Fix migration SQL for proper basename extraction

- Replace complex SQL with application logic to extract basenames
- Use TypeScript path.split() instead of SQL string manipulation
- Consistent with getOrCreateCollection() implementation
- Avoids SQLite function compatibility issues

Closes qmd-bx1

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

.beads/issues.jsonl

@@ -1,6 +1,6 @@
 {"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":"in_progress","priority":0,"issue_type":"task","created_at":"2025-12-12T15:29:53.911881-05:00","updated_at":"2025-12-12T15:30:10.835834-05:00","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-ama","title":"Refactor database system","description":"All documents should be stored as content addressable hash, e.g. hash, doc, created_at,\n┃ updated_at. documents should be a file system layer on top e.g. collection, path, hash,\n┃ created_at, updated_at. (collection,path)\n┃\n┃\n\n┃ All documents should be stored as content addressable hash, e.g. hash, doc, created_at,\n┃ updated_at. documents should be a file system layer on top e.g. collection_id, path, hash,\n┃ created_at, updated_at. (collection,path) is unique. There is also collection which stores PWD\n┃ + glob pattern, name (\\w+). Every document is treated as path qmd://collection.name/","notes":"## Completed\n- ✅ Implemented content-addressable storage (content table with hash→doc mapping)\n- ✅ Refactored documents table as file system layer (collection_id, path, hash)\n- ✅ Added collection names (e.g., \"pages\", \"journals\", \"archive\")\n- ✅ Implemented virtual paths (qmd://collection-name/path/to/file.md)\n- ✅ Added hierarchical context support (collection-scoped)\n- ✅ Successfully migrated existing database\n- ✅ Updated search functions to work with new schema\n- ✅ Updated indexing logic to use content-addressable storage\n- ✅ Orphaned content hash cleanup\n\n## Still TODO\n- Fix migration SQL to properly extract basename (currently needs manual fix)\n- Implement `qmd collection add . --name \u003cname\u003e --mask '**/*.md'`\n- Implement `qmd ls [path]` for exploring virtual file tree","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-10T10:57:35.497489-05:00","updated_at":"2025-12-12T15:39:48.879143-05:00","closed_at":"2025-12-12T15:39:48.879143-05:00"}
-{"id":"qmd-bx1","title":"Fix migration SQL for proper basename extraction","description":"The migration currently generates collection names incorrectly (uses full path instead of basename). Need to fix the SQL in migrateToContentAddressable to properly extract the directory basename.","status":"open","priority":1,"issue_type":"bug","created_at":"2025-12-12T15:29:53.757723-05:00","updated_at":"2025-12-12T15:29:53.757723-05:00","dependencies":[{"issue_id":"qmd-bx1","depends_on_id":"qmd-ama","type":"discovered-from","created_at":"2025-12-12T15:29:53.758524-05:00","created_by":"daemon"}]}
+{"id":"qmd-bx1","title":"Fix migration SQL for proper basename extraction","description":"The migration currently generates collection names incorrectly (uses full path instead of basename). Need to fix the SQL in migrateToContentAddressable to properly extract the directory basename.","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-12-12T15:29:53.757723-05:00","updated_at":"2025-12-12T15:50:29.349134-05:00","closed_at":"2025-12-12T15:50:29.349134-05:00","dependencies":[{"issue_id":"qmd-bx1","depends_on_id":"qmd-ama","type":"discovered-from","created_at":"2025-12-12T15:29:53.758524-05:00","created_by":"daemon"}]}
 {"id":"qmd-c0m","title":"Comprehensive CLI review and consistency pass","description":"Review entire CLI command structure:\n- Consistent naming (add vs create, remove vs delete)\n- Consistent flag usage (--name, --mask, etc)\n- Update help text for all commands\n- Ensure virtual paths work everywhere\n- Test all commands end-to-end","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-12T15:29:38.083564-05:00","updated_at":"2025-12-12T15:29:38.083564-05:00"}
 {"id":"qmd-deh","title":"Refactor database introduce qmd collection *","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-10T10:56:04.516137-05:00","updated_at":"2025-12-10T10:56:04.516137-05:00"}
 {"id":"qmd-dmi","title":"Implement 'qmd collection' commands","description":"Add explicit collection management:\n- qmd collection add . --name \u003cname\u003e --mask '**/*.md'\n- qmd collection list\n- qmd collection remove \u003cname\u003e\n\nThis gives users control over collection names and patterns.","status":"open","priority":1,"issue_type":"feature","created_at":"2025-12-12T15:29:53.810666-05:00","updated_at":"2025-12-12T15:29:53.810666-05:00","dependencies":[{"issue_id":"qmd-dmi","depends_on_id":"qmd-ama","type":"discovered-from","created_at":"2025-12-12T15:29:53.811294-05:00","created_by":"daemon"}]}

store.ts

@@ -380,15 +380,12 @@ function migrateToContentAddressable(db: Database): void {
 
     // 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,
-        CASE
-          WHEN INSTR(RTRIM(pwd, '/'), '/') > 0
-          THEN SUBSTR(RTRIM(pwd, '/'), INSTR(RTRIM(pwd, '/'), '/') + 1)
-          ELSE RTRIM(pwd, '/')
-        END as name,
+        pwd as name,
         pwd,
         glob_pattern,
         created_at,
@@ -396,6 +393,14 @@ function migrateToContentAddressable(db: Database): void {
       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