mermaid_label escapes both quotes and pipes", {
-  result <- putior:::sanitize_mermaid_label('Say "hello" | world')
-  expect_equal(result, '"Say #quot;hello#quot; #124; world"')
-})
-
-test_that("put_diagram handles labels with pipe characters", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_pipe_label")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-  create_test_file(c(
-    '# put id:"node1", label:"Parse TABLE|FAN|SPEED", node_type:"process"'
-  ), "test.R", test_dir)
-  workflow <- put(test_dir)
-  diagram <- put_diagram(workflow, output = "raw")
-  expect_true(grepl("#124;", diagram))
-  expect_false(grepl("\\|FAN\\|", diagram))
-})
-
-test_that("put_diagram handles labels with special characters", {
-  temp_dir <- tempdir()
-  test_dir <- file.path(temp_dir, "putior_test_special_chars")
-  dir.create(test_dir, showWarnings = FALSE)
-  on.exit(unlink(test_dir, recursive = TRUE))
-
-  create_test_file(c(
-    '# put id:"node1", label:"Load [v2] Data", node_type:"process"'
-  ), "test.R", test_dir)
-  workflow <- put(test_dir)
-  diagram <- put_diagram(workflow, output = "raw")
-
-  # Should not error and should contain the label
-  expect_true(grepl("Load", diagram))
+# Test suite for putior package
+library(testthat)
+library(putior)
+
+# Test basic functionality
+test_that("put() handles basic directory scanning", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_basic")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  # Create test files
+  r_content <- c(
+    "# Test R file",
+    "#put id:\"test_r\", label:\"Test R Node\", node_type:\"process\"",
+    "x <- 1"
+  )
+
+  py_content <- c(
+    "# Test Python file",
+    "#put id:\"test_py\", label:\"Test Python Node\", node_type:\"input\"",
+    "x = 1"
+  )
+
+  create_test_file(r_content, "test.R", test_dir)
+  create_test_file(py_content, "test.py", test_dir)
+
+  # Test the function
+  result <- put(test_dir)
+
+  expect_s3_class(result, "data.frame")
+  expect_equal(nrow(result), 2)
+  expect_true(all(c("file_name", "file_type", "id", "label", "node_type") %in% names(result)))
+  expect_equal(sort(result$id), c("test_py", "test_r"))
+  expect_equal(sort(result$file_type), c("py", "r"))
+})
+
+test_that("put() handles single file processing", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_single")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  content <- c(
+    "# Single file test",
+    "#put id:\"single\", label:\"Single Node\", output:\"result.csv\"",
+    "write.csv(data, 'result.csv')"
+  )
+
+  filepath <- create_test_file(content, "single.R", test_dir)
+
+  # Test single file processing
+  result <- put(filepath)
+
+  expect_s3_class(result, "data.frame")
+  expect_equal(nrow(result), 1)
+  expect_equal(result$id, "single")
+  expect_equal(result$output, "result.csv")
+})
+
+test_that("put() handles recursive directory scanning", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_recursive")
+  subdir <- file.path(test_dir, "subdir")
+  dir.create(test_dir, showWarnings = FALSE)
+  dir.create(subdir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  # Create files in main directory
+  create_test_file(c("#put id:\"main\", label:\"Main\""), "main.R", test_dir)
+
+  # Create files in subdirectory
+  create_test_file(c("#put id:\"sub\", label:\"Sub\""), "sub.py", subdir)
+
+  # Test non-recursive (should find 1)
+  result_non_recursive <- put(test_dir, recursive = FALSE)
+  expect_equal(nrow(result_non_recursive), 1)
+
+  # Test recursive (should find 2)
+  result_recursive <- put(test_dir, recursive = TRUE)
+  expect_equal(nrow(result_recursive), 2)
+  expect_true(all(c("main", "sub") %in% result_recursive$id))
+})
+
+test_that("put() defaults to recursive scanning", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_default_recursive")
+  subdir <- file.path(test_dir, "subdir")
+  dir.create(subdir, recursive = TRUE, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  create_test_file(c("#put id:\"top\", label:\"Top\""), "top.R", test_dir)
+  create_test_file(c("#put id:\"nested\", label:\"Nested\""), "nested.R", subdir)
+
+  # Default (no explicit recursive arg) should find both files
+  result <- put(test_dir)
+  expect_equal(nrow(result), 2)
+  expect_true(all(c("top", "nested") %in% result$id))
+})
+
+test_that("put() includes line numbers when requested", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_lines")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  content <- c(
+    "# Line 1",
+    "#put id:\"first\", label:\"First\"", # Line 2
+    "# Line 3",
+    "#put id:\"second\", label:\"Second\"" # Line 4
+  )
+
+  create_test_file(content, "test.R", test_dir)
+
+  # Without line numbers
+  result_no_lines <- put(test_dir, include_line_numbers = FALSE)
+  expect_false("line_number" %in% names(result_no_lines))
+
+  # With line numbers
+  result_with_lines <- put(test_dir, include_line_numbers = TRUE)
+  expect_true("line_number" %in% names(result_with_lines))
+  expect_equal(result_with_lines$line_number, c(2, 4))
+})
+
+# Test annotation parsing
+test_that("parse_put_annotation() handles various formats", {
+  # Basic format
+  result1 <- parse_put_annotation('#put id:"test", label:"Test Label"')
+  expect_equal(result1$id, "test")
+  expect_equal(result1$label, "Test Label")
+
+  # With spaces
+  result2 <- parse_put_annotation('# put id:"test2", node_type:"process"')
+  expect_equal(result2$id, "test2")
+  expect_equal(result2$node_type, "process")
+
+  # With pipe separator
+  result3 <- parse_put_annotation('#put| id:"test3", input:"data.csv"')
+  expect_equal(result3$id, "test3")
+  expect_equal(result3$input, "data.csv")
+
+  # Single quotes
+  result4 <- parse_put_annotation("#put id:'test4', label:'Single Quotes'")
+  expect_equal(result4$id, "test4")
+  expect_equal(result4$label, "Single Quotes")
+
+  # Mixed quotes
+  result5 <- parse_put_annotation('#put id:"test5", label:\'Mixed Quotes\'')
+  expect_equal(result5$id, "test5")
+  expect_equal(result5$label, "Mixed Quotes")
+})
+
+test_that("parse_put_annotation() handles edge cases", {
+  # Empty annotation
+  expect_null(parse_put_annotation("#put"))
+  expect_null(parse_put_annotation("# put "))
+
+  # Invalid syntax
+  expect_null(parse_put_annotation("#put invalid"))
+  expect_null(parse_put_annotation("#put no quotes"))
+
+  # Not a PUT annotation
+  expect_null(parse_put_annotation("# Regular comment"))
+  expect_null(parse_put_annotation("puts something"))
+})
+
+test_that("put() handles files with no annotations", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_no_annotations")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  # Create file without PUT annotations
+  content <- c(
+    "# Regular R file",
+    "x <- 1:10",
+    "mean(x)"
+  )
+
+  create_test_file(content, "no_annotations.R", test_dir)
+
+  result <- put(test_dir)
+  expect_s3_class(result, "data.frame")
+  expect_equal(nrow(result), 0)
+})
+
+test_that("put() validation works correctly", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_validation")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  # Create file with validation issues
+  content_with_issues <- c(
+    "#put label:\"No ID\"", # Missing id
+    "#put id:\"test\", node_type:\"invalid_type\"", # Invalid node type
+    "#put id:\"test2\", input:\"noextension\"", # File without extension
+    "#put id:\"good\", label:\"Good Annotation\", node_type:\"process\"" # Valid
+  )
+
+  create_test_file(content_with_issues, "test.R", test_dir)
+
+  # Test with validation enabled (should give warnings)
+  expect_warning({
+    result_with_validation <- put(test_dir, validate = TRUE)
+  })
+
+  # Should still return results for valid annotations
+  expect_gte(nrow(result_with_validation), 1)
+
+  # Test with validation disabled (should not give warnings)
+  expect_silent({
+    result_no_validation <- put(test_dir, validate = FALSE)
+  })
+})
+
+test_that("is_valid_put_annotation() correctly identifies valid annotations", {
+  # Valid annotations
+  expect_true(is_valid_put_annotation('#put id:"test", label:"Test"'))
+  expect_true(is_valid_put_annotation('# put id:"test"'))
+  expect_true(is_valid_put_annotation('#put| id:"test", type:"process"'))
+
+  # Invalid annotations
+  expect_false(is_valid_put_annotation("#put"))
+  expect_false(is_valid_put_annotation("#put invalid"))
+  expect_false(is_valid_put_annotation("#put id:noQuotes"))
+  expect_false(is_valid_put_annotation("not a put annotation"))
+})
+
+# Test error handling
+test_that("put() handles errors gracefully", {
+  # Non-existent directory
+  expect_error(put("/path/that/does/not/exist"), "Path does not exist")
+
+  # Invalid path type
+  expect_error(put(123), "'path' must be a single character string")
+  expect_error(put(c("path1", "path2")), "'path' must be a single character string")
+
+  # Empty directory
+  temp_dir <- tempdir()
+  empty_dir <- file.path(temp_dir, "empty_test_dir")
+  dir.create(empty_dir, showWarnings = FALSE)
+  on.exit(unlink(empty_dir, recursive = TRUE))
+
+  expect_warning(
+    {
+      result <- put(empty_dir)
+    },
+    "No files matching pattern"
+  )
+
+  expect_s3_class(result, "data.frame")
+  expect_equal(nrow(result), 0)
+})
+
+test_that("put() handles different file extensions", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_extensions")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  # Create files with different extensions
+  # Note: The default pattern is "\\.(R|r|py|sql|sh|jl)$"
+  # Each file type needs its appropriate comment prefix
+  extensions <- c("R", "py", "sql", "sh", "jl") # Removed lowercase "r" to avoid duplicates
+
+  for (ext in extensions) {
+    # Use the appropriate comment prefix for each file type
+    prefix <- get_comment_prefix(ext)
+    content <- paste0(prefix, "put id:\"test_", ext, "\", label:\"Test ", ext, "\"")
+    create_test_file(content, paste0("test.", ext), test_dir)
+  }
+
+  result <- put(test_dir)
+  expect_equal(nrow(result), length(extensions))
+  expect_true(all(tolower(extensions) %in% result$file_type))
+})
+
+test_that("put() preserves custom properties", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_custom")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  content <- c(
+    '#put id:"custom", label:"Custom Node", color:"blue", priority:"high", duration:"5min"'
+  )
+
+  create_test_file(content, "custom.R", test_dir)
+
+  result <- put(test_dir)
+  expect_equal(result$color, "blue")
+  expect_equal(result$priority, "high")
+  expect_equal(result$duration, "5min")
+})
+
+# Performance and stress tests
+test_that("put() handles multiple annotations efficiently", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_many")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  # Create file with many annotations
+  many_annotations <- character()
+  for (i in 1:50) {
+    many_annotations <- c(
+      many_annotations,
+      paste0('#put id:"node', i, '", label:"Node ', i, '", step:', i)
+    )
+  }
+
+  create_test_file(many_annotations, "many.R", test_dir)
+
+  # Should complete reasonably quickly
+  start_time <- Sys.time()
+  result <- put(test_dir)
+  end_time <- Sys.time()
+
+  expect_equal(nrow(result), 50)
+  expect_lt(as.numeric(end_time - start_time), 5) # Should take less than 5 seconds
+})
+
+test_that("put() column ordering is consistent", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_columns")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  content <- c(
+    '#put zebra:"z", alpha:"a", id:"test", beta:"b"'
+  )
+
+  create_test_file(content, "test.R", test_dir)
+
+  result <- put(test_dir)
+
+  # Standard columns should come first
+  expect_true(which(names(result) == "file_name") < which(names(result) == "alpha"))
+  expect_true(which(names(result) == "file_type") < which(names(result) == "alpha"))
+
+  # Custom columns should be alphabetically ordered
+  custom_cols <- names(result)[!names(result) %in% c("file_name", "file_path", "file_type")]
+  expect_equal(custom_cols, sort(custom_cols))
+})
+
+test_that("put() detects duplicate IDs", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_duplicates")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  content <- c(
+    '#put id:"test_dup", label:"First Duplicate"',
+    '#put id:"test_dup", label:"Second Duplicate"',
+    '#put id:"unique_node", label:"Unique Node"'
+  )
+
+  create_test_file(content, "test.R", test_dir)
+
+  # Should warn about duplicate IDs
+  expect_warning({
+    result <- put(test_dir, validate = TRUE)
+  }, "Duplicate node IDs found: test_dup")
+
+  # Should still return all nodes
+  expect_equal(nrow(result), 3)
+})
+
+test_that("put() defaults output to file_name when missing", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_output_default")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  # Create file where output is not specified
+  content <- c(
+    '#put label:"Process Step", node_type:"process", input:"data.csv"',
+    '# No output specified - should default to file name'
+  )
+
+  create_test_file(content, "process_script.R", test_dir)
+  
+  result <- put(test_dir)
+  
+  # Check that output was defaulted to the file name
+  expect_equal(nrow(result), 1)
+  expect_equal(result$output, "process_script.R")
+  expect_equal(result$file_name, "process_script.R")
+})
+
+# Tests for multiline annotations
+test_that("put() handles multiline annotations correctly", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_multiline")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+  
+  # Test file with multiline annotations
+  multiline_content <- c(
+    "#put id:\"multi1\", label:\"Multiline Test\", \\",
+    "#    input:\"file1.csv,file2.csv,file3.csv\", \\",
+    "#    output:\"result.csv\"",
+    "",
+    "# Some R code here",
+    "",
+    "#put id:\"multi2\", \\",
+    "#    label:\"Complex Process\", \\",
+    "#    node_type:\"process\", \\",
+    "#    input:\"data1.csv,data2.csv,data3.csv,data4.csv,data5.csv\", \\",
+    "#    output:\"processed_data.csv\"",
+    "",
+    "# More code",
+    "",
+    "# Single line annotation for comparison",
+    "#put id:\"single\", label:\"Single Line\", input:\"test.csv\""
+  )
+  
+  test_file <- create_test_file(multiline_content, "multiline_test.R", test_dir)
+  
+  # Extract annotations
+  result <- put(test_dir)
+  
+  # Should find 3 annotations
+  expect_equal(nrow(result), 3)
+  
+  # Check first multiline annotation
+  multi1 <- result[result$id == "multi1", ]
+  expect_equal(multi1$label, "Multiline Test")
+  expect_equal(multi1$input, "file1.csv,file2.csv,file3.csv")
+  expect_equal(multi1$output, "result.csv")
+  
+  # Check second multiline annotation
+  multi2 <- result[result$id == "multi2", ]
+  expect_equal(multi2$label, "Complex Process")
+  expect_equal(multi2$node_type, "process")
+  expect_equal(multi2$input, "data1.csv,data2.csv,data3.csv,data4.csv,data5.csv")
+  expect_equal(multi2$output, "processed_data.csv")
+  
+  # Check single line annotation still works
+  single <- result[result$id == "single", ]
+  expect_equal(single$label, "Single Line")
+  expect_equal(single$input, "test.csv")
+})
+
+test_that("put() handles edge cases in multiline annotations", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_multiline_edge")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+  
+  # Test edge cases
+  edge_case_content <- c(
+    "# Multiline with trailing backslash but no continuation",
+    "#put id:\"edge1\", label:\"Edge Case 1\" \\",
+    "",
+    "# Next annotation immediately after multiline",
+    "#put id:\"edge2\", label:\"Edge Case 2\" \\",
+    "#put id:\"edge3\", label:\"This is separate\"",
+    "",
+    "# Multiline with empty continuation lines",
+    "#put id:\"edge4\", label:\"With Empty Lines\", \\",
+    "#",
+    "#    input:\"test.csv\"",
+    "",
+    "# Backslash at end of file",
+    "#put id:\"edge5\", label:\"End of File\" \\"
+  )
+  
+  test_file <- create_test_file(edge_case_content, "edge_cases.R", test_dir)
+  
+  # Extract annotations
+  result <- put(test_dir)
+  
+  # Should find all annotations (at least 4)
+  expect_gte(nrow(result), 4)
+  
+  # Check that edge cases are handled
+  edge1 <- result[result$id == "edge1", ]
+  expect_equal(edge1$label, "Edge Case 1")
+  
+  edge3 <- result[result$id == "edge3", ]
+  expect_equal(edge3$label, "This is separate")
+  
+  edge4 <- result[result$id == "edge4", ]
+  expect_equal(edge4$label, "With Empty Lines")
+  expect_equal(edge4$input, "test.csv")
+})
+
+test_that("put() preserves line numbers with multiline annotations", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_multiline_lines")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+  
+  content <- c(
+    "# Line 1",
+    "#put id:\"first\", label:\"First\" \\",  # Line 2
+    "#    input:\"test.csv\"",              # Line 3
+    "",
+    "# Line 5",
+    "#put id:\"second\", label:\"Second\""   # Line 6
+  )
+  
+  test_file <- create_test_file(content, "line_test.R", test_dir)
+  
+  # Extract with line numbers
+  result <- put(test_dir, include_line_numbers = TRUE)
+  
+  # Check line numbers point to start of annotation
+  first <- result[result$id == "first", ]
+  expect_equal(first$line_number, 2)
+  
+  second <- result[result$id == "second", ]
+  expect_equal(second$line_number, 6)
+})
+
+test_that("put() handles different multiline syntax variations", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_multiline_syntax")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+  
+  # Test different syntax variations
+  syntax_content <- c(
+    "# Standard multiline with spaces",
+    "#put id:\"style1\", label:\"Style 1\" \\",
+    "#    input:\"file1.csv\"",
+    "",
+    "# Multiline with pipe separator",
+    "#put| id:\"style2\", label:\"Style 2\" \\",
+    "#     input:\"file2.csv\"",
+    "",
+    "# Multiline with colon separator",
+    "#put: id:\"style3\", label:\"Style 3\" \\",
+    "#     input:\"file3.csv\"",
+    "",
+    "# Backslash with trailing spaces",
+    "#put id:\"style4\", label:\"Style 4\"  \\   ",
+    "#    input:\"file4.csv\""
+  )
+  
+  test_file <- create_test_file(syntax_content, "syntax_test.R", test_dir)
+  
+  # Extract annotations
+  result <- put(test_dir)
+  
+  # Should find 4 annotations
+  expect_equal(nrow(result), 4)
+  
+  # Verify all styles work
+  for (i in 1:4) {
+    style <- result[result$id == paste0("style", i), ]
+    expect_equal(style$label, paste("Style", i))
+    expect_equal(style$input, paste0("file", i, ".csv"))
+  }
+})
+
+# =============================================================================
+# S3 Class Tests (putior_workflow)
+# =============================================================================
+
+test_that("put() returns a putior_workflow object", {
+  test_dir <- tempfile("putior_s3_test_")
+  dir.create(test_dir)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  create_test_file(c('# put label:"Step 1", output:"data.csv"'), "test.R", test_dir)
+  result <- put(test_dir)
+
+  expect_s3_class(result, "putior_workflow")
+  expect_s3_class(result, "data.frame")
+})
+
+test_that("print.putior_workflow shows header with counts", {
+  test_dir <- tempfile("putior_print_test_")
+  dir.create(test_dir)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  create_test_file(c(
+    '# put label:"Load", node_type:"input", output:"data.csv"',
+    '# put label:"Process", node_type:"process", input:"data.csv"'
+  ), "test.R", test_dir)
+  result <- put(test_dir)
+
+  output <- capture.output(print(result))
+  expect_true(any(grepl("putior workflow:", output)))
+  expect_true(any(grepl("2 node", output)))
+  expect_true(any(grepl("1 file", output)))
+  expect_true(any(grepl("Node types:", output)))
+})
+
+test_that("print.putior_workflow handles empty workflow", {
+  empty_wf <- putior:::as_putior_workflow(putior:::empty_result_df())
+  output <- capture.output(print(empty_wf))
+  expect_true(any(grepl("0 nodes", output)))
+})
+
+test_that("summary.putior_workflow returns structured list", {
+  test_dir <- tempfile("putior_summary_test_")
+  dir.create(test_dir)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  create_test_file(c(
+    '# put label:"Load", node_type:"input", output:"data.csv"',
+    '# put label:"Save", node_type:"output", input:"data.csv"'
+  ), "test.R", test_dir)
+  result <- put(test_dir)
+
+  output <- capture.output(summ <- summary(result))
+  expect_true(any(grepl("putior workflow summary", output)))
+  expect_true(any(grepl("Nodes: 2", output)))
+  expect_equal(summ$n_nodes, 2)
+  expect_equal(summ$n_files, 1)
+  expect_true(!is.null(summ$node_types))
+})
+
+# Tests for sanitize_mermaid_label
+test_that("sanitize_mermaid_label wraps labels in quotes", {
+  result <- putior:::sanitize_mermaid_label("Simple Label")
+  expect_equal(result, '"Simple Label"')
+})
+
+test_that("sanitize_mermaid_label escapes internal quotes", {
+  result <- putior:::sanitize_mermaid_label('Say "hello"')
+  expect_equal(result, '"Say #quot;hello#quot;"')
+})
+
+test_that("sanitize_mermaid_label handles empty/NA/NULL", {
+  expect_equal(putior:::sanitize_mermaid_label(""), "")
+  expect_true(is.na(putior:::sanitize_mermaid_label(NA)))
+  expect_null(putior:::sanitize_mermaid_label(NULL))
+})
+
+test_that("sanitize_mermaid_label handles special Mermaid characters", {
+  # Brackets, braces, parens are safe inside quotes
+  result <- putior:::sanitize_mermaid_label("data [v2] (final)")
+  expect_equal(result, '"data [v2] (final)"')
+})
+
+test_that("sanitize_mermaid_label escapes pipe characters", {
+  result <- putior:::sanitize_mermaid_label("Input | Output")
+  expect_equal(result, '"Input #124; Output"')
+  expect_false(grepl("\\|", result))
+})
+
+test_that("sanitize_mermaid_label escapes both quotes and pipes", {
+  result <- putior:::sanitize_mermaid_label('Say "hello" | world')
+  expect_equal(result, '"Say #quot;hello#quot; #124; world"')
+})
+
+test_that("put_diagram handles labels with pipe characters", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_pipe_label")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+  create_test_file(c(
+    '# put id:"node1", label:"Parse TABLE|FAN|SPEED", node_type:"process"'
+  ), "test.R", test_dir)
+  workflow <- put(test_dir)
+  diagram <- put_diagram(workflow, output = "raw")
+  expect_true(grepl("#124;", diagram))
+  expect_false(grepl("\\|FAN\\|", diagram))
+})
+
+test_that("put_diagram handles labels with special characters", {
+  temp_dir <- tempdir()
+  test_dir <- file.path(temp_dir, "putior_test_special_chars")
+  dir.create(test_dir, showWarnings = FALSE)
+  on.exit(unlink(test_dir, recursive = TRUE))
+
+  create_test_file(c(
+    '# put id:"node1", label:"Load [v2] Data", node_type:"process"'
+  ), "test.R", test_dir)
+  workflow <- put(test_dir)
+  diagram <- put_diagram(workflow, output = "raw")
+
+  # Should not error and should contain the label
+  expect_true(grepl("Load", diagram))
 })
\ No newline at end of file
diff --git a/tests/testthat/test-put_diagram.R b/tests/testthat/test-put_diagram.R
index efa8887..d8395da 100644
--- a/tests/testthat/test-put_diagram.R
+++ b/tests/testthat/test-put_diagram.R
@@ -1,936 +1,936 @@
-# Test suite for put_diagram() function
-library(testthat)
-
-# Helper function to create test workflow data
-create_test_workflow <- function() {
-  data.frame(
-    file_name = c("01_load.R", "02_process.py", "03_analyze.R"),
-    file_type = c("r", "py", "r"),
-    id = c("load_data", "process_data", "analyze_results"),
-    label = c("Load Raw Data", "Process Data", "Analyze Results"),
-    node_type = c("input", "process", "output"),
-    input = c(NA, "raw_data.csv", "processed_data.csv"),
-    output = c("raw_data.csv", "processed_data.csv", "final_report.html"),
-    stringsAsFactors = FALSE
-  )
-}
-
-# Helper function to create test workflow with terminal outputs
-create_test_workflow_with_terminal <- function() {
-  data.frame(
-    file_name = c("load.R", "process.R"),
-    file_type = c("r", "r"),
-    id = c("load", "process"),
-    label = c("Load Data", "Process Data"),
-    node_type = c("input", "process"),
-    input = c(NA, "data.csv"),
-    output = c("data.csv", "final_results.csv"),  # final_results.csv is terminal
-    stringsAsFactors = FALSE
-  )
-}
-
-test_that("put_diagram() creates basic mermaid diagram", {
-  workflow <- create_test_workflow()
-
-  # Capture output
-  result <- capture.output({
-    diagram_code <- put_diagram(workflow)
-  })
-
-  # Check that mermaid code block is created
-  expect_true(any(grepl("```mermaid", result)))
-  expect_true(any(grepl("flowchart TD", result)))
-  expect_true(any(grepl("```", result)))
-
-  # Check that diagram code is returned invisibly
-  expect_true(is.character(diagram_code))
-  expect_true(grepl("flowchart TD", diagram_code))
-})
-
-test_that("put_diagram() handles different directions", {
-  workflow <- create_test_workflow()
-
-  # Test different directions
-  directions <- c("TD", "LR", "BT", "RL")
-
-  for (dir in directions) {
-    diagram_code <- put_diagram(workflow, direction = dir, output = "none")
-    expect_true(grepl(paste0("flowchart ", dir), diagram_code))
-  }
-})
-
-test_that("put_diagram() handles different node label options", {
-  workflow <- create_test_workflow()
-
-  # Test ID labels (node_labels = "name" shows IDs)
-  diagram_id <- put_diagram(workflow, node_labels = "name", output = "none")
-  expect_true(grepl("load_data", diagram_id))
-
-  # Test description labels
-  diagram_label <- put_diagram(workflow, node_labels = "label", output = "none")
-  expect_true(grepl("Load Raw Data", diagram_label))
-
-  # Test both labels
-  diagram_both <- put_diagram(workflow, node_labels = "both", output = "none")
-  expect_true(grepl("load_data: Load Raw Data", diagram_both))
-})
-
-test_that("put_diagram() generates correct node shapes", {
-  workflow <- create_test_workflow()
-  diagram_code <- put_diagram(workflow, output = "none")
-
-  # Check shapes for different node types
-  expect_true(grepl("\\(\\[.*\\]\\)", diagram_code)) # Stadium shape for input
-  expect_true(grepl("\\[.*\\]", diagram_code)) # Rectangle for process
-  expect_true(grepl("\\[\\[.*\\]\\]", diagram_code)) # Subroutine for output
-})
-
-test_that("put_diagram() creates connections based on file flow", {
-  workflow <- create_test_workflow()
-  diagram_code <- put_diagram(workflow, output = "none")
-
-  # Should have connections between nodes that share files
-  expect_true(grepl("load_data --> process_data", diagram_code))
-  expect_true(grepl("process_data --> analyze_results", diagram_code))
-})
-
-test_that("put_diagram() shows file names on connections when requested", {
-  workflow <- create_test_workflow()
-
-  # Without file names
-  diagram_no_files <- put_diagram(workflow, show_files = FALSE, output = "none")
-  expect_true(grepl("load_data --> process_data", diagram_no_files))
-  expect_false(grepl("raw_data.csv", diagram_no_files))
-
-  # With file names
-  diagram_with_files <- put_diagram(workflow, show_files = TRUE, output = "none")
-  expect_true(grepl("\\|raw_data.csv\\|", diagram_with_files))
-  expect_true(grepl("\\|processed_data.csv\\|", diagram_with_files))
-})
-
-test_that("put_diagram() adds styling when requested", {
-  workflow <- create_test_workflow()
-
-  # With styling
-  diagram_styled <- put_diagram(workflow, style_nodes = TRUE, output = "none")
-  expect_true(grepl("classDef inputStyle", diagram_styled))
-  expect_true(grepl("classDef processStyle", diagram_styled))
-  expect_true(grepl("classDef outputStyle", diagram_styled))
-
-  # Without styling
-  diagram_unstyled <- put_diagram(workflow, style_nodes = FALSE, output = "none")
-  expect_false(grepl("classDef", diagram_unstyled))
-})
-
-test_that("put_diagram() includes title when provided", {
-  workflow <- create_test_workflow()
-
-  diagram_with_title <- put_diagram(workflow, title = "My Workflow", output = "none")
-  expect_true(grepl("title: My Workflow", diagram_with_title))
-
-  diagram_no_title <- put_diagram(workflow, title = NULL, output = "none")
-  expect_false(grepl("title:", diagram_no_title))
-})
-
-test_that("put_diagram() handles file output", {
-  workflow <- create_test_workflow()
-  temp_file <- tempfile(fileext = ".md")
-
-  # Test file output
-  expect_message(
-    {
-      put_diagram(workflow, output = "file", file = temp_file)
-    },
-    "Diagram saved to"
-  )
-
-  # Check file was created and has correct content
-  expect_true(file.exists(temp_file))
-
-  content <- readLines(temp_file)
-  expect_true(any(grepl("```mermaid", content)))
-  expect_true(any(grepl("flowchart TD", content)))
-
-  # Clean up
-  unlink(temp_file)
-})
-
-test_that("put_diagram() validates input", {
-  # Empty workflow
-  expect_error(put_diagram(data.frame()), "empty.*0 rows")
-
-  # Missing required columns
-  bad_workflow <- data.frame(x = 1, y = 2)
-  expect_error(put_diagram(bad_workflow), "missing required column")
-
-  # All IDs missing
-  workflow_no_ids <- data.frame(
-    id = c(NA, "", NA),
-    file_name = c("a.R", "b.py", "c.R"),
-    stringsAsFactors = FALSE
-  )
-  expect_error(put_diagram(workflow_no_ids), "No valid workflow nodes found")
-})
-
-test_that("sanitize_node_id() works correctly", {
-  # Test normal names
-  expect_equal(sanitize_node_id("load_data"), "load_data")
-  expect_equal(sanitize_node_id("process-data"), "process_data")
-  expect_equal(sanitize_node_id("analyze.results"), "analyze_results")
-
-  # Test names starting with numbers
-  expect_equal(sanitize_node_id("1_load_data"), "node_1_load_data")
-
-  # Test special characters
-  expect_equal(sanitize_node_id("load@data#1"), "load_data_1")
-})
-
-test_that("split_file_list() handles various inputs", {
-  # Single file
-  expect_equal(split_file_list("file.csv"), "file.csv")
-
-  # Multiple files
-  expect_equal(split_file_list("file1.csv,file2.json"), c("file1.csv", "file2.json"))
-
-  # With spaces
-  expect_equal(
-    split_file_list("file1.csv, file2.json, file3.txt"),
-    c("file1.csv", "file2.json", "file3.txt")
-  )
-
-  # Empty string
-  expect_equal(split_file_list(""), character(0))
-  expect_equal(split_file_list(NA), character(0))
-})
-
-test_that("get_node_shape() returns correct shapes", {
-  expect_equal(get_node_shape("input"), c("([", "])"))
-  expect_equal(get_node_shape("process"), c("[", "]"))
-  expect_equal(get_node_shape("output"), c("[[", "]]"))
-  expect_equal(get_node_shape("decision"), c("{", "}"))
-  expect_equal(get_node_shape(NA), c("[", "]"))
-  expect_equal(get_node_shape("unknown"), c("[", "]"))
-})
-
-test_that("put_diagram() handles complex workflows", {
-  # Create workflow with multiple inputs/outputs and various node types
-  complex_workflow <- data.frame(
-    file_name = c("collect.py", "clean.R", "analyze.R", "report.R", "decide.R"),
-    id = c("collect", "clean", "analyze", "report", "decide"),
-    label = c("Collect Data", "Clean Data", "Analyze", "Generate Report", "Make Decision"),
-    node_type = c("input", "process", "process", "output", "decision"),
-    input = c(NA, "raw.csv", "clean.csv", "analysis.rds", "analysis.rds"),
-    output = c("raw.csv", "clean.csv", "analysis.rds", "report.html", "decision.json"),
-    stringsAsFactors = FALSE
-  )
-
-  diagram_code <- put_diagram(complex_workflow, output = "none")
-
-  # Should handle all node types
-  expect_true(grepl("collect", diagram_code))
-  expect_true(grepl("clean", diagram_code))
-  expect_true(grepl("analyze", diagram_code))
-  expect_true(grepl("report", diagram_code))
-  expect_true(grepl("decide", diagram_code))
-
-  # Should have appropriate connections
-  expect_true(grepl("collect --> clean", diagram_code))
-  expect_true(grepl("clean --> analyze", diagram_code))
-})
-
-test_that("put_diagram() handles workflows with no connections", {
-  # Independent nodes with no shared files
-  independent_workflow <- data.frame(
-    file_name = c("task1.R", "task2.R", "task3.R"),
-    id = c("task1", "task2", "task3"),
-    label = c("Task 1", "Task 2", "Task 3"),
-    node_type = c("process", "process", "process"),
-    input = c("file1.csv", "file2.csv", "file3.csv"),
-    output = c("out1.csv", "out2.csv", "out3.csv"),
-    stringsAsFactors = FALSE
-  )
-
-  diagram_code <- put_diagram(independent_workflow, output = "none")
-
-  # Should still create valid diagram with nodes
-  expect_true(grepl("flowchart TD", diagram_code))
-  expect_true(grepl("task1", diagram_code))
-  expect_true(grepl("task2", diagram_code))
-  expect_true(grepl("task3", diagram_code))
-
-  # Should not have connections
-  expect_false(grepl("-->", diagram_code))
-})
-
-# Mock clipr for clipboard tests
-test_that("put_diagram() handles clipboard output", {
-  workflow <- create_test_workflow()
-
-  # Mock clipr not being available
-  if (!requireNamespace("clipr", quietly = TRUE)) {
-    expect_warning(
-      {
-        result <- capture.output({
-          put_diagram(workflow, output = "clipboard")
-        })
-      },
-      "clipr package not available"
-    )
-
-    # Should fall back to console output
-    expect_true(any(grepl("```mermaid", result)))
-  }
-})
-
-# ============================================================================
-# Artifact functionality tests
-# ============================================================================
-
-test_that("put_diagram() supports show_artifacts parameter", {
-  workflow <- create_test_workflow_with_terminal()
-  
-  # Test that show_artifacts parameter is accepted
-  expect_no_error({
-    diagram_simple <- put_diagram(workflow, output = "none")
-    diagram_artifacts <- put_diagram(workflow, show_artifacts = TRUE, output = "none")
-  })
-  
-  # Diagrams should be different
-  diagram_simple <- put_diagram(workflow, output = "none")
-  diagram_artifacts <- put_diagram(workflow, show_artifacts = TRUE, output = "none")
-  expect_false(identical(diagram_simple, diagram_artifacts))
-})
-
-test_that("create_artifact_nodes() identifies data files correctly", {
-  workflow <- create_test_workflow_with_terminal()
-  artifacts <- create_artifact_nodes(workflow)
-  
-  # Should identify final_results.csv as an artifact (terminal output)
-  expect_true(nrow(artifacts) > 0)
-  expect_true("final_results.csv" %in% artifacts$file_name)
-  expect_true(all(artifacts$node_type == "artifact"))
-  expect_true(all(artifacts$is_artifact == TRUE))
-})
-
-test_that("artifact nodes have correct shape", {
-  # Test artifact node shape
-  expect_equal(get_node_shape("artifact"), c("[(", ")]"))
-})
-
-test_that("show_artifacts creates artifact nodes in diagram", {
-  workflow <- create_test_workflow_with_terminal()
-  diagram_code <- put_diagram(workflow, show_artifacts = TRUE, output = "none")
-  
-  # Should contain artifact node for terminal output
-  expect_true(grepl("artifact_final_results_csv", diagram_code))
-  expect_true(grepl("final_results\\.csv", diagram_code))
-})
-
-test_that("show_artifacts creates correct connections", {
-  workflow <- create_test_workflow_with_terminal()
-  diagram_code <- put_diagram(workflow, show_artifacts = TRUE, output = "none")
-  
-  # Should have BOTH script-to-script AND script-to-artifact connections
-  # Script-to-script connection (preserved from simple mode)
-  expect_true(grepl("load --> process", diagram_code))
-  
-  # Script-to-artifact and artifact-to-script connections
-  expect_true(grepl("load --> artifact_data_csv", diagram_code))
-  expect_true(grepl("artifact_data_csv --> process", diagram_code))
-  expect_true(grepl("process --> artifact_final_results_csv", diagram_code))
-})
-
-test_that("artifact styling is applied correctly", {
-  workflow <- create_test_workflow_with_terminal()
-  diagram_code <- put_diagram(workflow, show_artifacts = TRUE, output = "none")
-  
-  # Should contain artifact styling
-  expect_true(grepl("classDef artifactStyle", diagram_code))
-  expect_true(grepl("class artifact_", diagram_code))
-})
-
-test_that("show_artifacts with show_files shows file labels", {
-  workflow <- create_test_workflow_with_terminal()
-  diagram_code <- put_diagram(workflow, show_artifacts = TRUE, show_files = TRUE, output = "none")
-  
-  # Should have file labels on connections
-  expect_true(grepl("-->\\|.*\\|", diagram_code))  # Should have |file| labels
-})
-
-test_that("show_artifacts works with different themes", {
-  workflow <- create_test_workflow_with_terminal()
-  
-  # Test multiple themes
-  themes <- c("light", "dark", "github", "minimal", "auto")
-  
-  for (theme in themes) {
-    expect_no_error({
-      diagram_code <- put_diagram(workflow, show_artifacts = TRUE, theme = theme, output = "none")
-      expect_true(grepl("artifact", diagram_code))
-    })
-  }
-})
-
-test_that("show_artifacts handles workflow with no artifacts", {
-  # Create workflow where all outputs are script files
-  workflow <- data.frame(
-    file_name = c("main.R", "utils.R"),
-    id = c("main", "utils"),
-    label = c("Main", "Utils"),
-    node_type = c("process", "input"),
-    input = c("utils.R", NA),
-    output = c("results.txt", "utils.R"),  # utils.R is script, not artifact
-    stringsAsFactors = FALSE
-  )
-  
-  diagram_code <- put_diagram(workflow, show_artifacts = TRUE, output = "none")
-  
-  # Should handle gracefully and show results.txt artifact
-  expect_true(grepl("artifact_results_txt", diagram_code))
-})
-
-test_that("show_artifacts combines with existing node_type styling", {
-  workflow <- create_test_workflow_with_terminal()
-  diagram_code <- put_diagram(workflow, show_artifacts = TRUE, style_nodes = TRUE, output = "none")
-  
-  # Should have both script node styling and artifact styling
-  expect_true(grepl("classDef inputStyle", diagram_code))
-  expect_true(grepl("classDef processStyle", diagram_code))
-  expect_true(grepl("classDef artifactStyle", diagram_code))
-})
-
-# ============================================================================
-# Workflow boundary functionality tests
-# ============================================================================
-
-test_that("put_diagram() supports show_workflow_boundaries parameter", {
-  workflow <- data.frame(
-    file_name = c("start.R", "process.R", "end.R"),
-    id = c("start_node", "process_node", "end_node"),
-    label = c("Start", "Process", "End"),
-    node_type = c("start", "process", "end"),
-    stringsAsFactors = FALSE
-  )
-  
-  # Test that show_workflow_boundaries parameter is accepted
-  expect_no_error({
-    diagram_boundaries <- put_diagram(workflow, show_workflow_boundaries = TRUE, output = "none")
-    diagram_no_boundaries <- put_diagram(workflow, show_workflow_boundaries = FALSE, output = "none")
-  })
-  
-  # Diagrams should be different
-  diagram_boundaries <- put_diagram(workflow, show_workflow_boundaries = TRUE, output = "none")
-  diagram_no_boundaries <- put_diagram(workflow, show_workflow_boundaries = FALSE, output = "none")
-  expect_false(identical(diagram_boundaries, diagram_no_boundaries))
-})
-
-test_that("workflow boundaries show special icons when enabled", {
-  workflow <- data.frame(
-    file_name = c("start.R", "end.R"),
-    id = c("start_node", "end_node"),
-    label = c("Pipeline Start", "Pipeline End"),
-    node_type = c("start", "end"),
-    stringsAsFactors = FALSE
-  )
-  
-  diagram_code <- put_diagram(workflow, show_workflow_boundaries = TRUE, output = "none")
-  
-  # Should contain start and end nodes with special styling
-  expect_true(grepl("startStyle", diagram_code))  # Special start styling
-  expect_true(grepl("endStyle", diagram_code))  # Special end styling
-})
-
-test_that("workflow boundaries hide icons when disabled", {
-  workflow <- data.frame(
-    file_name = c("start.R", "end.R"),
-    id = c("start_node", "end_node"),
-    label = c("Pipeline Start", "Pipeline End"),
-    node_type = c("start", "end"),
-    stringsAsFactors = FALSE
-  )
-  
-  diagram_code <- put_diagram(workflow, show_workflow_boundaries = FALSE, output = "none")
-  
-  # Should NOT contain special styling when boundaries are disabled
-  expect_false(grepl("startStyle", diagram_code))  # No start styling
-  expect_false(grepl("endStyle", diagram_code))  # No end styling
-})
-
-test_that("workflow boundary styling is applied when enabled", {
-  workflow <- data.frame(
-    file_name = c("start.R", "end.R"),
-    id = c("start_node", "end_node"),
-    label = c("Start", "End"),
-    node_type = c("start", "end"),
-    stringsAsFactors = FALSE
-  )
-  
-  diagram_code <- put_diagram(workflow, show_workflow_boundaries = TRUE, output = "none")
-  
-  # Should contain start and end styling
-  expect_true(grepl("classDef startStyle", diagram_code))
-  expect_true(grepl("classDef endStyle", diagram_code))
-  expect_true(grepl("class start_node startStyle", diagram_code))
-  expect_true(grepl("class end_node endStyle", diagram_code))
-})
-
-test_that("workflow boundary styling is hidden when disabled", {
-  workflow <- data.frame(
-    file_name = c("start.R", "end.R"),
-    id = c("start_node", "end_node"),
-    label = c("Start", "End"),
-    node_type = c("start", "end"),
-    stringsAsFactors = FALSE
-  )
-  
-  diagram_code <- put_diagram(workflow, show_workflow_boundaries = FALSE, output = "none")
-  
-  # Should NOT contain start and end styling when boundaries are disabled
-  expect_false(grepl("classDef startStyle", diagram_code))
-  expect_false(grepl("classDef endStyle", diagram_code))
-})
-
-test_that("get_node_shape handles workflow boundaries correctly", {
-  # With boundaries enabled, should get stadium shapes (no special characters)
-  expect_equal(get_node_shape("start", TRUE), c("([", "])"))
-  expect_equal(get_node_shape("end", TRUE), c("([", "])"))
-  
-  # With boundaries disabled, should get regular shapes
-  expect_equal(get_node_shape("start", FALSE), c("([", "])"))
-  expect_equal(get_node_shape("end", FALSE), c("([", "])"))
-})
-
-test_that("workflow boundaries work with different themes", {
-  workflow <- data.frame(
-    file_name = c("start.R", "end.R"),
-    id = c("start_node", "end_node"),
-    label = c("Start", "End"),
-    node_type = c("start", "end"),
-    stringsAsFactors = FALSE
-  )
-  
-  # Test multiple themes with workflow boundaries
-  themes <- c("light", "dark", "github", "minimal", "auto")
-  
-  for (theme in themes) {
-    expect_no_error({
-      diagram_code <- put_diagram(workflow, show_workflow_boundaries = TRUE, theme = theme, output = "none")
-      expect_true(grepl("startStyle", diagram_code))
-      expect_true(grepl("endStyle", diagram_code))
-    })
-  }
-})
-
-# ============================================================================
-# Metadata Display (show_source_info) Tests - GitHub Issue #3
-# ============================================================================
-
-test_that("show_source_info adds file names inline", {
-  workflow <- create_test_workflow()
-
-  # Without source info
-  diagram_no_info <- put_diagram(workflow, show_source_info = FALSE, output = "none")
-  expect_false(grepl("<br/>", diagram_no_info))
-  expect_false(grepl("01_load\\.R", diagram_no_info))
-
-  # With source info inline
-  diagram_with_info <- put_diagram(workflow, show_source_info = TRUE, output = "none")
-  expect_true(grepl("<br/>", diagram_with_info))
-  expect_true(grepl("01_load\\.R", diagram_with_info))
-  expect_true(grepl("01_load\\.R", diagram_with_info))
-})
-
-test_that("source_info_style='subgraph' groups nodes by file", {
-  workflow <- create_test_workflow()
-
-  diagram_code <- put_diagram(
-    workflow,
-    show_source_info = TRUE,
-    source_info_style = "subgraph",
-    output = "none"
-  )
-
-  # Should contain subgraph declarations
-  expect_true(grepl("subgraph", diagram_code))
-  expect_true(grepl("end", diagram_code))
-
-  # Should have file names as subgraph labels
-  expect_true(grepl("01_load\\.R", diagram_code))
-  expect_true(grepl("02_process\\.py", diagram_code))
-})
-
-test_that("show_source_info handles missing file_name", {
-  workflow <- data.frame(
-    file_name = c("test.R", NA, ""),
-    id = c("node1", "node2", "node3"),
-    label = c("Node 1", "Node 2", "Node 3"),
-    node_type = c("process", "process", "process"),
-    stringsAsFactors = FALSE
-  )
-
-  # Should not error with NA or empty file names
-  expect_no_error({
-    diagram_code <- put_diagram(workflow, show_source_info = TRUE, output = "none")
-  })
-
-  diagram_code <- put_diagram(workflow, show_source_info = TRUE, output = "none")
-  # Only test.R should show source info
-  expect_true(grepl("test\\.R", diagram_code))
-})
-
-test_that("show_source_info with invalid source_info_style warns and uses default", {
-  workflow <- create_test_workflow()
-
-  expect_warning(
-    put_diagram(workflow, show_source_info = TRUE, source_info_style = "invalid", output = "none"),
-    "Invalid source_info_style"
-  )
-})
-
-test_that("show_source_info excludes artifact nodes from source info", {
-  workflow <- create_test_workflow_with_terminal()
-
-  diagram_code <- put_diagram(
-    workflow,
-    show_artifacts = TRUE,
-    show_source_info = TRUE,
-    output = "none"
-  )
-
-  # Artifact nodes should NOT have source info appended
-  # Script nodes should have source info
-  expect_true(grepl("load\\.R", diagram_code))
-  # The artifact label should be clean (final_results.csv without additional source info)
-  expect_true(grepl("final_results\\.csv", diagram_code))
-})
-
-# ============================================================================
-# Clickable Hyperlinks (enable_clicks) Tests - GitHub Issue #4
-# ============================================================================
-
-test_that("enable_clicks adds click directives", {
-  workflow <- create_test_workflow()
-
-  # Without clicks
-  diagram_no_clicks <- put_diagram(workflow, enable_clicks = FALSE, output = "none")
-  expect_false(grepl("click ", diagram_no_clicks))
-
-  # With clicks
-  diagram_with_clicks <- put_diagram(workflow, enable_clicks = TRUE, output = "none")
-  expect_true(grepl("click ", diagram_with_clicks))
-  expect_true(grepl("%% Click Actions", diagram_with_clicks))
-})
-
-test_that("click_protocol='vscode' generates correct URLs", {
-  workflow <- create_test_workflow()
-
-  diagram_code <- put_diagram(
-    workflow,
-    enable_clicks = TRUE,
-    click_protocol = "vscode",
-    output = "none"
-  )
-
-  # Should have vscode:// protocol
-  expect_true(grepl("vscode://file/", diagram_code))
-  expect_true(grepl('click load_data "vscode://file/', diagram_code))
-})
-
-test_that("click_protocol='file' generates correct URLs", {
-  workflow <- create_test_workflow()
-
-  diagram_code <- put_diagram(
-    workflow,
-    enable_clicks = TRUE,
-    click_protocol = "file",
-    output = "none"
-  )
-
-  # Should have file:/// protocol
-  expect_true(grepl("file:///", diagram_code))
-})
-
-test_that("click_protocol='rstudio' generates correct URLs", {
-  workflow <- create_test_workflow()
-
-  diagram_code <- put_diagram(
-    workflow,
-    enable_clicks = TRUE,
-    click_protocol = "rstudio",
-    output = "none"
-  )
-
-  # Should have rstudio:// protocol
-  expect_true(grepl("rstudio://open-file\\?path=", diagram_code))
-})
-
-test_that("enable_clicks with invalid protocol warns and uses default", {
-  workflow <- create_test_workflow()
-
-  expect_warning(
-    put_diagram(workflow, enable_clicks = TRUE, click_protocol = "invalid", output = "none"),
-    "Invalid click_protocol"
-  )
-})
-
-test_that("normalize_path_for_url handles various inputs", {
-  # Empty and NA inputs
-  expect_equal(normalize_path_for_url(""), "")
-  expect_equal(normalize_path_for_url(NA), "")
-  expect_equal(normalize_path_for_url(NULL), "")
-
-  # Normal paths (just check it returns a string and converts slashes)
-  result <- normalize_path_for_url("test/path/file.R")
-  expect_true(is.character(result))
-  expect_false(grepl("\\\\", result))  # No backslashes
-})
-
-test_that("generate_click_url creates proper URLs for each protocol", {
-  # VS Code without line number
-  url_vscode <- generate_click_url("test.R", protocol = "vscode")
-  expect_true(grepl("vscode://file/", url_vscode))
-
-  # VS Code with line number
-  url_vscode_line <- generate_click_url("test.R", line_number = 42, protocol = "vscode")
-  expect_true(grepl(":42$", url_vscode_line))
-
-  # File protocol
-  url_file <- generate_click_url("test.R", protocol = "file")
-  expect_true(grepl("file:///", url_file))
-
-  # RStudio protocol
-  url_rstudio <- generate_click_url("test.R", protocol = "rstudio")
-  expect_true(grepl("rstudio://open-file\\?path=", url_rstudio))
-
-  # RStudio with line number
-  url_rstudio_line <- generate_click_url("test.R", line_number = 10, protocol = "rstudio")
-  expect_true(grepl("&line=10", url_rstudio_line))
-})
-
-test_that("click directives include tooltips", {
-  workflow <- create_test_workflow()
-
-  diagram_code <- put_diagram(workflow, enable_clicks = TRUE, output = "none")
-
-  # Should have tooltip format: click nodeId "url" "tooltip"
-  expect_true(grepl('click load_data "[^"]*" "Open 01_load\\.R"', diagram_code))
-})
-
-test_that("click directives respect line_number when available", {
-  workflow <- create_test_workflow()
-  workflow$line_number <- c(10, 25, 40)
-
-  diagram_code <- put_diagram(workflow, enable_clicks = TRUE, output = "none")
-
-  # Should include line numbers in URLs (for vscode)
-  expect_true(grepl(":10", diagram_code))
-  expect_true(grepl(":25", diagram_code))
-  expect_true(grepl(":40", diagram_code))
-
-  # Tooltips should mention line numbers
-  expect_true(grepl("at line 10", diagram_code))
-})
-
-test_that("click directives skip artifact nodes", {
-  workflow <- create_test_workflow_with_terminal()
-
-  diagram_code <- put_diagram(
-    workflow,
-    show_artifacts = TRUE,
-    enable_clicks = TRUE,
-    output = "none"
-  )
-
-  # Script nodes should have click directives
-  expect_true(grepl("click load ", diagram_code))
-  expect_true(grepl("click process ", diagram_code))
-
-  # Artifact nodes should NOT have click directives
-  expect_false(grepl("click artifact_", diagram_code))
-})
-
-test_that("enable_clicks works with all themes", {
-  workflow <- create_test_workflow()
-  themes <- c("light", "dark", "github", "minimal", "auto",
-              "viridis", "magma", "plasma", "cividis")
-
-  for (theme in themes) {
-    expect_no_error({
-      diagram_code <- put_diagram(
-        workflow,
-        enable_clicks = TRUE,
-        theme = theme,
-        output = "none"
-      )
-      expect_true(grepl("click ", diagram_code))
-    })
-  }
-})
-
-test_that("show_source_info and enable_clicks work together", {
-  workflow <- create_test_workflow()
-
-  diagram_code <- put_diagram(
-    workflow,
-    show_source_info = TRUE,
-    enable_clicks = TRUE,
-    output = "none"
-  )
-
-  # Should have both source info and click directives
-  expect_true(grepl("<br/>", diagram_code))
-  expect_true(grepl("01_load\\.R", diagram_code))
-  expect_true(grepl("click ", diagram_code))
-  expect_true(grepl("vscode://file/", diagram_code))
-})
-
-# ===========================================================================
-# Colorblind-Safe Viridis Theme Tests
-# ===========================================================================
-
-test_that("viridis theme produces valid diagram with correct styling", {
-  workflow <- create_test_workflow()
-
-  diagram_code <- put_diagram(workflow, theme = "viridis", output = "none")
-
-  # Should contain mermaid code
-
-  expect_true(grepl("flowchart", diagram_code))
-  expect_true(grepl("classDef", diagram_code))
-
-  # Check viridis-specific colors (deep purple for input)
-  expect_true(grepl("#440154", diagram_code))
-})
-
-test_that("magma theme produces valid diagram with correct styling", {
-  workflow <- create_test_workflow()
-
-  diagram_code <- put_diagram(workflow, theme = "magma", output = "none")
-
-  expect_true(grepl("flowchart", diagram_code))
-  expect_true(grepl("classDef", diagram_code))
-
-  # Check magma-specific colors (deep purple for input)
-  expect_true(grepl("#3b0f70", diagram_code))
-})
-
-test_that("plasma theme produces valid diagram with correct styling", {
-  workflow <- create_test_workflow()
-
-  diagram_code <- put_diagram(workflow, theme = "plasma", output = "none")
-
-  expect_true(grepl("flowchart", diagram_code))
-  expect_true(grepl("classDef", diagram_code))
-
-  # Check plasma-specific colors (deep blue for input)
-  expect_true(grepl("#0d0887", diagram_code))
-})
-
-test_that("cividis theme produces valid diagram with correct styling", {
-  workflow <- create_test_workflow()
-
-  diagram_code <- put_diagram(workflow, theme = "cividis", output = "none")
-
-  expect_true(grepl("flowchart", diagram_code))
-  expect_true(grepl("classDef", diagram_code))
-
-  # Check cividis-specific colors (navy for input)
-  expect_true(grepl("#00204d", diagram_code))
-})
-
-test_that("get_diagram_themes includes viridis family themes", {
-  themes <- get_diagram_themes()
-
-  # Check all viridis family themes are present
-  expect_true("viridis" %in% names(themes))
-  expect_true("magma" %in% names(themes))
-  expect_true("plasma" %in% names(themes))
-  expect_true("cividis" %in% names(themes))
-
-  # Check descriptions mention colorblind-safe
-  expect_true(grepl("colorblind", tolower(themes$viridis)))
-  expect_true(grepl("colorblind", tolower(themes$magma)))
-  expect_true(grepl("colorblind", tolower(themes$plasma)))
-  expect_true(grepl("colorblind", tolower(themes$cividis)))
-})
-
-test_that("viridis themes work with all node types", {
-  # Create workflow with all node types
-  workflow <- data.frame(
-    id = c("start_node", "input_node", "process_node", "decision_node",
-           "output_node", "end_node"),
-    label = c("Start", "Input Data", "Process", "Decision",
-              "Output Data", "End"),
-    node_type = c("start", "input", "process", "decision", "output", "end"),
-    file_path = rep("/test/file.R", 6),
-    file_name = rep("file.R", 6),
-    line_number = 1:6,
-    input = rep(NA_character_, 6),
-    output = rep(NA_character_, 6),
-    stringsAsFactors = FALSE
-  )
-
-  viridis_themes <- c("viridis", "magma", "plasma", "cividis")
-
-  for (theme in viridis_themes) {
-    expect_no_error({
-      diagram_code <- put_diagram(workflow, theme = theme, output = "none")
-      # All node types should have class definitions
-      expect_true(grepl("classDef input", diagram_code))
-      expect_true(grepl("classDef process", diagram_code))
-      expect_true(grepl("classDef output", diagram_code))
-      expect_true(grepl("classDef decision", diagram_code))
-      expect_true(grepl("classDef start", diagram_code))
-      expect_true(grepl("classDef end", diagram_code))
-    })
-  }
-})
-
-test_that("viridis themes work with artifacts", {
-  workflow <- create_test_workflow()
-
-  viridis_themes <- c("viridis", "magma", "plasma", "cividis")
-
-  for (theme in viridis_themes) {
-    expect_no_error({
-      diagram_code <- put_diagram(
-        workflow,
-        theme = theme,
-        show_artifacts = TRUE,
-        output = "none"
-      )
-      # Should have artifact class definition
-      expect_true(grepl("classDef artifact", diagram_code))
-    })
-  }
-})
-
-test_that("enable_clicks works with viridis themes", {
-  workflow <- create_test_workflow()
-
-  viridis_themes <- c("viridis", "magma", "plasma", "cividis")
-
-  for (theme in viridis_themes) {
-    expect_no_error({
-      diagram_code <- put_diagram(
-        workflow,
-        enable_clicks = TRUE,
-        theme = theme,
-        output = "none"
-      )
-      expect_true(grepl("click ", diagram_code))
-    })
-  }
-})
-
-test_that("invalid theme falls back to light with warning", {
-  workflow <- create_test_workflow()
-
-  expect_warning(
-    diagram_code <- put_diagram(workflow, theme = "nonexistent", output = "none"),
-    "Invalid theme"
-  )
-
-  # Should still produce valid diagram
-  expect_true(grepl("flowchart", diagram_code))
-})
+# Test suite for put_diagram() function
+library(testthat)
+
+# Helper function to create test workflow data
+create_test_workflow <- function() {
+  data.frame(
+    file_name = c("01_load.R", "02_process.py", "03_analyze.R"),
+    file_type = c("r", "py", "r"),
+    id = c("load_data", "process_data", "analyze_results"),
+    label = c("Load Raw Data", "Process Data", "Analyze Results"),
+    node_type = c("input", "process", "output"),
+    input = c(NA, "raw_data.csv", "processed_data.csv"),
+    output = c("raw_data.csv", "processed_data.csv", "final_report.html"),
+    stringsAsFactors = FALSE
+  )
+}
+
+# Helper function to create test workflow with terminal outputs
+create_test_workflow_with_terminal <- function() {
+  data.frame(
+    file_name = c("load.R", "process.R"),
+    file_type = c("r", "r"),
+    id = c("load", "process"),
+    label = c("Load Data", "Process Data"),
+    node_type = c("input", "process"),
+    input = c(NA, "data.csv"),
+    output = c("data.csv", "final_results.csv"),  # final_results.csv is terminal
+    stringsAsFactors = FALSE
+  )
+}
+
+test_that("put_diagram() creates basic mermaid diagram", {
+  workflow <- create_test_workflow()
+
+  # Capture output
+  result <- capture.output({
+    diagram_code <- put_diagram(workflow)
+  })
+
+  # Check that mermaid code block is created
+  expect_true(any(grepl("```mermaid", result)))
+  expect_true(any(grepl("flowchart TD", result)))
+  expect_true(any(grepl("```", result)))
+
+  # Check that diagram code is returned invisibly
+  expect_true(is.character(diagram_code))
+  expect_true(grepl("flowchart TD", diagram_code))
+})
+
+test_that("put_diagram() handles different directions", {
+  workflow <- create_test_workflow()
+
+  # Test different directions
+  directions <- c("TD", "LR", "BT", "RL")
+
+  for (dir in directions) {
+    diagram_code <- put_diagram(workflow, direction = dir, output = "none")
+    expect_true(grepl(paste0("flowchart ", dir), diagram_code))
+  }
+})
+
+test_that("put_diagram() handles different node label options", {
+  workflow <- create_test_workflow()
+
+  # Test ID labels (node_labels = "name" shows IDs)
+  diagram_id <- put_diagram(workflow, node_labels = "name", output = "none")
+  expect_true(grepl("load_data", diagram_id))
+
+  # Test description labels
+  diagram_label <- put_diagram(workflow, node_labels = "label", output = "none")
+  expect_true(grepl("Load Raw Data", diagram_label))
+
+  # Test both labels
+  diagram_both <- put_diagram(workflow, node_labels = "both", output = "none")
+  expect_true(grepl("load_data: Load Raw Data", diagram_both))
+})
+
+test_that("put_diagram() generates correct node shapes", {
+  workflow <- create_test_workflow()
+  diagram_code <- put_diagram(workflow, output = "none")
+
+  # Check shapes for different node types
+  expect_true(grepl("\\(\\[.*\\]\\)", diagram_code)) # Stadium shape for input
+  expect_true(grepl("\\[.*\\]", diagram_code)) # Rectangle for process
+  expect_true(grepl("\\[\\[.*\\]\\]", diagram_code)) # Subroutine for output
+})
+
+test_that("put_diagram() creates connections based on file flow", {
+  workflow <- create_test_workflow()
+  diagram_code <- put_diagram(workflow, output = "none")
+
+  # Should have connections between nodes that share files
+  expect_true(grepl("load_data --> process_data", diagram_code))
+  expect_true(grepl("process_data --> analyze_results", diagram_code))
+})
+
+test_that("put_diagram() shows file names on connections when requested", {
+  workflow <- create_test_workflow()
+
+  # Without file names
+  diagram_no_files <- put_diagram(workflow, show_files = FALSE, output = "none")
+  expect_true(grepl("load_data --> process_data", diagram_no_files))
+  expect_false(grepl("raw_data.csv", diagram_no_files))
+
+  # With file names
+  diagram_with_files <- put_diagram(workflow, show_files = TRUE, output = "none")
+  expect_true(grepl("\\|raw_data.csv\\|", diagram_with_files))
+  expect_true(grepl("\\|processed_data.csv\\|", diagram_with_files))
+})
+
+test_that("put_diagram() adds styling when requested", {
+  workflow <- create_test_workflow()
+
+  # With styling
+  diagram_styled <- put_diagram(workflow, style_nodes = TRUE, output = "none")
+  expect_true(grepl("classDef inputStyle", diagram_styled))
+  expect_true(grepl("classDef processStyle", diagram_styled))
+  expect_true(grepl("classDef outputStyle", diagram_styled))
+
+  # Without styling
+  diagram_unstyled <- put_diagram(workflow, style_nodes = FALSE, output = "none")
+  expect_false(grepl("classDef", diagram_unstyled))
+})
+
+test_that("put_diagram() includes title when provided", {
+  workflow <- create_test_workflow()
+
+  diagram_with_title <- put_diagram(workflow, title = "My Workflow", output = "none")
+  expect_true(grepl("title: My Workflow", diagram_with_title))
+
+  diagram_no_title <- put_diagram(workflow, title = NULL, output = "none")
+  expect_false(grepl("title:", diagram_no_title))
+})
+
+test_that("put_diagram() handles file output", {
+  workflow <- create_test_workflow()
+  temp_file <- tempfile(fileext = ".md")
+
+  # Test file output
+  expect_message(
+    {
+      put_diagram(workflow, output = "file", file = temp_file)
+    },
+    "Diagram saved to"
+  )
+
+  # Check file was created and has correct content
+  expect_true(file.exists(temp_file))
+
+  content <- readLines(temp_file)
+  expect_true(any(grepl("```mermaid", content)))
+  expect_true(any(grepl("flowchart TD", content)))
+
+  # Clean up
+  unlink(temp_file)
+})
+
+test_that("put_diagram() validates input", {
+  # Empty workflow
+  expect_error(put_diagram(data.frame()), "empty.*0 rows")
+
+  # Missing required columns
+  bad_workflow <- data.frame(x = 1, y = 2)
+  expect_error(put_diagram(bad_workflow), "missing required column")
+
+  # All IDs missing
+  workflow_no_ids <- data.frame(
+    id = c(NA, "", NA),
+    file_name = c("a.R", "b.py", "c.R"),
+    stringsAsFactors = FALSE
+  )
+  expect_error(put_diagram(workflow_no_ids), "No valid workflow nodes found")
+})
+
+test_that("sanitize_node_id() works correctly", {
+  # Test normal names
+  expect_equal(sanitize_node_id("load_data"), "load_data")
+  expect_equal(sanitize_node_id("process-data"), "process_data")
+  expect_equal(sanitize_node_id("analyze.results"), "analyze_results")
+
+  # Test names starting with numbers
+  expect_equal(sanitize_node_id("1_load_data"), "node_1_load_data")
+
+  # Test special characters
+  expect_equal(sanitize_node_id("load@data#1"), "load_data_1")
+})
+
+test_that("split_file_list() handles various inputs", {
+  # Single file
+  expect_equal(split_file_list("file.csv"), "file.csv")
+
+  # Multiple files
+  expect_equal(split_file_list("file1.csv,file2.json"), c("file1.csv", "file2.json"))
+
+  # With spaces
+  expect_equal(
+    split_file_list("file1.csv, file2.json, file3.txt"),
+    c("file1.csv", "file2.json", "file3.txt")
+  )
+
+  # Empty string
+  expect_equal(split_file_list(""), character(0))
+  expect_equal(split_file_list(NA), character(0))
+})
+
+test_that("get_node_shape() returns correct shapes", {
+  expect_equal(get_node_shape("input"), c("([", "])"))
+  expect_equal(get_node_shape("process"), c("[", "]"))
+  expect_equal(get_node_shape("output"), c("[[", "]]"))
+  expect_equal(get_node_shape("decision"), c("{", "}"))
+  expect_equal(get_node_shape(NA), c("[", "]"))
+  expect_equal(get_node_shape("unknown"), c("[", "]"))
+})
+
+test_that("put_diagram() handles complex workflows", {
+  # Create workflow with multiple inputs/outputs and various node types
+  complex_workflow <- data.frame(
+    file_name = c("collect.py", "clean.R", "analyze.R", "report.R", "decide.R"),
+    id = c("collect", "clean", "analyze", "report", "decide"),
+    label = c("Collect Data", "Clean Data", "Analyze", "Generate Report", "Make Decision"),
+    node_type = c("input", "process", "process", "output", "decision"),
+    input = c(NA, "raw.csv", "clean.csv", "analysis.rds", "analysis.rds"),
+    output = c("raw.csv", "clean.csv", "analysis.rds", "report.html", "decision.json"),
+    stringsAsFactors = FALSE
+  )
+
+  diagram_code <- put_diagram(complex_workflow, output = "none")
+
+  # Should handle all node types
+  expect_true(grepl("collect", diagram_code))
+  expect_true(grepl("clean", diagram_code))
+  expect_true(grepl("analyze", diagram_code))
+  expect_true(grepl("report", diagram_code))
+  expect_true(grepl("decide", diagram_code))
+
+  # Should have appropriate connections
+  expect_true(grepl("collect --> clean", diagram_code))
+  expect_true(grepl("clean --> analyze", diagram_code))
+})
+
+test_that("put_diagram() handles workflows with no connections", {
+  # Independent nodes with no shared files
+  independent_workflow <- data.frame(
+    file_name = c("task1.R", "task2.R", "task3.R"),
+    id = c("task1", "task2", "task3"),
+    label = c("Task 1", "Task 2", "Task 3"),
+    node_type = c("process", "process", "process"),
+    input = c("file1.csv", "file2.csv", "file3.csv"),
+    output = c("out1.csv", "out2.csv", "out3.csv"),
+    stringsAsFactors = FALSE
+  )
+
+  diagram_code <- put_diagram(independent_workflow, output = "none")
+
+  # Should still create valid diagram with nodes
+  expect_true(grepl("flowchart TD", diagram_code))
+  expect_true(grepl("task1", diagram_code))
+  expect_true(grepl("task2", diagram_code))
+  expect_true(grepl("task3", diagram_code))
+
+  # Should not have connections
+  expect_false(grepl("-->", diagram_code))
+})
+
+# Mock clipr for clipboard tests
+test_that("put_diagram() handles clipboard output", {
+  workflow <- create_test_workflow()
+
+  # Mock clipr not being available
+  if (!requireNamespace("clipr", quietly = TRUE)) {
+    expect_warning(
+      {
+        result <- capture.output({
+          put_diagram(workflow, output = "clipboard")
+        })
+      },
+      "clipr package not available"
+    )
+
+    # Should fall back to console output
+    expect_true(any(grepl("```mermaid", result)))
+  }
+})
+
+# ============================================================================
+# Artifact functionality tests
+# ============================================================================
+
+test_that("put_diagram() supports show_artifacts parameter", {
+  workflow <- create_test_workflow_with_terminal()
+  
+  # Test that show_artifacts parameter is accepted
+  expect_no_error({
+    diagram_simple <- put_diagram(workflow, output = "none")
+    diagram_artifacts <- put_diagram(workflow, show_artifacts = TRUE, output = "none")
+  })
+  
+  # Diagrams should be different
+  diagram_simple <- put_diagram(workflow, output = "none")
+  diagram_artifacts <- put_diagram(workflow, show_artifacts = TRUE, output = "none")
+  expect_false(identical(diagram_simple, diagram_artifacts))
+})
+
+test_that("create_artifact_nodes() identifies data files correctly", {
+  workflow <- create_test_workflow_with_terminal()
+  artifacts <- create_artifact_nodes(workflow)
+  
+  # Should identify final_results.csv as an artifact (terminal output)
+  expect_true(nrow(artifacts) > 0)
+  expect_true("final_results.csv" %in% artifacts$file_name)
+  expect_true(all(artifacts$node_type == "artifact"))
+  expect_true(all(artifacts$is_artifact == TRUE))
+})
+
+test_that("artifact nodes have correct shape", {
+  # Test artifact node shape
+  expect_equal(get_node_shape("artifact"), c("[(", ")]"))
+})
+
+test_that("show_artifacts creates artifact nodes in diagram", {
+  workflow <- create_test_workflow_with_terminal()
+  diagram_code <- put_diagram(workflow, show_artifacts = TRUE, output = "none")
+  
+  # Should contain artifact node for terminal output
+  expect_true(grepl("artifact_final_results_csv", diagram_code))
+  expect_true(grepl("final_results\\.csv", diagram_code))
+})
+
+test_that("show_artifacts creates correct connections", {
+  workflow <- create_test_workflow_with_terminal()
+  diagram_code <- put_diagram(workflow, show_artifacts = TRUE, output = "none")
+  
+  # Should have BOTH script-to-script AND script-to-artifact connections
+  # Script-to-script connection (preserved from simple mode)
+  expect_true(grepl("load --> process", diagram_code))
+  
+  # Script-to-artifact and artifact-to-script connections
+  expect_true(grepl("load --> artifact_data_csv", diagram_code))
+  expect_true(grepl("artifact_data_csv --> process", diagram_code))
+  expect_true(grepl("process --> artifact_final_results_csv", diagram_code))
+})
+
+test_that("artifact styling is applied correctly", {
+  workflow <- create_test_workflow_with_terminal()
+  diagram_code <- put_diagram(workflow, show_artifacts = TRUE, output = "none")
+  
+  # Should contain artifact styling
+  expect_true(grepl("classDef artifactStyle", diagram_code))
+  expect_true(grepl("class artifact_", diagram_code))
+})
+
+test_that("show_artifacts with show_files shows file labels", {
+  workflow <- create_test_workflow_with_terminal()
+  diagram_code <- put_diagram(workflow, show_artifacts = TRUE, show_files = TRUE, output = "none")
+  
+  # Should have file labels on connections
+  expect_true(grepl("-->\\|.*\\|", diagram_code))  # Should have |file| labels
+})
+
+test_that("show_artifacts works with different themes", {
+  workflow <- create_test_workflow_with_terminal()
+  
+  # Test multiple themes
+  themes <- c("light", "dark", "github", "minimal", "auto")
+  
+  for (theme in themes) {
+    expect_no_error({
+      diagram_code <- put_diagram(workflow, show_artifacts = TRUE, theme = theme, output = "none")
+      expect_true(grepl("artifact", diagram_code))
+    })
+  }
+})
+
+test_that("show_artifacts handles workflow with no artifacts", {
+  # Create workflow where all outputs are script files
+  workflow <- data.frame(
+    file_name = c("main.R", "utils.R"),
+    id = c("main", "utils"),
+    label = c("Main", "Utils"),
+    node_type = c("process", "input"),
+    input = c("utils.R", NA),
+    output = c("results.txt", "utils.R"),  # utils.R is script, not artifact
+    stringsAsFactors = FALSE
+  )
+  
+  diagram_code <- put_diagram(workflow, show_artifacts = TRUE, output = "none")
+  
+  # Should handle gracefully and show results.txt artifact
+  expect_true(grepl("artifact_results_txt", diagram_code))
+})
+
+test_that("show_artifacts combines with existing node_type styling", {
+  workflow <- create_test_workflow_with_terminal()
+  diagram_code <- put_diagram(workflow, show_artifacts = TRUE, style_nodes = TRUE, output = "none")
+  
+  # Should have both script node styling and artifact styling
+  expect_true(grepl("classDef inputStyle", diagram_code))
+  expect_true(grepl("classDef processStyle", diagram_code))
+  expect_true(grepl("classDef artifactStyle", diagram_code))
+})
+
+# ============================================================================
+# Workflow boundary functionality tests
+# ============================================================================
+
+test_that("put_diagram() supports show_workflow_boundaries parameter", {
+  workflow <- data.frame(
+    file_name = c("start.R", "process.R", "end.R"),
+    id = c("start_node", "process_node", "end_node"),
+    label = c("Start", "Process", "End"),
+    node_type = c("start", "process", "end"),
+    stringsAsFactors = FALSE
+  )
+  
+  # Test that show_workflow_boundaries parameter is accepted
+  expect_no_error({
+    diagram_boundaries <- put_diagram(workflow, show_workflow_boundaries = TRUE, output = "none")
+    diagram_no_boundaries <- put_diagram(workflow, show_workflow_boundaries = FALSE, output = "none")
+  })
+  
+  # Diagrams should be different
+  diagram_boundaries <- put_diagram(workflow, show_workflow_boundaries = TRUE, output = "none")
+  diagram_no_boundaries <- put_diagram(workflow, show_workflow_boundaries = FALSE, output = "none")
+  expect_false(identical(diagram_boundaries, diagram_no_boundaries))
+})
+
+test_that("workflow boundaries show special icons when enabled", {
+  workflow <- data.frame(
+    file_name = c("start.R", "end.R"),
+    id = c("start_node", "end_node"),
+    label = c("Pipeline Start", "Pipeline End"),
+    node_type = c("start", "end"),
+    stringsAsFactors = FALSE
+  )
+  
+  diagram_code <- put_diagram(workflow, show_workflow_boundaries = TRUE, output = "none")
+  
+  # Should contain start and end nodes with special styling
+  expect_true(grepl("startStyle", diagram_code))  # Special start styling
+  expect_true(grepl("endStyle", diagram_code))  # Special end styling
+})
+
+test_that("workflow boundaries hide icons when disabled", {
+  workflow <- data.frame(
+    file_name = c("start.R", "end.R"),
+    id = c("start_node", "end_node"),
+    label = c("Pipeline Start", "Pipeline End"),
+    node_type = c("start", "end"),
+    stringsAsFactors = FALSE
+  )
+  
+  diagram_code <- put_diagram(workflow, show_workflow_boundaries = FALSE, output = "none")
+  
+  # Should NOT contain special styling when boundaries are disabled
+  expect_false(grepl("startStyle", diagram_code))  # No start styling
+  expect_false(grepl("endStyle", diagram_code))  # No end styling
+})
+
+test_that("workflow boundary styling is applied when enabled", {
+  workflow <- data.frame(
+    file_name = c("start.R", "end.R"),
+    id = c("start_node", "end_node"),
+    label = c("Start", "End"),
+    node_type = c("start", "end"),
+    stringsAsFactors = FALSE
+  )
+  
+  diagram_code <- put_diagram(workflow, show_workflow_boundaries = TRUE, output = "none")
+  
+  # Should contain start and end styling
+  expect_true(grepl("classDef startStyle", diagram_code))
+  expect_true(grepl("classDef endStyle", diagram_code))
+  expect_true(grepl("class start_node startStyle", diagram_code))
+  expect_true(grepl("class end_node endStyle", diagram_code))
+})
+
+test_that("workflow boundary styling is hidden when disabled", {
+  workflow <- data.frame(
+    file_name = c("start.R", "end.R"),
+    id = c("start_node", "end_node"),
+    label = c("Start", "End"),
+    node_type = c("start", "end"),
+    stringsAsFactors = FALSE
+  )
+  
+  diagram_code <- put_diagram(workflow, show_workflow_boundaries = FALSE, output = "none")
+  
+  # Should NOT contain start and end styling when boundaries are disabled
+  expect_false(grepl("classDef startStyle", diagram_code))
+  expect_false(grepl("classDef endStyle", diagram_code))
+})
+
+test_that("get_node_shape handles workflow boundaries correctly", {
+  # With boundaries enabled, should get stadium shapes (no special characters)
+  expect_equal(get_node_shape("start", TRUE), c("([", "])"))
+  expect_equal(get_node_shape("end", TRUE), c("([", "])"))
+  
+  # With boundaries disabled, should get regular shapes
+  expect_equal(get_node_shape("start", FALSE), c("([", "])"))
+  expect_equal(get_node_shape("end", FALSE), c("([", "])"))
+})
+
+test_that("workflow boundaries work with different themes", {
+  workflow <- data.frame(
+    file_name = c("start.R", "end.R"),
+    id = c("start_node", "end_node"),
+    label = c("Start", "End"),
+    node_type = c("start", "end"),
+    stringsAsFactors = FALSE
+  )
+  
+  # Test multiple themes with workflow boundaries
+  themes <- c("light", "dark", "github", "minimal", "auto")
+  
+  for (theme in themes) {
+    expect_no_error({
+      diagram_code <- put_diagram(workflow, show_workflow_boundaries = TRUE, theme = theme, output = "none")
+      expect_true(grepl("startStyle", diagram_code))
+      expect_true(grepl("endStyle", diagram_code))
+    })
+  }
+})
+
+# ============================================================================
+# Metadata Display (show_source_info) Tests - GitHub Issue #3
+# ============================================================================
+
+test_that("show_source_info adds file names inline", {
+  workflow <- create_test_workflow()
+
+  # Without source info
+  diagram_no_info <- put_diagram(workflow, show_source_info = FALSE, output = "none")
+  expect_false(grepl("<br/>", diagram_no_info))
+  expect_false(grepl("01_load\\.R", diagram_no_info))
+
+  # With source info inline
+  diagram_with_info <- put_diagram(workflow, show_source_info = TRUE, output = "none")
+  expect_true(grepl("<br/>", diagram_with_info))
+  expect_true(grepl("01_load\\.R", diagram_with_info))
+  expect_true(grepl("01_load\\.R", diagram_with_info))
+})
+
+test_that("source_info_style='subgraph' groups nodes by file", {
+  workflow <- create_test_workflow()
+
+  diagram_code <- put_diagram(
+    workflow,
+    show_source_info = TRUE,
+    source_info_style = "subgraph",
+    output = "none"
+  )
+
+  # Should contain subgraph declarations
+  expect_true(grepl("subgraph", diagram_code))
+  expect_true(grepl("end", diagram_code))
+
+  # Should have file names as subgraph labels
+  expect_true(grepl("01_load\\.R", diagram_code))
+  expect_true(grepl("02_process\\.py", diagram_code))
+})
+
+test_that("show_source_info handles missing file_name", {
+  workflow <- data.frame(
+    file_name = c("test.R", NA, ""),
+    id = c("node1", "node2", "node3"),
+    label = c("Node 1", "Node 2", "Node 3"),
+    node_type = c("process", "process", "process"),
+    stringsAsFactors = FALSE
+  )
+
+  # Should not error with NA or empty file names
+  expect_no_error({
+    diagram_code <- put_diagram(workflow, show_source_info = TRUE, output = "none")
+  })
+
+  diagram_code <- put_diagram(workflow, show_source_info = TRUE, output = "none")
+  # Only test.R should show source info
+  expect_true(grepl("test\\.R", diagram_code))
+})
+
+test_that("show_source_info with invalid source_info_style warns and uses default", {
+  workflow <- create_test_workflow()
+
+  expect_warning(
+    put_diagram(workflow, show_source_info = TRUE, source_info_style = "invalid", output = "none"),
+    "Invalid source_info_style"
+  )
+})
+
+test_that("show_source_info excludes artifact nodes from source info", {
+  workflow <- create_test_workflow_with_terminal()
+
+  diagram_code <- put_diagram(
+    workflow,
+    show_artifacts = TRUE,
+    show_source_info = TRUE,
+    output = "none"
+  )
+
+  # Artifact nodes should NOT have source info appended
+  # Script nodes should have source info
+  expect_true(grepl("load\\.R", diagram_code))
+  # The artifact label should be clean (final_results.csv without additional source info)
+  expect_true(grepl("final_results\\.csv", diagram_code))
+})
+
+# ============================================================================
+# Clickable Hyperlinks (enable_clicks) Tests - GitHub Issue #4
+# ============================================================================
+
+test_that("enable_clicks adds click directives", {
+  workflow <- create_test_workflow()
+
+  # Without clicks
+  diagram_no_clicks <- put_diagram(workflow, enable_clicks = FALSE, output = "none")
+  expect_false(grepl("click ", diagram_no_clicks))
+
+  # With clicks
+  diagram_with_clicks <- put_diagram(workflow, enable_clicks = TRUE, output = "none")
+  expect_true(grepl("click ", diagram_with_clicks))
+  expect_true(grepl("%% Click Actions", diagram_with_clicks))
+})
+
+test_that("click_protocol='vscode' generates correct URLs", {
+  workflow <- create_test_workflow()
+
+  diagram_code <- put_diagram(
+    workflow,
+    enable_clicks = TRUE,
+    click_protocol = "vscode",
+    output = "none"
+  )
+
+  # Should have vscode:// protocol
+  expect_true(grepl("vscode://file/", diagram_code))
+  expect_true(grepl('click load_data "vscode://file/', diagram_code))
+})
+
+test_that("click_protocol='file' generates correct URLs", {
+  workflow <- create_test_workflow()
+
+  diagram_code <- put_diagram(
+    workflow,
+    enable_clicks = TRUE,
+    click_protocol = "file",
+    output = "none"
+  )
+
+  # Should have file:/// protocol
+  expect_true(grepl("file:///", diagram_code))
+})
+
+test_that("click_protocol='rstudio' generates correct URLs", {
+  workflow <- create_test_workflow()
+
+  diagram_code <- put_diagram(
+    workflow,
+    enable_clicks = TRUE,
+    click_protocol = "rstudio",
+    output = "none"
+  )
+
+  # Should have rstudio:// protocol
+  expect_true(grepl("rstudio://open-file\\?path=", diagram_code))
+})
+
+test_that("enable_clicks with invalid protocol warns and uses default", {
+  workflow <- create_test_workflow()
+
+  expect_warning(
+    put_diagram(workflow, enable_clicks = TRUE, click_protocol = "invalid", output = "none"),
+    "Invalid click_protocol"
+  )
+})
+
+test_that("normalize_path_for_url handles various inputs", {
+  # Empty and NA inputs
+  expect_equal(normalize_path_for_url(""), "")
+  expect_equal(normalize_path_for_url(NA), "")
+  expect_equal(normalize_path_for_url(NULL), "")
+
+  # Normal paths (just check it returns a string and converts slashes)
+  result <- normalize_path_for_url("test/path/file.R")
+  expect_true(is.character(result))
+  expect_false(grepl("\\\\", result))  # No backslashes
+})
+
+test_that("generate_click_url creates proper URLs for each protocol", {
+  # VS Code without line number
+  url_vscode <- generate_click_url("test.R", protocol = "vscode")
+  expect_true(grepl("vscode://file/", url_vscode))
+
+  # VS Code with line number
+  url_vscode_line <- generate_click_url("test.R", line_number = 42, protocol = "vscode")
+  expect_true(grepl(":42$", url_vscode_line))
+
+  # File protocol
+  url_file <- generate_click_url("test.R", protocol = "file")
+  expect_true(grepl("file:///", url_file))
+
+  # RStudio protocol
+  url_rstudio <- generate_click_url("test.R", protocol = "rstudio")
+  expect_true(grepl("rstudio://open-file\\?path=", url_rstudio))
+
+  # RStudio with line number
+  url_rstudio_line <- generate_click_url("test.R", line_number = 10, protocol = "rstudio")
+  expect_true(grepl("&line=10", url_rstudio_line))
+})
+
+test_that("click directives include tooltips", {
+  workflow <- create_test_workflow()
+
+  diagram_code <- put_diagram(workflow, enable_clicks = TRUE, output = "none")
+
+  # Should have tooltip format: click nodeId "url" "tooltip"
+  expect_true(grepl('click load_data "[^"]*" "Open 01_load\\.R"', diagram_code))
+})
+
+test_that("click directives respect line_number when available", {
+  workflow <- create_test_workflow()
+  workflow$line_number <- c(10, 25, 40)
+
+  diagram_code <- put_diagram(workflow, enable_clicks = TRUE, output = "none")
+
+  # Should include line numbers in URLs (for vscode)
+  expect_true(grepl(":10", diagram_code))
+  expect_true(grepl(":25", diagram_code))
+  expect_true(grepl(":40", diagram_code))
+
+  # Tooltips should mention line numbers
+  expect_true(grepl("at line 10", diagram_code))
+})
+
+test_that("click directives skip artifact nodes", {
+  workflow <- create_test_workflow_with_terminal()
+
+  diagram_code <- put_diagram(
+    workflow,
+    show_artifacts = TRUE,
+    enable_clicks = TRUE,
+    output = "none"
+  )
+
+  # Script nodes should have click directives
+  expect_true(grepl("click load ", diagram_code))
+  expect_true(grepl("click process ", diagram_code))
+
+  # Artifact nodes should NOT have click directives
+  expect_false(grepl("click artifact_", diagram_code))
+})
+
+test_that("enable_clicks works with all themes", {
+  workflow <- create_test_workflow()
+  themes <- c("light", "dark", "github", "minimal", "auto",
+              "viridis", "magma", "plasma", "cividis")
+
+  for (theme in themes) {
+    expect_no_error({
+      diagram_code <- put_diagram(
+        workflow,
+        enable_clicks = TRUE,
+        theme = theme,
+        output = "none"
+      )
+      expect_true(grepl("click ", diagram_code))
+    })
+  }
+})
+
+test_that("show_source_info and enable_clicks work together", {
+  workflow <- create_test_workflow()
+
+  diagram_code <- put_diagram(
+    workflow,
+    show_source_info = TRUE,
+    enable_clicks = TRUE,
+    output = "none"
+  )
+
+  # Should have both source info and click directives
+  expect_true(grepl("<br/>", diagram_code))
+  expect_true(grepl("01_load\\.R", diagram_code))
+  expect_true(grepl("click ", diagram_code))
+  expect_true(grepl("vscode://file/", diagram_code))
+})
+
+# ===========================================================================
+# Colorblind-Safe Viridis Theme Tests
+# ===========================================================================
+
+test_that("viridis theme produces valid diagram with correct styling", {
+  workflow <- create_test_workflow()
+
+  diagram_code <- put_diagram(workflow, theme = "viridis", output = "none")
+
+  # Should contain mermaid code
+
+  expect_true(grepl("flowchart", diagram_code))
+  expect_true(grepl("classDef", diagram_code))
+
+  # Check viridis-specific colors (deep purple for input)
+  expect_true(grepl("#440154", diagram_code))
+})
+
+test_that("magma theme produces valid diagram with correct styling", {
+  workflow <- create_test_workflow()
+
+  diagram_code <- put_diagram(workflow, theme = "magma", output = "none")
+
+  expect_true(grepl("flowchart", diagram_code))
+  expect_true(grepl("classDef", diagram_code))
+
+  # Check magma-specific colors (deep purple for input)
+  expect_true(grepl("#3b0f70", diagram_code))
+})
+
+test_that("plasma theme produces valid diagram with correct styling", {
+  workflow <- create_test_workflow()
+
+  diagram_code <- put_diagram(workflow, theme = "plasma", output = "none")
+
+  expect_true(grepl("flowchart", diagram_code))
+  expect_true(grepl("classDef", diagram_code))
+
+  # Check plasma-specific colors (deep blue for input)
+  expect_true(grepl("#0d0887", diagram_code))
+})
+
+test_that("cividis theme produces valid diagram with correct styling", {
+  workflow <- create_test_workflow()
+
+  diagram_code <- put_diagram(workflow, theme = "cividis", output = "none")
+
+  expect_true(grepl("flowchart", diagram_code))
+  expect_true(grepl("classDef", diagram_code))
+
+  # Check cividis-specific colors (navy for input)
+  expect_true(grepl("#00204d", diagram_code))
+})
+
+test_that("get_diagram_themes includes viridis family themes", {
+  themes <- get_diagram_themes()
+
+  # Check all viridis family themes are present
+  expect_true("viridis" %in% names(themes))
+  expect_true("magma" %in% names(themes))
+  expect_true("plasma" %in% names(themes))
+  expect_true("cividis" %in% names(themes))
+
+  # Check descriptions mention colorblind-safe
+  expect_true(grepl("colorblind", tolower(themes$viridis)))
+  expect_true(grepl("colorblind", tolower(themes$magma)))
+  expect_true(grepl("colorblind", tolower(themes$plasma)))
+  expect_true(grepl("colorblind", tolower(themes$cividis)))
+})
+
+test_that("viridis themes work with all node types", {
+  # Create workflow with all node types
+  workflow <- data.frame(
+    id = c("start_node", "input_node", "process_node", "decision_node",
+           "output_node", "end_node"),
+    label = c("Start", "Input Data", "Process", "Decision",
+              "Output Data", "End"),
+    node_type = c("start", "input", "process", "decision", "output", "end"),
+    file_path = rep("/test/file.R", 6),
+    file_name = rep("file.R", 6),
+    line_number = 1:6,
+    input = rep(NA_character_, 6),
+    output = rep(NA_character_, 6),
+    stringsAsFactors = FALSE
+  )
+
+  viridis_themes <- c("viridis", "magma", "plasma", "cividis")
+
+  for (theme in viridis_themes) {
+    expect_no_error({
+      diagram_code <- put_diagram(workflow, theme = theme, output = "none")
+      # All node types should have class definitions
+      expect_true(grepl("classDef input", diagram_code))
+      expect_true(grepl("classDef process", diagram_code))
+      expect_true(grepl("classDef output", diagram_code))
+      expect_true(grepl("classDef decision", diagram_code))
+      expect_true(grepl("classDef start", diagram_code))
+      expect_true(grepl("classDef end", diagram_code))
+    })
+  }
+})
+
+test_that("viridis themes work with artifacts", {
+  workflow <- create_test_workflow()
+
+  viridis_themes <- c("viridis", "magma", "plasma", "cividis")
+
+  for (theme in viridis_themes) {
+    expect_no_error({
+      diagram_code <- put_diagram(
+        workflow,
+        theme = theme,
+        show_artifacts = TRUE,
+        output = "none"
+      )
+      # Should have artifact class definition
+      expect_true(grepl("classDef artifact", diagram_code))
+    })
+  }
+})
+
+test_that("enable_clicks works with viridis themes", {
+  workflow <- create_test_workflow()
+
+  viridis_themes <- c("viridis", "magma", "plasma", "cividis")
+
+  for (theme in viridis_themes) {
+    expect_no_error({
+      diagram_code <- put_diagram(
+        workflow,
+        enable_clicks = TRUE,
+        theme = theme,
+        output = "none"
+      )
+      expect_true(grepl("click ", diagram_code))
+    })
+  }
+})
+
+test_that("invalid theme falls back to light with warning", {
+  workflow <- create_test_workflow()
+
+  expect_warning(
+    diagram_code <- put_diagram(workflow, theme = "nonexistent", output = "none"),
+    "Invalid theme"
+  )
+
+  # Should still produce valid diagram
+  expect_true(grepl("flowchart", diagram_code))
+})