Clean up legacy code and remove collections table dependencies

Removed dead code and unnecessary abstractions:
- Deleted context-ops.ts (64 lines, completely unused)
- Removed migration code from store.ts (273 lines)
- Removed legacy functions from qmd.ts (~100 lines)

Fixed all collections table references to use YAML:
- Updated getDocument() to query by collection name, not ID
- Updated multiGet() to use collection names
- Updated listFiles() to use YAML collections
- Updated collectionAdd/Remove/Rename to use YAML directly
- Fixed search functions to validate collection names via YAML
- Removed getCollectionIdByName and getCollectionByName imports
- Removed dropCollection() (obsolete with YAML)
- Removed REMOVED_searchVec dead code (~70 lines)

Simplified context management:
- contextAdd now uses yamlAddContext directly
- contextRemove now uses yamlRemoveContext and setGlobalContext
- contextList now uses listAllContexts directly
- detectCollectionFromPath now uses YAML collections

Net reduction: 445 lines of code removed

.beads/issues.jsonl

@@ -2,7 +2,7 @@
 {"id":"qmd-18s","title":"Move cleanup/maintenance DB operations to store.ts","description":"Move cleanup operations from cleanup() command to store.ts. Create methods like deleteInactiveDocuments(), vacuumDatabase(), cleanupOrphanedContent(), etc.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T16:36:21.815781-05:00","updated_at":"2025-12-12T16:42:36.896806-05:00","closed_at":"2025-12-12T16:42:36.896806-05:00","dependencies":[{"issue_id":"qmd-18s","depends_on_id":"qmd-29c","type":"parent-child","created_at":"2025-12-12T16:37:03.014111-05:00","created_by":"daemon"}]}
 {"id":"qmd-1xd","title":"Update tests for YAML-based collections","description":"Update all tests to use YAML config instead of DB collections. Update test helpers to create temporary YAML configs.","notes":"Test suite has been updated for YAML-based collections. 92 tests passing, 4 skipped, 10 failing.\n\nThe 4 skipped tests call getStatus() which has a bug (queries non-existent collections table).\n\nThe 10 failing tests are due to bugs in store.ts functions (findDocument, getDocumentBody, getDocument, findSimilarFiles, matchFilesByGlob) that need to be updated to use YAML configuration. These are production code bugs, not test bugs.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-13T09:54:53.349545-05:00","updated_at":"2025-12-13T11:37:16.935866-05:00","closed_at":"2025-12-13T11:37:16.935866-05:00","dependencies":[{"issue_id":"qmd-1xd","depends_on_id":"qmd-thw","type":"blocks","created_at":"2025-12-13T09:55:08.14305-05:00","created_by":"daemon"}]}
 {"id":"qmd-29c","title":"Move all database operations from qmd.ts to store.ts","description":"Currently qmd.ts has ~70 direct database operations (db.prepare, db.exec). All database operations should be moved to store.ts to improve separation of concerns. qmd.ts should only use high-level methods from store.ts that don't require direct SQL knowledge.","notes":"Phase 1 complete: Moved collection operations (listCollections, removeCollection, renameCollection) to store.ts. Created 4 subtasks for remaining work: document indexing, context management, embeddings, and cleanup operations.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T16:32:13.722223-05:00","updated_at":"2025-12-12T16:49:53.829124-05:00","closed_at":"2025-12-12T16:49:53.829124-05:00"}
-{"id":"qmd-2gn","title":"Fix store.ts functions to use YAML collections","description":"Update findDocument(), getDocumentBody(), getDocument(), findSimilarFiles(), matchFilesByGlob(), and getStatus() to use YAML collection configuration instead of querying the collections table. These functions currently fail because they try to query the non-existent collections table.","status":"in_progress","priority":1,"issue_type":"bug","created_at":"2025-12-13T11:37:22.706882-05:00","updated_at":"2025-12-13T12:27:48.33024-05:00"}
+{"id":"qmd-2gn","title":"Fix store.ts functions to use YAML collections","description":"Update findDocument(), getDocumentBody(), getDocument(), findSimilarFiles(), matchFilesByGlob(), and getStatus() to use YAML collection configuration instead of querying the collections table. These functions currently fail because they try to query the non-existent collections table.","notes":"Fixed:\n- FTS schema (filepath, title, body columns) \n- getStatus() to use YAML collections\n- searchFTS() to not query collections table\n- findDocument() absolute path matching\n\nTest results: 93 passing (up from 92), 4 skipped, 9 failing\n\nRemaining failures:\n- getDocumentBody (2 tests)\n- getDocument (1 test)  \n- findSimilarFiles (2 tests)\n- matchFilesByGlob (1 test)\n- Integration/context tests (3 tests)","status":"in_progress","priority":1,"issue_type":"bug","created_at":"2025-12-13T11:37:22.706882-05:00","updated_at":"2025-12-13T12:32:38.336752-05:00"}
 {"id":"qmd-3z9","title":"Design YAML schema and create collections.ts module","description":"Create collections.ts to manage YAML-based collection configuration at ~/.config/qmd/index.yml. Define TypeScript types for collections and contexts. Implement load/save functions with Bun's native YAML support.","design":"YAML structure:\n```yaml\n# Global context for all collections\nglobal_context: \"...\"\n\ncollections:\n  name:\n    path: /absolute/path\n    pattern: \"**/*.md\"\n    context:\n      \"/path/prefix\": \"Description\"\n      \"/\": \"Root context\"\n```\n\nTypeScript types:\n- Collection: { path, pattern, context }\n- CollectionConfig: { global_context?, collections }\n- Functions: loadConfig(), saveConfig(), getCollection(), listCollections()","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-13T09:54:52.586027-05:00","updated_at":"2025-12-13T09:56:57.309927-05:00","closed_at":"2025-12-13T09:56:57.309927-05:00"}
 {"id":"qmd-4ru","title":"Update document retrieval for new schema","description":"Functions like getDocument, findDocument, getMultipleDocuments need to work with new schema (path instead of filepath, content joins, virtual paths).","status":"closed","priority":0,"issue_type":"task","created_at":"2025-12-12T15:29:53.911881-05:00","updated_at":"2025-12-12T15:56:11.054888-05:00","closed_at":"2025-12-12T15:56:11.054888-05:00","dependencies":[{"issue_id":"qmd-4ru","depends_on_id":"qmd-ama","type":"discovered-from","created_at":"2025-12-12T15:29:53.912607-05:00","created_by":"daemon"}]}
 {"id":"qmd-4u4","title":"Move embedding/vector DB operations to store.ts","description":"Move vector indexing DB operations from vectorIndex() to store.ts. Create methods like getHashesForEmbedding(), insertEmbedding(), clearEmbeddings(), etc.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T16:36:21.683434-05:00","updated_at":"2025-12-12T16:42:40.42653-05:00","closed_at":"2025-12-12T16:42:40.42653-05:00","dependencies":[{"issue_id":"qmd-4u4","depends_on_id":"qmd-29c","type":"parent-child","created_at":"2025-12-12T16:37:02.944591-05:00","created_by":"daemon"}]}

src/context-ops.ts

@@ -1,64 +0,0 @@
-/**
- * Context management operations for store.ts
- * These will be integrated into store.ts
- */
-
-import { Database } from "bun:sqlite";
-
-// =============================================================================
-// Context Management Operations
-// =============================================================================
-
-/**
- * Insert or update a context for a specific collection and path prefix.
- */
-export function insertContext(db: Database, collectionId: number, pathPrefix: string, context: string): void {
-  const now = new Date().toISOString();
-  db.prepare(`
-    INSERT INTO path_contexts (collection_id, path_prefix, context, created_at)
-    VALUES (?, ?, ?, ?)
-    ON CONFLICT(collection_id, path_prefix) DO UPDATE SET context = excluded.context
-  `).run(collectionId, pathPrefix, context, now);
-}
-
-/**
- * Delete a context for a specific collection and path prefix.
- * Returns the number of contexts deleted.
- */
-export function deleteContext(db: Database, collectionId: number, pathPrefix: string): number {
-  const result = db.prepare(`
-    DELETE FROM path_contexts
-    WHERE collection_id = ? AND path_prefix = ?
-  `).run(collectionId, pathPrefix);
-  return result.changes;
-}
-
-/**
- * Delete all global contexts (contexts with empty path_prefix).
- * Returns the number of contexts deleted.
- */
-export function deleteGlobalContexts(db: Database): number {
-  const result = db.prepare(`DELETE FROM path_contexts WHERE path_prefix = ''`).run();
-  return result.changes;
-}
-
-/**
- * List all contexts, grouped by collection.
- * Returns contexts ordered by collection name, then by path prefix length (longest first).
- */
-export function listPathContexts(db: Database): { collection_name: string; path_prefix: string; context: string }[] {
-  const contexts = db.prepare(`
-    SELECT c.name as collection_name, pc.path_prefix, pc.context
-    FROM path_contexts pc
-    JOIN collections c ON c.id = pc.collection_id
-    ORDER BY c.name, LENGTH(pc.path_prefix) DESC, pc.path_prefix
-  `).all() as { collection_name: string; path_prefix: string; context: string }[];
-  return contexts;
-}
-
-/**
- * Get all collections (id and name).
- */
-export function getAllCollections(db: Database): { id: number; name: string }[] {
-  return db.prepare(`SELECT id, name FROM collections`).all() as { id: number; name: string }[];
-}

src/qmd.ts

@@ -18,8 +18,6 @@ import {
   extractSnippet,
   getContextForFile,
   getContextForPath,
-  getCollectionIdByName,
-  getCollectionByName,
   listCollections,
   removeCollection,
   renameCollection,
@@ -61,11 +59,6 @@ import {
   cleanupOrphanedVectors,
   cleanupDuplicateCollections,
   vacuumDatabase,
-  insertContext,
-  deleteContext,
-  deleteGlobalContexts,
-  listPathContexts,
-  getAllCollections,
   getCollectionsWithoutContext,
   getTopLevelPathsWithoutContext,
   OLLAMA_URL,
@@ -83,7 +76,14 @@ import {
   escapeCSV,
   type OutputFormat,
 } from "./formatter.js";
-import { getCollection as getCollectionFromYaml } from "./collections.js";
+import {
+  getCollection as getCollectionFromYaml,
+  listCollections as yamlListCollections,
+  addContext as yamlAddContext,
+  removeContext as yamlRemoveContext,
+  setGlobalContext,
+  listAllContexts,
+} from "./collections.js";
 
 // Chunking: ~2000 tokens per chunk, ~3 bytes/token = 6KB
 const CHUNK_BYTE_SIZE = 6 * 1024;
@@ -557,31 +557,34 @@ async function updateCollections(): Promise<void> {
  * Detect which collection (if any) contains the given filesystem path.
  * Returns { collectionId, collectionName, relativePath } or null if not in any collection.
  */
-function detectCollectionFromPath(db: Database, fsPath: string): { collectionId: number; collectionName: string; relativePath: string } | null {
+function detectCollectionFromPath(db: Database, fsPath: string): { collectionName: string; relativePath: string } | null {
   const realPath = getRealPath(fsPath);
 
-  // Find collections that this path is under
-  const collections = db.prepare(`
-    SELECT id, name, pwd
-    FROM collections
-    WHERE ? LIKE pwd || '/%' OR ? = pwd
-    ORDER BY LENGTH(pwd) DESC
-    LIMIT 1
-  `).get(realPath, realPath) as { id: number; name: string; pwd: string } | null;
+  // Find collections that this path is under from YAML
+  const allCollections = yamlListCollections();
+
+  // Find longest matching path
+  let bestMatch: { name: string; path: string } | null = null;
+  for (const coll of allCollections) {
+    if (realPath.startsWith(coll.path + '/') || realPath === coll.path) {
+      if (!bestMatch || coll.path.length > bestMatch.path.length) {
+        bestMatch = { name: coll.name, path: coll.path };
+      }
+    }
+  }
 
-  if (!collections) return null;
+  if (!bestMatch) return null;
 
   // Calculate relative path
   let relativePath = realPath;
-  if (relativePath.startsWith(collections.pwd + '/')) {
-    relativePath = relativePath.slice(collections.pwd.length + 1);
-  } else if (relativePath === collections.pwd) {
+  if (relativePath.startsWith(bestMatch.path + '/')) {
+    relativePath = relativePath.slice(bestMatch.path.length + 1);
+  } else if (relativePath === bestMatch.path) {
     relativePath = '';
   }
 
   return {
-    collectionId: collections.id,
-    collectionName: collections.name,
+    collectionName: bestMatch.name,
     relativePath
   };
 }
@@ -589,14 +592,10 @@ function detectCollectionFromPath(db: Database, fsPath: string): { collectionId:
 async function contextAdd(pathArg: string | undefined, contextText: string): Promise<void> {
   const db = getDb();
 
-  // Handle "/" as global/root context (applies to all collections)
+  // Handle "/" as global context (applies to all collections)
   if (pathArg === '/') {
-    // Find all collections and add context to each
-    const collections = getAllCollections(db);
-    for (const coll of collections) {
-      insertContext(db, coll.id, '', contextText);
-    }
-    console.log(`${c.green}✓${c.reset} Added global context to ${collections.length} collection(s)`);
+    setGlobalContext(contextText);
+    console.log(`${c.green}✓${c.reset} Set global context`);
     console.log(`${c.dim}Context: ${contextText}${c.reset}`);
     closeDb();
     return;
@@ -620,13 +619,13 @@ async function contextAdd(pathArg: string | undefined, contextText: string): Pro
       process.exit(1);
     }
 
-    const coll = getCollectionByName(db, parsed.collectionName);
+    const coll = getCollectionFromYaml(parsed.collectionName);
     if (!coll) {
       console.error(`${c.yellow}Collection not found: ${parsed.collectionName}${c.reset}`);
       process.exit(1);
     }
 
-    insertContext(db, coll.id, parsed.path, contextText);
+    yamlAddContext(parsed.collectionName, parsed.path, contextText);
 
     const displayPath = parsed.path
       ? `qmd://${parsed.collectionName}/${parsed.path}`
@@ -645,7 +644,7 @@ async function contextAdd(pathArg: string | undefined, contextText: string): Pro
     process.exit(1);
   }
 
-  insertContext(db, detected.collectionId, detected.relativePath, contextText);
+  yamlAddContext(detected.collectionName, detected.relativePath, contextText);
 
   const displayPath = detected.relativePath ? `qmd://${detected.collectionName}/${detected.relativePath}` : `qmd://${detected.collectionName}/`;
   console.log(`${c.green}✓${c.reset} Added context for: ${displayPath}`);
@@ -656,9 +655,9 @@ async function contextAdd(pathArg: string | undefined, contextText: string): Pro
 function contextList(): void {
   const db = getDb();
 
-  const contexts = listPathContexts(db);
+  const allContexts = listAllContexts();
 
-  if (contexts.length === 0) {
+  if (allContexts.length === 0) {
     console.log(`${c.dim}No contexts configured. Use 'qmd context add' to add one.${c.reset}`);
     closeDb();
     return;
@@ -667,14 +666,13 @@ function contextList(): void {
   console.log(`\n${c.bold}Configured Contexts${c.reset}\n`);
 
   let lastCollection = '';
-  for (const ctx of contexts) {
-    if (ctx.collection_name !== lastCollection) {
-      console.log(`${c.cyan}${ctx.collection_name}${c.reset}`);
-      lastCollection = ctx.collection_name;
+  for (const ctx of allContexts) {
+    if (ctx.collection !== lastCollection) {
+      console.log(`${c.cyan}${ctx.collection}${c.reset}`);
+      lastCollection = ctx.collection;
     }
 
-    const path = ctx.path_prefix || '/';
-    const displayPath = ctx.path_prefix ? `  ${path}` : '  / (root)';
+    const displayPath = ctx.path ? `  ${ctx.path}` : '  / (root)';
     console.log(`${displayPath}`);
     console.log(`    ${c.dim}${ctx.context}${c.reset}`);
   }
@@ -683,13 +681,10 @@ function contextList(): void {
 }
 
 function contextRemove(pathArg: string): void {
-  const db = getDb();
-
   if (pathArg === '/') {
-    // Remove all root contexts
-    const changes = deleteGlobalContexts(db);
-    console.log(`${c.green}✓${c.reset} Removed ${changes} global context(s)`);
-    closeDb();
+    // Remove global context
+    setGlobalContext(undefined);
+    console.log(`${c.green}✓${c.reset} Removed global context`);
     return;
   }
 
@@ -701,21 +696,20 @@ function contextRemove(pathArg: string): void {
       process.exit(1);
     }
 
-    const coll = getCollectionByName(db, parsed.collectionName);
+    const coll = getCollectionFromYaml(parsed.collectionName);
     if (!coll) {
       console.error(`${c.yellow}Collection not found: ${parsed.collectionName}${c.reset}`);
       process.exit(1);
     }
 
-    const changes = deleteContext(db, coll.name, parsed.path);
+    const success = yamlRemoveContext(coll.name, parsed.path);
 
-    if (changes === 0) {
+    if (!success) {
       console.error(`${c.yellow}No context found for: ${pathArg}${c.reset}`);
       process.exit(1);
     }
 
     console.log(`${c.green}✓${c.reset} Removed context for: ${pathArg}`);
-    closeDb();
     return;
   }
 
@@ -729,21 +723,23 @@ function contextRemove(pathArg: string): void {
     fsPath = resolve(getPwd(), fsPath);
   }
 
+  const db = getDb();
   const detected = detectCollectionFromPath(db, fsPath);
+  closeDb();
+
   if (!detected) {
     console.error(`${c.yellow}Path is not in any indexed collection: ${fsPath}${c.reset}`);
     process.exit(1);
   }
 
-  const changes = deleteContext(db, detected.collectionName, detected.relativePath);
+  const success = yamlRemoveContext(detected.collectionName, detected.relativePath);
 
-  if (changes === 0) {
+  if (!success) {
     console.error(`${c.yellow}No context found for: qmd://${detected.collectionName}/${detected.relativePath}${c.reset}`);
     process.exit(1);
   }
 
   console.log(`${c.green}✓${c.reset} Removed context for: qmd://${detected.collectionName}/${detected.relativePath}`);
-  closeDb();
 }
 
 function contextCheck(): void {
@@ -815,7 +811,7 @@ function getDocument(filename: string, fromLine?: number, maxLines?: number): vo
     inputPath = inputPath.slice(0, -colonMatch[0].length);
   }
 
-  let doc: { collectionId: number; collectionName: string; path: string; body: string } | null = null;
+  let doc: { collectionName: string; path: string; body: string } | null = null;
   let virtualPath: string;
 
   // Handle virtual paths (qmd://collection/path)
@@ -829,21 +825,19 @@ function getDocument(filename: string, fromLine?: number, maxLines?: number): vo
 
     // Try exact match on collection + path
     doc = db.prepare(`
-      SELECT c.id as collectionId, c.name as collectionName, d.path, content.doc as body
+      SELECT d.collection as collectionName, d.path, content.doc as body
       FROM documents d
-      JOIN collections c ON c.id = d.collection_id
       JOIN content ON content.hash = d.hash
-      WHERE c.name = ? AND d.path = ? AND d.active = 1
+      WHERE d.collection = ? AND d.path = ? AND d.active = 1
     `).get(parsed.collectionName, parsed.path) as typeof doc;
 
     if (!doc) {
       // Try fuzzy match by path ending
       doc = db.prepare(`
-        SELECT c.id as collectionId, c.name as collectionName, d.path, content.doc as body
+        SELECT d.collection as collectionName, d.path, content.doc as body
         FROM documents d
-        JOIN collections c ON c.id = d.collection_id
         JOIN content ON content.hash = d.hash
-        WHERE c.name = ? AND d.path LIKE ? AND d.active = 1
+        WHERE d.collection = ? AND d.path LIKE ? AND d.active = 1
         LIMIT 1
       `).get(parsed.collectionName, `%${parsed.path}`) as typeof doc;
     }
@@ -866,23 +860,21 @@ function getDocument(filename: string, fromLine?: number, maxLines?: number): vo
     const detected = detectCollectionFromPath(db, fsPath);
 
     if (detected) {
-      // Found collection - query by collection_id + relative path
+      // Found collection - query by collection name + relative path
       doc = db.prepare(`
-        SELECT c.id as collectionId, c.name as collectionName, d.path, content.doc as body
+        SELECT d.collection as collectionName, d.path, content.doc as body
         FROM documents d
-        JOIN collections c ON c.id = d.collection_id
         JOIN content ON content.hash = d.hash
-        WHERE c.id = ? AND d.path = ? AND d.active = 1
-      `).get(detected.collectionId, detected.relativePath) as typeof doc;
+        WHERE d.collection = ? AND d.path = ? AND d.active = 1
+      `).get(detected.collectionName, detected.relativePath) as typeof doc;
     }
 
     // Fuzzy match by filename (last component of path)
     if (!doc) {
       const filename = inputPath.split('/').pop() || inputPath;
       doc = db.prepare(`
-        SELECT c.id as collectionId, c.name as collectionName, d.path, content.doc as body
+        SELECT d.collection as collectionName, d.path, content.doc as body
         FROM documents d
-        JOIN collections c ON c.id = d.collection_id
         JOIN content ON content.hash = d.hash
         WHERE d.path LIKE ? AND d.active = 1
         LIMIT 1
@@ -903,7 +895,7 @@ function getDocument(filename: string, fromLine?: number, maxLines?: number): vo
   }
 
   // Get context for this file
-  const context = getContextForPath(db, doc.collectionId, doc.path);
+  const context = getContextForPath(db, doc.collectionName, doc.path);
 
   let output = doc.body;
 
@@ -930,14 +922,14 @@ function multiGet(pattern: string, maxLines?: number, maxBytes: number = DEFAULT
   // Check if it's a comma-separated list or a glob pattern
   const isCommaSeparated = pattern.includes(',') && !pattern.includes('*') && !pattern.includes('?');
 
-  let files: { filepath: string; displayPath: string; bodyLength: number; collectionId?: number; path?: string }[];
+  let files: { filepath: string; displayPath: string; bodyLength: number; collection?: string; path?: string }[];
 
   if (isCommaSeparated) {
     // Comma-separated list of files (can be virtual paths or relative paths)
     const names = pattern.split(',').map(s => s.trim()).filter(Boolean);
     files = [];
     for (const name of names) {
-      let doc: { virtual_path: string; body_length: number; collection_id: number; path: string } | null = null;
+      let doc: { virtual_path: string; body_length: number; collection: string; path: string } | null = null;
 
       // Handle virtual paths
       if (isVirtualPath(name)) {
@@ -946,26 +938,24 @@ function multiGet(pattern: string, maxLines?: number, maxBytes: number = DEFAULT
           // Try exact match on collection + path
           doc = db.prepare(`
             SELECT
-              'qmd://' || c.name || '/' || d.path as virtual_path,
+              'qmd://' || d.collection || '/' || d.path as virtual_path,
               LENGTH(content.doc) as body_length,
-              d.collection_id,
+              d.collection,
               d.path
             FROM documents d
-            JOIN collections c ON c.id = d.collection_id
             JOIN content ON content.hash = d.hash
-            WHERE c.name = ? AND d.path = ? AND d.active = 1
+            WHERE d.collection = ? AND d.path = ? AND d.active = 1
           `).get(parsed.collectionName, parsed.path) as typeof doc;
         }
       } else {
         // Try exact match on path
         doc = db.prepare(`
           SELECT
-            'qmd://' || c.name || '/' || d.path as virtual_path,
+            'qmd://' || d.collection || '/' || d.path as virtual_path,
             LENGTH(content.doc) as body_length,
-            d.collection_id,
+            d.collection,
             d.path
           FROM documents d
-          JOIN collections c ON c.id = d.collection_id
           JOIN content ON content.hash = d.hash
           WHERE d.path = ? AND d.active = 1
           LIMIT 1
@@ -975,12 +965,11 @@ function multiGet(pattern: string, maxLines?: number, maxBytes: number = DEFAULT
         if (!doc) {
           doc = db.prepare(`
             SELECT
-              'qmd://' || c.name || '/' || d.path as virtual_path,
+              'qmd://' || d.collection || '/' || d.path as virtual_path,
               LENGTH(content.doc) as body_length,
-              d.collection_id,
+              d.collection,
               d.path
             FROM documents d
-            JOIN collections c ON c.id = d.collection_id
             JOIN content ON content.hash = d.hash
             WHERE d.path LIKE ? AND d.active = 1
             LIMIT 1
@@ -993,7 +982,7 @@ function multiGet(pattern: string, maxLines?: number, maxBytes: number = DEFAULT
           filepath: doc.virtual_path,
           displayPath: doc.virtual_path,
           bodyLength: doc.body_length,
-          collectionId: doc.collection_id,
+          collection: doc.collection,
           path: doc.path
         });
       } else {
@@ -1004,7 +993,7 @@ function multiGet(pattern: string, maxLines?: number, maxBytes: number = DEFAULT
     // Glob pattern - matchFilesByGlob now returns virtual paths
     files = matchFilesByGlob(db, pattern).map(f => ({
       ...f,
-      collectionId: undefined,  // Will be fetched later if needed
+      collection: undefined,  // Will be fetched later if needed
       path: undefined
     }));
     if (files.length === 0) {
@@ -1019,22 +1008,19 @@ function multiGet(pattern: string, maxLines?: number, maxBytes: number = DEFAULT
 
   for (const file of files) {
     // Parse virtual path to get collection info if not already available
-    let collectionId = file.collectionId;
+    let collection = file.collection;
     let path = file.path;
 
-    if (!collectionId || !path) {
+    if (!collection || !path) {
       const parsed = parseVirtualPath(file.displayPath);
       if (parsed) {
-        const coll = getCollectionByName(db, parsed.collectionName);
-        if (coll) {
-          collectionId = coll.id;
-          path = parsed.path;
-        }
+        collection = parsed.collectionName;
+        path = parsed.path;
       }
     }
 
     // Get context using collection-scoped function
-    const context = collectionId && path ? getContextForPath(db, collectionId, path) : null;
+    const context = collection && path ? getContextForPath(db, collection, path) : null;
 
     // Check size limit
     if (file.bodyLength > maxBytes) {
@@ -1057,9 +1043,8 @@ function multiGet(pattern: string, maxLines?: number, maxBytes: number = DEFAULT
     const doc = db.prepare(`
       SELECT content.doc as body, d.title
       FROM documents d
-      JOIN collections c ON c.id = d.collection_id
       JOIN content ON content.hash = d.hash
-      WHERE c.name = ? AND d.path = ? AND d.active = 1
+      WHERE d.collection = ? AND d.path = ? AND d.active = 1
     `).get(parsed.collectionName, parsed.path) as { body: string; title: string } | null;
 
     if (!doc) continue;
@@ -1171,20 +1156,28 @@ function listFiles(pathArg?: string): void {
 
   if (!pathArg) {
     // No argument - list all collections
-    const collections = db.prepare(`
-      SELECT name, COUNT(d.id) as file_count
-      FROM collections c
-      LEFT JOIN documents d ON d.collection_id = c.id AND d.active = 1
-      GROUP BY c.id, c.name
-      ORDER BY c.name
-    `).all() as { name: string; file_count: number }[];
-
-    if (collections.length === 0) {
+    const yamlCollections = yamlListCollections();
+
+    if (yamlCollections.length === 0) {
       console.log("No collections found. Run 'qmd add .' to index files.");
       closeDb();
       return;
     }
 
+    // Get file counts from database for each collection
+    const collections = yamlCollections.map(coll => {
+      const stats = db.prepare(`
+        SELECT COUNT(*) as file_count
+        FROM documents d
+        WHERE d.collection = ? AND d.active = 1
+      `).get(coll.name) as { file_count: number } | null;
+
+      return {
+        name: coll.name,
+        file_count: stats?.file_count || 0
+      };
+    });
+
     console.log(`${c.bold}Collections:${c.reset}\n`);
     for (const coll of collections) {
       console.log(`  ${c.dim}qmd://${c.reset}${c.cyan}${coll.name}/${c.reset}  ${c.dim}(${coll.file_count} files)${c.reset}`);
@@ -1217,7 +1210,7 @@ function listFiles(pathArg?: string): void {
   }
 
   // Get the collection
-  const coll = getCollectionByName(db, collectionName);
+  const coll = getCollectionFromYaml(collectionName);
   if (!coll) {
     console.error(`Collection not found: ${collectionName}`);
     console.error(`Run 'qmd ls' to see available collections.`);
@@ -1235,20 +1228,20 @@ function listFiles(pathArg?: string): void {
       SELECT d.path, d.title, d.modified_at, LENGTH(ct.doc) as size
       FROM documents d
       JOIN content ct ON d.hash = ct.hash
-      WHERE d.collection_id = ? AND d.path LIKE ? AND d.active = 1
+      WHERE d.collection = ? AND d.path LIKE ? AND d.active = 1
       ORDER BY d.path
     `;
-    params = [coll.id, `${pathPrefix}%`];
+    params = [coll.name, `${pathPrefix}%`];
   } else {
     // List all files in the collection
     query = `
       SELECT d.path, d.title, d.modified_at, LENGTH(ct.doc) as size
       FROM documents d
       JOIN content ct ON d.hash = ct.hash
-      WHERE d.collection_id = ? AND d.active = 1
+      WHERE d.collection = ? AND d.active = 1
       ORDER BY d.path
     `;
-    params = [coll.id];
+    params = [coll.name];
   }
 
   const files = db.prepare(query).all(...params) as { path: string; title: string; modified_at: string; size: number }[];
@@ -1328,39 +1321,36 @@ function collectionList(): void {
 }
 
 async function collectionAdd(pwd: string, globPattern: string, name?: string): Promise<void> {
-  const db = getDb();
-
   // If name not provided, generate from pwd basename
   if (!name) {
     const parts = pwd.split('/').filter(Boolean);
     name = parts[parts.length - 1] || 'root';
   }
 
-  // Check if collection with this name already exists
-  const existing = getCollectionByName(db, name);
+  // Check if collection with this name already exists in YAML
+  const existing = getCollectionFromYaml(name);
   if (existing) {
     console.error(`${c.yellow}Collection '${name}' already exists.${c.reset}`);
     console.error(`Use a different name with --name <name>`);
-    closeDb();
     process.exit(1);
   }
 
-  // Check if a collection with this pwd+glob already exists
-  const existingPwdGlob = db.prepare(`
-    SELECT id, name FROM collections WHERE pwd = ? AND glob_pattern = ?
-  `).get(pwd, globPattern) as { id: number; name: string } | null;
+  // Check if a collection with this pwd+glob already exists in YAML
+  const allCollections = yamlListCollections();
+  const existingPwdGlob = allCollections.find(c => c.path === pwd && c.pattern === globPattern);
 
   if (existingPwdGlob) {
     console.error(`${c.yellow}A collection already exists for this path and pattern:${c.reset}`);
     console.error(`  Name: ${existingPwdGlob.name}`);
     console.error(`  Path: ${pwd}`);
     console.error(`  Pattern: ${globPattern}`);
-    console.error(`\nUse 'qmd add ${globPattern}' to update it, or remove it first with 'qmd collection remove ${existingPwdGlob.name}'`);
-    closeDb();
+    console.error(`\nUse 'qmd update' to re-index it, or remove it first with 'qmd collection remove ${existingPwdGlob.name}'`);
     process.exit(1);
   }
 
-  closeDb();
+  // Add to YAML config
+  const { addCollection } = await import("./collections.js");
+  addCollection(name, pwd, globPattern);
 
   // Create the collection and index files
   console.log(`Creating collection '${name}'...`);
@@ -1369,77 +1359,48 @@ async function collectionAdd(pwd: string, globPattern: string, name?: string): P
 }
 
 function collectionRemove(name: string): void {
-  const db = getDb();
-
-  const coll = getCollectionByName(db, name);
+  // Check if collection exists in YAML
+  const coll = getCollectionFromYaml(name);
   if (!coll) {
     console.error(`${c.yellow}Collection not found: ${name}${c.reset}`);
     console.error(`Run 'qmd collection list' to see available collections.`);
-    closeDb();
     process.exit(1);
   }
 
+  const db = getDb();
   const result = removeCollection(db, name);
+  closeDb();
 
   console.log(`${c.green}✓${c.reset} Removed collection '${name}'`);
   console.log(`  Deleted ${result.deletedDocs} documents`);
   if (result.cleanedHashes > 0) {
     console.log(`  Cleaned up ${result.cleanedHashes} orphaned content hashes`);
   }
-
-  closeDb();
 }
 
 function collectionRename(oldName: string, newName: string): void {
-  const db = getDb();
-
-  // Check if old collection exists
-  const coll = getCollectionByName(db, oldName);
+  // Check if old collection exists in YAML
+  const coll = getCollectionFromYaml(oldName);
   if (!coll) {
     console.error(`${c.yellow}Collection not found: ${oldName}${c.reset}`);
     console.error(`Run 'qmd collection list' to see available collections.`);
-    closeDb();
     process.exit(1);
   }
 
-  // Check if new name already exists
-  const existing = getCollectionByName(db, newName);
+  // Check if new name already exists in YAML
+  const existing = getCollectionFromYaml(newName);
   if (existing) {
     console.error(`${c.yellow}Collection name already exists: ${newName}${c.reset}`);
     console.error(`Choose a different name or remove the existing collection first.`);
-    closeDb();
     process.exit(1);
   }
 
+  const db = getDb();
   renameCollection(db, oldName, newName);
+  closeDb();
 
   console.log(`${c.green}✓${c.reset} Renamed collection '${oldName}' to '${newName}'`);
   console.log(`  Virtual paths updated: ${c.cyan}qmd://${oldName}/${c.reset} → ${c.cyan}qmd://${newName}/${c.reset}`);
-
-  closeDb();
-}
-
-async function dropCollection(globPattern: string): Promise<void> {
-  const db = getDb();
-  const pwd = getPwd();
-
-  const collection = db.prepare(`SELECT id FROM collections WHERE pwd = ? AND glob_pattern = ?`).get(pwd, globPattern) as { id: number } | null;
-
-  if (!collection) {
-    // No collection to drop - this is fine, we'll create one during indexing
-    return;
-  }
-
-  // Delete documents in this collection
-  const deleted = db.prepare(`DELETE FROM documents WHERE collection_id = ?`).run(collection.id);
-
-  // Delete the collection
-  db.prepare(`DELETE FROM collections WHERE id = ?`).run(collection.id);
-
-  console.log(`Dropped collection: ${pwd} (${globPattern})`);
-  console.log(`Removed ${deleted.changes} documents`);
-  console.log(`(Vectors kept for potential reuse)`);
-  // Don't close db - indexFiles will use it and close at the end
 }
 
 async function indexFiles(pwd?: string, globPattern: string = DEFAULT_GLOB, collectionName?: string): Promise<void> {
@@ -1736,80 +1697,6 @@ function normalizeBM25(score: number): number {
   return 1 / (1 + Math.exp(-(absScore - 5) / 3));
 }
 
-// Get collection ID by name (matches pwd or glob_pattern suffix)
-function getCollectionIdByName(db: Database, name: string): number | null {
-  // Search both pwd and glob_pattern columns for the name
-  const result = db.prepare(`
-    SELECT id FROM collections
-    WHERE pwd LIKE ? OR glob_pattern LIKE ?
-    ORDER BY LENGTH(pwd) DESC
-    LIMIT 1
-  `).get(`%${name}%`, `%${name}%`) as { id: number } | null;
-  return result?.id || null;
-}
-
-// searchFTS and searchVec are now imported from store.ts with updated schema
-
-// Removed duplicate searchFTS and searchVec functions - using store.ts versions instead
-async function REMOVED_searchVec(db: Database, query: string, model: string, limit: number = 20, collectionId?: number): Promise<SearchResult[]> {
-  const tableExists = db.prepare(`SELECT name FROM sqlite_master WHERE type='table' AND name='vectors_vec'`).get();
-  if (!tableExists) return [];
-
-  const queryEmbedding = await getEmbedding(query, model, true);
-  const queryVec = new Float32Array(queryEmbedding);
-
-  // Join: vectors_vec -> content_vectors -> documents
-  // Over-retrieve to handle multiple chunks per document, then dedupe
-  let sql = `
-    SELECT d.filepath, d.display_path, d.title, d.body, vec.distance, cv.pos
-    FROM vectors_vec vec
-    JOIN content_vectors cv ON vec.hash_seq = cv.hash || '_' || cv.seq
-    JOIN documents d ON d.hash = cv.hash AND d.active = 1
-    WHERE vec.embedding MATCH ? AND k = ?
-  `;
-  if (collectionId !== undefined) {
-    sql += ` AND d.collection_id = ${collectionId}`;
-  }
-  sql += ` ORDER BY vec.distance`;
-
-  const stmt = db.prepare(sql);
-  const rawResults = stmt.all(queryVec, limit * 3) as { filepath: string; display_path: string; title: string; body: string; distance: number; pos: number }[];
-
-  // Aggregate chunks per document: max score + small bonus for additional matches
-  const byFile = new Map<string, { filepath: string; displayPath: string; title: string; body: string; chunkCount: number; bestPos: number; bestDist: number }>();
-  for (const r of rawResults) {
-    const existing = byFile.get(r.filepath);
-    if (!existing) {
-      byFile.set(r.filepath, { filepath: r.filepath, displayPath: r.display_path, title: r.title, body: r.body, chunkCount: 1, bestPos: r.pos, bestDist: r.distance });
-    } else {
-      existing.chunkCount++;
-      if (r.distance < existing.bestDist) {
-        existing.bestDist = r.distance;
-        existing.bestPos = r.pos;
-      }
-    }
-  }
-
-  // Score = max chunk score + 0.02 bonus per additional chunk (capped at +0.1)
-  return Array.from(byFile.values())
-    .map(r => {
-      const maxScore = 1 / (1 + r.bestDist);
-      const bonusChunks = Math.min(r.chunkCount - 1, 5);
-      const bonus = bonusChunks * 0.02;
-      return {
-        file: r.filepath,
-        displayPath: r.displayPath,
-        title: r.title,
-        body: r.body,
-        score: maxScore + bonus,
-        source: "vec" as const,
-        chunkPos: r.bestPos,
-      };
-    })
-    .sort((a, b) => b.score - a.score)
-    .slice(0, limit);
-}
-
 function normalizeScores(results: SearchResult[]): SearchResult[] {
   if (results.length === 0) return results;
   const maxScore = Math.max(...results.map(r => r.score));
@@ -2029,20 +1916,22 @@ function outputResults(results: { file: string; displayPath: string; title: stri
 function search(query: string, opts: OutputOptions): void {
   const db = getDb();
 
-  // Resolve collection filter if specified
-  let collectionId: number | undefined;
+  // Validate collection filter if specified
+  let collectionName: string | undefined;
   if (opts.collection) {
-    collectionId = getCollectionIdByName(db, opts.collection) ?? undefined;
-    if (collectionId === undefined) {
+    const coll = getCollectionFromYaml(opts.collection);
+    if (!coll) {
       console.error(`Collection not found: ${opts.collection}`);
       closeDb();
       process.exit(1);
     }
+    collectionName = opts.collection;
   }
 
   // Use large limit for --all, otherwise fetch more than needed and let outputResults filter
   const fetchLimit = opts.all ? 100000 : Math.max(50, opts.limit * 2);
-  const results = searchFTS(db, query, fetchLimit, collectionId);
+  // searchFTS accepts collection name as number parameter for legacy reasons (will be fixed in store.ts)
+  const results = searchFTS(db, query, fetchLimit, collectionName as any);
 
   // Add context to results
   const resultsWithContext = results.map(r => ({
@@ -2062,15 +1951,16 @@ function search(query: string, opts: OutputOptions): void {
 async function vectorSearch(query: string, opts: OutputOptions, model: string = DEFAULT_EMBED_MODEL): Promise<void> {
   const db = getDb();
 
-  // Resolve collection filter if specified
-  let collectionId: number | undefined;
+  // Validate collection filter if specified
+  let collectionName: string | undefined;
   if (opts.collection) {
-    collectionId = getCollectionIdByName(db, opts.collection) ?? undefined;
-    if (collectionId === undefined) {
+    const coll = getCollectionFromYaml(opts.collection);
+    if (!coll) {
       console.error(`Collection not found: ${opts.collection}`);
       closeDb();
       process.exit(1);
     }
+    collectionName = opts.collection;
   }
 
   const tableExists = db.prepare(`SELECT name FROM sqlite_master WHERE type='table' AND name='vectors_vec'`).get();
@@ -2093,7 +1983,8 @@ async function vectorSearch(query: string, opts: OutputOptions, model: string =
   const allResults = new Map<string, { file: string; displayPath: string; title: string; body: string; score: number }>();
 
   for (const q of queries) {
-    const vecResults = await searchVec(db, q, model, perQueryLimit, collectionId);
+    // searchVec accepts collection name as number parameter for legacy reasons (will be fixed in store.ts)
+    const vecResults = await searchVec(db, q, model, perQueryLimit, collectionName as any);
     for (const r of vecResults) {
       const existing = allResults.get(r.file);
       if (!existing || r.score > existing.score) {
@@ -2187,15 +2078,16 @@ Output exactly 2 variations, one per line, no numbering or bullets:`;
 async function querySearch(query: string, opts: OutputOptions, embedModel: string = DEFAULT_EMBED_MODEL, rerankModel: string = DEFAULT_RERANK_MODEL): Promise<void> {
   const db = getDb();
 
-  // Resolve collection filter if specified
-  let collectionId: number | undefined;
+  // Validate collection filter if specified
+  let collectionName: string | undefined;
   if (opts.collection) {
-    collectionId = getCollectionIdByName(db, opts.collection) ?? undefined;
-    if (collectionId === undefined) {
+    const coll = getCollectionFromYaml(opts.collection);
+    if (!coll) {
       console.error(`Collection not found: ${opts.collection}`);
       closeDb();
       process.exit(1);
     }
+    collectionName = opts.collection;
   }
 
   // Check index health and warn about issues
@@ -2211,14 +2103,16 @@ async function querySearch(query: string, opts: OutputOptions, embedModel: strin
 
   for (const q of queries) {
     // FTS search - get ranked results
-    const ftsResults = searchFTS(db, q, 20, collectionId);
+    // searchFTS accepts collection name as number parameter for legacy reasons (will be fixed in store.ts)
+    const ftsResults = searchFTS(db, q, 20, collectionName as any);
     if (ftsResults.length > 0) {
       rankedLists.push(ftsResults.map(r => ({ file: r.file, displayPath: r.displayPath, title: r.title, body: r.body, score: r.score })));
     }
 
     // Vector search - get ranked results
     if (hasVectors) {
-      const vecResults = await searchVec(db, q, embedModel, 20, collectionId);
+      // searchVec accepts collection name as number parameter for legacy reasons (will be fixed in store.ts)
+      const vecResults = await searchVec(db, q, embedModel, 20, collectionName as any);
       if (vecResults.length > 0) {
         rankedLists.push(vecResults.map(r => ({ file: r.file, displayPath: r.displayPath, title: r.title, body: r.body, score: r.score })));
       }

src/store.ts

@@ -207,16 +207,6 @@ function initializeDatabase(db: Database): void {
   db.exec("PRAGMA journal_mode = WAL");
   db.exec("PRAGMA foreign_keys = ON");
 
-  // Check if we need to migrate from old schema
-  const tables = db.prepare(`SELECT name FROM sqlite_master WHERE type='table'`).all() as { name: string }[];
-  const tableNames = tables.map(t => t.name);
-  const needsMigration = tableNames.includes('documents') && !tableNames.includes('content');
-
-  if (needsMigration) {
-    migrateToContentAddressable(db);
-    return; // Migration will call initializeDatabase again
-  }
-
   // Drop legacy tables that are now managed in YAML
   db.exec(`DROP TABLE IF EXISTS path_contexts`);
   db.exec(`DROP TABLE IF EXISTS collections`);
@@ -325,271 +315,6 @@ function initializeDatabase(db: Database): void {
   `);
 }
 
-function migrateToContentAddressable(db: Database): void {
-  console.log("Migrating database to content-addressable schema...");
-
-  // Start transaction
-  db.exec("BEGIN TRANSACTION");
-
-  try {
-    // Rename old tables
-    db.exec("ALTER TABLE documents RENAME TO documents_old");
-    db.exec("ALTER TABLE collections RENAME TO collections_old");
-    db.exec("ALTER TABLE path_contexts RENAME TO path_contexts_old");
-    db.exec("DROP TABLE IF EXISTS documents_fts");
-    db.exec("DROP TRIGGER IF EXISTS documents_ai");
-    db.exec("DROP TRIGGER IF EXISTS documents_ad");
-    db.exec("DROP TRIGGER IF EXISTS documents_au");
-
-    // Create new schema
-    db.exec(`
-      CREATE TABLE content (
-        hash TEXT PRIMARY KEY,
-        doc TEXT NOT NULL,
-        created_at TEXT NOT NULL
-      )
-    `);
-
-    db.exec(`
-      CREATE TABLE collections (
-        id INTEGER PRIMARY KEY AUTOINCREMENT,
-        name TEXT NOT NULL UNIQUE,
-        pwd TEXT NOT NULL,
-        glob_pattern TEXT NOT NULL,
-        created_at TEXT NOT NULL,
-        updated_at TEXT NOT NULL,
-        UNIQUE(pwd, glob_pattern)
-      )
-    `);
-
-    db.exec(`
-      CREATE TABLE documents (
-        id INTEGER PRIMARY KEY AUTOINCREMENT,
-        collection TEXT NOT NULL,
-        path TEXT NOT NULL,
-        title TEXT NOT NULL,
-        hash TEXT NOT NULL,
-        created_at TEXT NOT NULL,
-        modified_at TEXT NOT NULL,
-        active INTEGER NOT NULL DEFAULT 1,
-        FOREIGN KEY (hash) REFERENCES content(hash) ON DELETE CASCADE,
-        UNIQUE(collection, path)
-      )
-    `);
-
-    db.exec(`
-      CREATE TABLE path_contexts (
-        id INTEGER PRIMARY KEY AUTOINCREMENT,
-        collection_id INTEGER NOT NULL,
-        path_prefix TEXT NOT NULL,
-        context TEXT NOT NULL,
-        created_at TEXT NOT NULL,
-        FOREIGN KEY (collection_id) REFERENCES collections(id) ON DELETE CASCADE,
-        UNIQUE(collection_id, path_prefix)
-      )
-    `);
-
-    // Migrate data: Extract unique content hashes
-    console.log("Migrating content...");
-    db.exec(`
-      INSERT INTO content (hash, doc, created_at)
-      SELECT hash, body, MIN(created_at) as created_at
-      FROM documents_old
-      WHERE active = 1
-      GROUP BY hash
-    `);
-
-    // Migrate collections: generate names from pwd basename
-    console.log("Migrating collections...");
-    // First insert with pwd as temporary name
-    db.exec(`
-      INSERT INTO collections (id, name, pwd, glob_pattern, created_at, updated_at)
-      SELECT
-        id,
-        pwd as name,
-        pwd,
-        glob_pattern,
-        created_at,
-        created_at as updated_at
-      FROM collections_old
-    `);
-
-    // Then update names to basenames using application logic
-    const collections = db.prepare(`SELECT id, pwd FROM collections`).all() as { id: number; pwd: string }[];
-    for (const coll of collections) {
-      const parts = coll.pwd.split('/').filter(Boolean);
-      const name = parts[parts.length - 1] || 'root';
-      db.prepare(`UPDATE collections SET name = ? WHERE id = ?`).run(name, coll.id);
-    }
-
-    // Handle duplicate collection names by appending collection_id
-    const duplicates = db.prepare(`
-      SELECT name, COUNT(*) as cnt
-      FROM collections
-      GROUP BY name
-      HAVING cnt > 1
-    `).all() as { name: string; cnt: number }[];
-
-    for (const dup of duplicates) {
-      const rows = db.prepare(`SELECT id FROM collections WHERE name = ? ORDER BY id`).all(dup.name) as { id: number }[];
-      for (let i = 1; i < rows.length; i++) {
-        db.prepare(`UPDATE collections SET name = ? WHERE id = ?`).run(`${dup.name}-${rows[i].id}`, rows[i].id);
-      }
-    }
-
-    // Migrate documents: convert filepath to relative path within collection
-    console.log("Migrating documents...");
-    const oldDocs = db.prepare(`
-      SELECT d.id, d.collection_id, d.filepath, d.title, d.hash, d.created_at, d.modified_at, c.pwd, c.name
-      FROM documents_old d
-      JOIN collections c ON c.id = d.collection_id
-      WHERE d.active = 1
-    `).all() as Array<{
-      id: number;
-      collection_id: number;
-      filepath: string;
-      title: string;
-      hash: string;
-      created_at: string;
-      modified_at: string;
-      pwd: string;
-      name: string;
-    }>;
-
-    const insertDoc = db.prepare(`
-      INSERT INTO documents (collection, path, title, hash, created_at, modified_at, active)
-      VALUES (?, ?, ?, ?, ?, ?, 1)
-    `);
-
-    for (const doc of oldDocs) {
-      // Convert absolute filepath to relative path within collection
-      let path = doc.filepath;
-      if (path.startsWith(doc.pwd + '/')) {
-        path = path.slice(doc.pwd.length + 1);
-      } else if (path.startsWith(doc.pwd)) {
-        path = path.slice(doc.pwd.length);
-      }
-      // Remove leading slash if present
-      path = path.replace(/^\/+/, '');
-
-      try {
-        insertDoc.run(doc.name, path, doc.title, doc.hash, doc.created_at, doc.modified_at);
-      } catch (e) {
-        console.warn(`Skipping duplicate path: ${path} in collection ${doc.name}`);
-      }
-    }
-
-    // Migrate path_contexts: associate with collections based on path prefix
-    console.log("Migrating path contexts...");
-    const oldContexts = db.prepare(`SELECT * FROM path_contexts_old`).all() as Array<{
-      path_prefix: string;
-      context: string;
-      created_at: string;
-    }>;
-
-    const insertContext = db.prepare(`
-      INSERT INTO path_contexts (collection_id, path_prefix, context, created_at)
-      VALUES (?, ?, ?, ?)
-    `);
-
-    const allCollections = db.prepare(`SELECT id, pwd FROM collections`).all() as Array<{ id: number; pwd: string }>;
-
-    for (const ctx of oldContexts) {
-      // Find collection(s) that match this path prefix
-      for (const coll of allCollections) {
-        if (ctx.path_prefix.startsWith(coll.pwd)) {
-          // Convert absolute path_prefix to relative within collection
-          let relPath = ctx.path_prefix;
-          if (relPath.startsWith(coll.pwd + '/')) {
-            relPath = relPath.slice(coll.pwd.length + 1);
-          } else if (relPath.startsWith(coll.pwd)) {
-            relPath = relPath.slice(coll.pwd.length);
-          }
-          relPath = relPath.replace(/^\/+/, '');
-
-          try {
-            insertContext.run(coll.id, relPath, ctx.context, ctx.created_at);
-          } catch (e) {
-            // Ignore duplicates
-          }
-        }
-      }
-    }
-
-    // Drop old tables
-    db.exec("DROP TABLE documents_old");
-    db.exec("DROP TABLE collections_old");
-    db.exec("DROP TABLE path_contexts_old");
-
-    // Recreate FTS and triggers (matching migrated schema)
-    db.exec(`
-      CREATE VIRTUAL TABLE documents_fts USING fts5(
-        filepath, title, body,
-        tokenize='porter unicode61'
-      )
-    `);
-
-    db.exec(`
-      CREATE TRIGGER documents_ai AFTER INSERT ON documents
-      WHEN new.active = 1
-      BEGIN
-        INSERT INTO documents_fts(rowid, filepath, title, body)
-        SELECT
-          new.id,
-          new.collection || '/' || new.path,
-          new.title,
-          (SELECT doc FROM content WHERE hash = new.hash)
-        WHERE new.active = 1;
-      END
-    `);
-
-    db.exec(`
-      CREATE TRIGGER documents_ad AFTER DELETE ON documents BEGIN
-        DELETE FROM documents_fts WHERE rowid = old.id;
-      END
-    `);
-
-    db.exec(`
-      CREATE TRIGGER documents_au AFTER UPDATE ON documents
-      BEGIN
-        -- Delete from FTS if no longer active
-        DELETE FROM documents_fts WHERE rowid = old.id AND new.active = 0;
-
-        -- Update FTS if still/newly active
-        INSERT OR REPLACE INTO documents_fts(rowid, filepath, title, body)
-        SELECT
-          new.id,
-          new.collection || '/' || new.path,
-          new.title,
-          (SELECT doc FROM content WHERE hash = new.hash)
-        WHERE new.active = 1;
-      END
-    `);
-
-    // Populate FTS from migrated data
-    console.log("Rebuilding full-text search index...");
-    db.exec(`
-      INSERT INTO documents_fts(rowid, filepath, title, body)
-      SELECT d.id, d.collection || '/' || d.path, d.title, c.doc
-      FROM documents d
-      JOIN content c ON c.hash = d.hash
-      WHERE d.active = 1
-    `);
-
-    // Create indexes
-    db.exec(`CREATE INDEX idx_documents_collection ON documents(collection, active)`);
-    db.exec(`CREATE INDEX idx_documents_hash ON documents(hash)`);
-    db.exec(`CREATE INDEX idx_documents_path ON documents(path, active)`);
-
-    db.exec("COMMIT");
-    console.log("Migration complete!");
-
-  } catch (e) {
-    db.exec("ROLLBACK");
-    console.error("Migration failed:", e);
-    throw e;
-  }
-}
 
 function ensureVecTableInternal(db: Database, dimensions: number): void {
   const tableInfo = db.prepare(`SELECT sql FROM sqlite_master WHERE type='table' AND name='vectors_vec'`).get() as { sql: string } | null;