Fix embed command for new content-addressable schema

- Updated vectorIndex() to work with new schema:
  * Join with content table to get document body
  * Use 'path' column instead of 'filepath'/'display_path'
  * Query now: SELECT d.hash, c.doc as body, MIN(d.path) as path
- Documents table no longer has body column (in content table)
- Documents table uses 'path' not 'filepath' or 'display_path'
- Embedding functionality now compatible with hash-based storage

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

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

.beads/issues.jsonl

@@ -3,7 +3,7 @@
 {"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":"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":"closed","priority":1,"issue_type":"task","created_at":"2025-12-12T15:29:38.083564-05:00","updated_at":"2025-12-12T16:06:51.544695-05:00","closed_at":"2025-12-12T16:06:51.544695-05:00"}
-{"id":"qmd-clr","title":"fix embed","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-12T16:14:55.292114-05:00","updated_at":"2025-12-12T16:14:55.292114-05:00"}
+{"id":"qmd-clr","title":"fix embed","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T16:14:55.292114-05:00","updated_at":"2025-12-12T16:31:27.661829-05:00","closed_at":"2025-12-12T16:31:27.661829-05:00"}
 {"id":"qmd-deh","title":"Refactor database introduce qmd collection *","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-10T10:56:04.516137-05:00","updated_at":"2025-12-12T16:12:12.349428-05:00","closed_at":"2025-12-12T16:12:12.349428-05:00"}
 {"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":"closed","priority":1,"issue_type":"feature","created_at":"2025-12-12T15:29:53.810666-05:00","updated_at":"2025-12-12T16:02:08.079158-05:00","closed_at":"2025-12-12T16:02:08.079158-05:00","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"}]}
 {"id":"qmd-e2c","title":"Implement 'qmd ls' command","description":"Add command to explore virtual file tree:\n- qmd ls → list all collections\n- qmd ls \u003ccollection\u003e → list files in collection\n- qmd ls \u003ccollection\u003e/\u003cpath\u003e → list files under path\nOutput: flat list of qmd:// paths","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-12-12T15:29:53.859804-05:00","updated_at":"2025-12-12T15:55:12.777701-05:00","closed_at":"2025-12-12T15:55:12.777701-05:00","dependencies":[{"issue_id":"qmd-e2c","depends_on_id":"qmd-ama","type":"discovered-from","created_at":"2025-12-12T15:29:53.860535-05:00","created_by":"daemon"}]}

qmd.ts

@@ -1582,14 +1582,15 @@ async function vectorIndex(model: string = DEFAULT_EMBED_MODEL, force: boolean =
   }
 
   // Find unique hashes that need embedding (from active documents)
-  // Use MIN(filepath) to get one representative filepath per hash
+  // Join with content table to get document body
   const hashesToEmbed = db.prepare(`
-    SELECT d.hash, d.body, MIN(d.filepath) as filepath, MIN(d.display_path) as display_path
+    SELECT d.hash, c.doc as body, MIN(d.path) as path
     FROM documents d
+    JOIN content c ON d.hash = c.hash
     LEFT JOIN content_vectors v ON d.hash = v.hash AND v.seq = 0
     WHERE d.active = 1 AND v.hash IS NULL
     GROUP BY d.hash
-  `).all() as { hash: string; body: string; filepath: string; display_path: string }[];
+  `).all() as { hash: string; body: string; path: string }[];
 
   if (hashesToEmbed.length === 0) {
     console.log(`${c.green}✓ All content hashes already have embeddings.${c.reset}`);
@@ -1607,8 +1608,8 @@ async function vectorIndex(model: string = DEFAULT_EMBED_MODEL, force: boolean =
     const bodyBytes = encoder.encode(item.body).length;
     if (bodyBytes === 0) continue; // Skip empty
 
-    const title = extractTitle(item.body, item.filepath);
-    const displayName = item.display_path || item.filepath;
+    const title = extractTitle(item.body, item.path);
+    const displayName = item.path;
     const chunks = chunkDocument(item.body, CHUNK_BYTE_SIZE);
 
     if (chunks.length > 1) multiChunkDocs++;