Update qmd.ts commands to use YAML-based collection management

- Changed removeCollection() call to use collection name instead of ID
- Changed renameCollection() call to use oldName, newName instead of ID
- Both commands now work with YAML config via store.ts

All collection commands now fully integrated with YAML configuration.

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

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

.beads/issues.jsonl

@@ -23,13 +23,13 @@
 {"id":"qmd-j9z","title":"Add unit tests for content addressable hashes","description":"add same file from multiple places and verify that they both point at same hash. drop one collection and the content stays.","status":"closed","priority":3,"issue_type":"task","created_at":"2025-12-12T15:39:15.459504-05:00","updated_at":"2025-12-12T16:21:35.473776-05:00","closed_at":"2025-12-12T16:21:35.473776-05:00"}
 {"id":"qmd-kf8","title":"Move document indexing DB operations to store.ts","description":"Move INSERT/UPDATE/DELETE operations for documents and content tables from indexFiles() to store.ts. Create methods like insertDocument(), updateDocument(), deactivateDocuments(), etc.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T16:36:14.558702-05:00","updated_at":"2025-12-12T16:45:38.830978-05:00","closed_at":"2025-12-12T16:45:38.830978-05:00","dependencies":[{"issue_id":"qmd-kf8","depends_on_id":"qmd-29c","type":"parent-child","created_at":"2025-12-12T16:37:02.770251-05:00","created_by":"daemon"}]}
 {"id":"qmd-ltg","title":"look for missing context","description":"i ran qmd context list and thats only one bit of context, i had a lot more. i think the path matching isn't quite working right","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T16:42:57.324769-05:00","updated_at":"2025-12-12T17:16:27.835047-05:00","closed_at":"2025-12-12T17:16:27.835047-05:00"}
-{"id":"qmd-oxy","title":"Update context system to use YAML","description":"Remove path_contexts table. Implement context management in collections.ts. Update context add/list/rm commands to modify YAML file instead of database.","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-13T09:54:53.042839-05:00","updated_at":"2025-12-13T09:54:53.042839-05:00","dependencies":[{"issue_id":"qmd-oxy","depends_on_id":"qmd-3z9","type":"blocks","created_at":"2025-12-13T09:55:07.842488-05:00","created_by":"daemon"}]}
+{"id":"qmd-oxy","title":"Update context system to use YAML","description":"Remove path_contexts table. Implement context management in collections.ts. Update context add/list/rm commands to modify YAML file instead of database.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-13T09:54:53.042839-05:00","updated_at":"2025-12-13T10:16:07.680285-05:00","closed_at":"2025-12-13T10:16:07.680285-05:00","dependencies":[{"issue_id":"qmd-oxy","depends_on_id":"qmd-3z9","type":"blocks","created_at":"2025-12-13T09:55:07.842488-05:00","created_by":"daemon"}]}
 {"id":"qmd-p1h","title":"Create collection add|remove","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-10T10:57:00.717864-05:00","updated_at":"2025-12-12T16:12:00.557003-05:00","closed_at":"2025-12-12T16:12:00.557003-05:00"}
 {"id":"qmd-rck","title":"move the source files to src/*, clean up teh directory","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T16:40:19.198119-05:00","updated_at":"2025-12-12T17:12:22.502746-05:00","closed_at":"2025-12-12T17:12:22.502746-05:00"}
 {"id":"qmd-rhd","title":"Fix 'qmd status' output for new schema","description":"Update status to show collections by name, cleaner context display, virtual path examples.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T15:29:54.020596-05:00","updated_at":"2025-12-12T16:13:28.08389-05:00","closed_at":"2025-12-12T16:13:28.08389-05:00","dependencies":[{"issue_id":"qmd-rhd","depends_on_id":"qmd-ama","type":"discovered-from","created_at":"2025-12-12T15:29:54.021095-05:00","created_by":"daemon"}]}
 {"id":"qmd-s1y","title":"Update 'qmd add-context' for collection scoping","description":"Update add-context to work with collection-scoped contexts using new path_contexts schema.","notes":"Refactoring to:\n- qmd context add [path] \"text\" (defaults to current collection if in one)\n- qmd context list\n- qmd context rm \u003cpath\u003e\n- Support \"/\" for global/system context\n- Auto-detect collection from pwd","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T15:29:54.076582-05:00","updated_at":"2025-12-12T15:37:47.683263-05:00","closed_at":"2025-12-12T15:37:47.683263-05:00"}
 {"id":"qmd-thw","title":"Drop collections and path_contexts tables","description":"Remove collections and path_contexts tables from schema. Update initDb() to not create these tables. Only keep documents, content, and search indices.","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-13T09:54:53.247136-05:00","updated_at":"2025-12-13T09:54:53.247136-05:00","dependencies":[{"issue_id":"qmd-thw","depends_on_id":"qmd-9ua","type":"blocks","created_at":"2025-12-13T09:55:08.027101-05:00","created_by":"daemon"}]}
-{"id":"qmd-u84","title":"Refactor store.ts to use collections.ts","description":"Replace all collection DB queries with collections.ts calls. Remove getCollectionById, getCollectionByName, listCollections DB functions. Use YAML config instead.","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-13T09:54:52.936782-05:00","updated_at":"2025-12-13T09:54:52.936782-05:00","dependencies":[{"issue_id":"qmd-u84","depends_on_id":"qmd-3z9","type":"blocks","created_at":"2025-12-13T09:55:07.720439-05:00","created_by":"daemon"},{"issue_id":"qmd-u84","depends_on_id":"qmd-8eu","type":"blocks","created_at":"2025-12-13T09:55:07.782051-05:00","created_by":"daemon"}]}
+{"id":"qmd-u84","title":"Refactor store.ts to use collections.ts","description":"Replace all collection DB queries with collections.ts calls. Remove getCollectionById, getCollectionByName, listCollections DB functions. Use YAML config instead.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-13T09:54:52.936782-05:00","updated_at":"2025-12-13T10:16:07.681047-05:00","closed_at":"2025-12-13T10:16:07.681047-05:00","dependencies":[{"issue_id":"qmd-u84","depends_on_id":"qmd-3z9","type":"blocks","created_at":"2025-12-13T09:55:07.720439-05:00","created_by":"daemon"},{"issue_id":"qmd-u84","depends_on_id":"qmd-8eu","type":"blocks","created_at":"2025-12-13T09:55:07.782051-05:00","created_by":"daemon"}]}
 {"id":"qmd-vro","title":"Update 'qmd get' to support virtual paths","description":"Allow qmd get to accept both virtual paths (qmd://journals/...) and filesystem paths, plus fuzzy matching by filename.","status":"closed","priority":0,"issue_type":"task","created_at":"2025-12-12T15:29:53.963113-05:00","updated_at":"2025-12-12T15:47:29.178955-05:00","closed_at":"2025-12-12T15:47:29.178955-05:00","dependencies":[{"issue_id":"qmd-vro","depends_on_id":"qmd-ama","type":"discovered-from","created_at":"2025-12-12T15:29:53.963641-05:00","created_by":"daemon"}]}
 {"id":"qmd-x19","title":"Update 'qmd add-context' for collection-scoped contexts","description":"Update add-context to work with collections:\n- qmd add-context \u003ccollection\u003e/\u003cpath\u003e \"context description\"\n- Support both virtual and filesystem paths\n- Update to use new path_contexts schema","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T15:29:38.142575-05:00","updated_at":"2025-12-12T15:53:00.525001-05:00","closed_at":"2025-12-12T15:53:00.525001-05:00"}
 {"id":"qmd-x64","title":"for each collection, on update, check if there is a .git directory, if so write out the git status, add --pull as a qmd update --pull parameter which also executes git pull before reindexing\n","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T17:04:15.994054-05:00","updated_at":"2025-12-12T17:14:40.107181-05:00","closed_at":"2025-12-12T17:14:40.107181-05:00"}

bun.lock

@@ -7,6 +7,7 @@
       "dependencies": {
         "@modelcontextprotocol/sdk": "^1.24.3",
         "sqlite-vec": "^0.1.7-alpha.2",
+        "yaml": "^2.8.2",
         "zod": "^4.1.13",
       },
       "devDependencies": {
@@ -216,6 +217,8 @@
 
     "wrappy": ["wrappy@1.0.2", "", {}, "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ=="],
 
+    "yaml": ["yaml@2.8.2", "", { "bin": { "yaml": "bin.mjs" } }, "sha512-mplynKqc1C2hTVYxd0PU2xQAc22TI1vShAYGksCCfxbn/dFwnHTNi1bvYsBTkhdUNtGIf5xNOg938rrSSYvS9A=="],
+
     "zod": ["zod@4.1.13", "", {}, "sha512-AvvthqfqrAhNH9dnfmrfKzX5upOdjUVJYFqNSlkmGf64gRaTzlPwz99IHYnVs28qYAybvAlBV+H7pn0saFY4Ig=="],
 
     "zod-to-json-schema": ["zod-to-json-schema@3.25.0", "", { "peerDependencies": { "zod": "^3.25 || ^4" } }, "sha512-HvWtU2UG41LALjajJrML6uQejQhNJx+JBO9IflpSja4R03iNWfKXrj6W2h7ljuLyc1nKS+9yDyL/9tD1U/yBnQ=="],

src/qmd.ts

@@ -1440,7 +1440,7 @@ function collectionRemove(name: string): void {
     process.exit(1);
   }
 
-  const result = removeCollection(db, coll.id);
+  const result = removeCollection(db, name);
 
   console.log(`${c.green}✓${c.reset} Removed collection '${name}'`);
   console.log(`  Deleted ${result.deletedDocs} documents`);
@@ -1472,7 +1472,7 @@ function collectionRename(oldName: string, newName: string): void {
     process.exit(1);
   }
 
-  renameCollection(db, coll.id, newName);
+  renameCollection(db, oldName, newName);
 
   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}`);