Refactor documentation and templates for clarity

R/AGENTS.md

@@ -6,7 +6,7 @@
 ## Namespace Management
 
 - **Prefer `@importFrom` over `@import`**: Always use `@importFrom package_name specific_functions` rather than `@import package_name` for all packages. This keeps the namespace clean and makes dependencies explicit by only importing the functions actually used in the codebase.
-- **Centralize imports in `r1099894-package.R`**: Declare all `@importFrom` statements in `R/r1099894-package.R` instead of in individual function roxygen comments. This provides a single source of truth for all package dependencies.
+- **Centralize imports in `<pkg-name>-package.R`**: Declare all `@importFrom` statements in `R/<pkg-name>-package.R` instead of in individual function roxygen comments. This provides a single source of truth for all package dependencies.
 - **Exception**: Only use `@import` in rare cases where a package is used extensively throughout the codebase (e.g., `rlang` for error handling utilities across many functions).
 
 ## Shiny App

inst/tasks/deploy_to_shinyio.R

@@ -30,6 +30,6 @@ golem::add_shinyappsio_file(open = FALSE)
 
 # Deploy
 # Use appPrimaryDoc to treat this as a document deployment (not a package)
-# This prevents rsconnect from trying to reinstall the r1099894 package
+# This prevents rsconnect from trying to reinstall the package
 rsconnect::setAccountInfo(name = Sys.getenv('SHINYAPPS_NAME'), token = Sys.getenv('SHINYAPPS_TOKEN'), secret = Sys.getenv('SHINYAPPS_SECRET'))
 rsconnect::deployApp(appName = Sys.getenv('SHINYAPPS_APPNAME'), forceUpdate = TRUE, logLevel = 'normal', launch.browser = FALSE, appMode = "shiny")

inst/tasks/run_local.R

@@ -5,7 +5,7 @@
 # Set development options for hot reload
 options(
   shiny.autoreload = TRUE,
-  shiny.port = 1023
+  shiny.port = 8000
 )     
 
 # Load the package in development mode

vignettes/adr/adr-001-module-structure-and-organisation.Rmd

@@ -1,6 +1,4 @@
----
-title: "ADR-001: Module Structure and Organisation"
----
+# ADR-001: Module Structure and Organisation
 
 ## Decision
 

vignettes/adr/adr-002-dashboard-page-component-extraction.Rmd

@@ -1,11 +1,4 @@
----
-title: "ADR-004: Dashboard Page Component Extraction"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{ADR-004: Dashboard Page Component Extraction}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
+# ADR-001: Dashboard Page Component Extraction
 
 ## Decision
 

vignettes/adr/adr-template.Rmd

@@ -1,4 +1,4 @@
-# Architecture Decision Record Template
+# ADR-XXX: Architecture Decision Record Template
 
 ## Decision