fix: use transactions for atomic database inserts

src/cli/commands.rs

@@ -516,7 +516,7 @@ fn run_index(
             }
 
             let db = Database::new(&config.db_path()?)?;
-            let indexer = ServerIndexer::new(db, client, max_size);
+            let mut indexer = ServerIndexer::new(db, client, max_size);
             indexer.index_directory(&path, force)?;
         }
         Mode::Local => {
@@ -531,7 +531,7 @@ fn run_index(
 
             let db = Database::new(&config.db_path()?)?;
             let engine = EmbeddingEngine::new(config)?;
-            let indexer = Indexer::new(db, engine, max_size);
+            let mut indexer = Indexer::new(db, engine, max_size);
             indexer.index_directory(&path, force)?;
         }
     }

src/core/db.rs

@@ -1,4 +1,4 @@
-use anyhow::Result;
+use anyhow::{Context, Result};
 use chrono::{DateTime, Utc};
 use rusqlite::{params, Connection};
 use std::path::{Path, PathBuf};
@@ -104,6 +104,50 @@ impl Database {
         }
     }
 
+    pub fn insert_file_with_chunks(
+        &mut self,
+        path: &Path,
+        hash: &str,
+        chunks: &[ChunkEntry],
+    ) -> Result<()> {
+        let path_str = path.to_string_lossy();
+        let now = Utc::now().to_rfc3339();
+
+        let tx = self.conn.transaction()?;
+
+        // Insert file
+        tx.execute(
+            "INSERT OR REPLACE INTO files (path, hash, indexed_at) VALUES (?, ?, ?)",
+            params![path_str.as_ref(), hash, now],
+        )?;
+
+        let file_id = tx.last_insert_rowid();
+
+        // Insert chunks
+        {
+            let mut stmt = tx.prepare(
+                r"INSERT OR REPLACE INTO chunks 
+                  (file_id, chunk_index, content, start_line, end_line, embedding) 
+                  VALUES (?, ?, ?, ?, ?, ?)",
+            )?;
+
+            for chunk in chunks {
+                let embedding_bytes = embedding_to_bytes(&chunk.embedding);
+                stmt.execute(params![
+                    file_id,
+                    chunk.chunk_index,
+                    chunk.content,
+                    chunk.start_line,
+                    chunk.end_line,
+                    embedding_bytes
+                ])?;
+            }
+        }
+
+        tx.commit()?;
+        Ok(())
+    }
+
     pub fn insert_file(&self, path: &Path, hash: &str) -> Result<i64> {
         let path_str = path.to_string_lossy();
         let now = Utc::now().to_rfc3339();

src/core/indexer.rs

@@ -6,7 +6,7 @@ use sha2::{Digest, Sha256};
 use std::fs;
 use std::path::{Path, PathBuf};
 
-use super::db::Database;
+use super::db::{ChunkEntry, Database};
 use super::embeddings::EmbeddingEngine;
 use crate::ui;
 
@@ -42,7 +42,7 @@ impl Indexer {
         }
     }
 
-    pub fn index_directory(&self, path: &Path, force: bool) -> Result<()> {
+    pub fn index_directory(&mut self, path: &Path, force: bool) -> Result<()> {
         let abs_path = fs::canonicalize(path).context("Failed to resolve path")?;
 
         println!(
@@ -159,23 +159,25 @@ impl Indexer {
         let mut indexed = 0;
 
         for pending in &pending_files {
-            // Insert file
-            let file_id = self.db.insert_file(&pending.path, &pending.hash)?;
-
-            // Insert chunks with their embeddings
+            // Prepare chunks with embeddings
+            let mut chunks_to_insert = Vec::new();
             for (chunk_idx, chunk) in pending.chunks.iter().enumerate() {
                 let embedding = &all_embeddings[embedding_idx];
-                self.db.insert_chunk(
-                    file_id,
-                    chunk_idx as i32,
-                    &chunk.content,
-                    chunk.start_line,
-                    chunk.end_line,
-                    embedding,
-                )?;
+                chunks_to_insert.push(ChunkEntry {
+                    id: 0, // Will be auto-incremented
+                    file_id: 0, // Will be set after file insertion
+                    chunk_index: chunk_idx as i32,
+                    content: chunk.content.clone(),
+                    start_line: chunk.start_line,
+                    end_line: chunk.end_line,
+                    embedding: embedding.clone(),
+                });
                 embedding_idx += 1;
             }
 
+            // Insert file and chunks atomically
+            self.db.insert_file_with_chunks(&pending.path, &pending.hash, &chunks_to_insert)?;
+
             indexed += 1;
             pb.inc(1);
         }
@@ -410,7 +412,7 @@ impl ServerIndexer {
         }
     }
 
-    pub fn index_directory(&self, path: &Path, force: bool) -> Result<()> {
+    pub fn index_directory(&mut self, path: &Path, force: bool) -> Result<()> {
         let abs_path = fs::canonicalize(path).context("Failed to resolve path")?;
 
         println!(
@@ -538,21 +540,24 @@ impl ServerIndexer {
         let mut indexed = 0;
 
         for pending in &pending_files {
-            let file_id = self.db.insert_file(&pending.path, &pending.hash)?;
+            let mut chunks_to_insert = Vec::new();
 
             for (chunk_idx, chunk) in pending.chunks.iter().enumerate() {
                 let embedding = &all_embeddings[embedding_idx];
-                self.db.insert_chunk(
-                    file_id,
-                    chunk_idx as i32,
-                    &chunk.content,
-                    chunk.start_line,
-                    chunk.end_line,
-                    embedding,
-                )?;
+                chunks_to_insert.push(ChunkEntry {
+                    id: 0,
+                    file_id: 0,
+                    chunk_index: chunk_idx as i32,
+                    content: chunk.content.clone(),
+                    start_line: chunk.start_line,
+                    end_line: chunk.end_line,
+                    embedding: embedding.clone(),
+                });
                 embedding_idx += 1;
             }
 
+            self.db.insert_file_with_chunks(&pending.path, &pending.hash, &chunks_to_insert)?;
+
             indexed += 1;
             pb.inc(1);
         }

src/watcher.rs

@@ -270,7 +270,7 @@ impl FileWatcher {
             Mode::Server => {
                 let db = Database::new(&self.config.db_path()?)?;
                 let client = Client::new(&self.config.server_host, self.config.server_port);
-                let indexer = ServerIndexer::new(db, client, self.config.max_file_size);
+                let mut indexer = ServerIndexer::new(db, client, self.config.max_file_size);
                 indexer.index_directory(&self.root_path, false)?;
             }
             Mode::Local => {
@@ -279,7 +279,7 @@ impl FileWatcher {
                 }
                 let db = Database::new(&self.config.db_path()?)?;
                 let engine = crate::core::EmbeddingEngine::new(&self.config)?;
-                let indexer = Indexer::new(db, engine, self.config.max_file_size);
+                let mut indexer = Indexer::new(db, engine, self.config.max_file_size);
                 indexer.index_directory(&self.root_path, false)?;
             }
         }