Fix YAML parsing and context grouping in qmd status

- Fixed YAML syntax: Quote all context strings containing colons
- Fixed context grouping: Use collection names instead of IDs
- contextsByCollection now uses Map<string, ...> keyed by name
- Removed collection.id references (collections from YAML have no ID)

YAML now properly parses and contexts display correctly per collection.

🤖 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-0ic","title":"in qmd status, list all the additonal contexts under the collections that match","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T16:41:42.126194-05:00","updated_at":"2025-12-12T17:14:48.268119-05:00","closed_at":"2025-12-12T17:14:48.268119-05:00"}
 {"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.","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-13T09:54:53.349545-05:00","updated_at":"2025-12-13T09:54:53.349545-05:00","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-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.","status":"in_progress","priority":1,"issue_type":"task","created_at":"2025-12-13T09:54:53.349545-05:00","updated_at":"2025-12-13T10:27:15.760204-05:00","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-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"}]}
@@ -28,7 +28,7 @@
 {"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":"in_progress","priority":1,"issue_type":"task","created_at":"2025-12-13T09:54:53.247136-05:00","updated_at":"2025-12-13T10:20:15.923202-05:00","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-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":"closed","priority":1,"issue_type":"task","created_at":"2025-12-13T09:54:53.247136-05:00","updated_at":"2025-12-13T10:27:06.54374-05:00","closed_at":"2025-12-13T10:27:06.54374-05:00","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":"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"}

src/qmd.ts

@@ -463,27 +463,24 @@ function showStatus(): void {
 
   // Get all contexts grouped by collection
   const allContexts = listPathContexts(db);
-  const contextsByCollection = new Map<number, { path_prefix: string; context: string }[]>();
+  const contextsByCollection = new Map<string, { path_prefix: string; context: string }[]>();
 
   for (const ctx of allContexts) {
-    // Find collection by name
-    const collection = collections.find(col => col.name === ctx.collection_name);
-    if (collection) {
-      if (!contextsByCollection.has(collection.id)) {
-        contextsByCollection.set(collection.id, []);
-      }
-      contextsByCollection.get(collection.id)!.push({
-        path_prefix: ctx.path_prefix,
-        context: ctx.context
-      });
+    // Group contexts by collection name
+    if (!contextsByCollection.has(ctx.collection_name)) {
+      contextsByCollection.set(ctx.collection_name, []);
     }
+    contextsByCollection.get(ctx.collection_name)!.push({
+      path_prefix: ctx.path_prefix,
+      context: ctx.context
+    });
   }
 
   if (collections.length > 0) {
     console.log(`\n${c.bold}Collections${c.reset}`);
     for (const col of collections) {
       const lastMod = col.last_modified ? formatTimeAgo(new Date(col.last_modified)) : "never";
-      const contexts = contextsByCollection.get(col.id) || [];
+      const contexts = contextsByCollection.get(col.name) || [];
 
       console.log(`  ${c.cyan}${col.name}${c.reset} ${c.dim}(qmd://${col.name}/)${c.reset}`);
       console.log(`    ${c.dim}Path:${c.reset}     ${col.pwd}`);