Add 'qmd context check' command to identify missing contexts

This commit implements a diagnostic command to help users find collections
and paths that don't have context strings defined.

Changes:
1. New 'qmd context check' command that:
   - Lists collections without any context configured
   - Identifies top-level directories in collections missing context
   - Provides actionable suggestions with example commands

2. Updated help text and command documentation in CLAUDE.md

3. Enhanced error messages to include the new 'check' subcommand

The command provides helpful output showing:
- Collections without context (with document counts and suggestions)
- Top-level paths within collections that lack context
- Suggestions for adding context using virtual path syntax

This addresses the issue where users had contexts but couldn't find them,
by providing a clear diagnostic tool to identify what's missing.

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

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

.beads/issues.jsonl

@@ -15,7 +15,7 @@
 {"id":"qmd-i3t","title":"Move context management DB operations to store.ts","description":"Move path_contexts INSERT/DELETE/SELECT operations from addContext(), listContexts(), removeContext() to store.ts. Create methods like insertContext(), deleteContext(), etc.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T16:36:21.561746-05:00","updated_at":"2025-12-12T16:48:57.271485-05:00","closed_at":"2025-12-12T16:48:57.271485-05:00","dependencies":[{"issue_id":"qmd-i3t","depends_on_id":"qmd-29c","type":"parent-child","created_at":"2025-12-12T16:37:02.866006-05:00","created_by":"daemon"}]}
 {"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":"in_progress","priority":2,"issue_type":"task","created_at":"2025-12-12T16:42:57.324769-05:00","updated_at":"2025-12-12T17:08:43.356423-05:00"}
+{"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-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"}]}

CLAUDE.md

@@ -14,6 +14,7 @@ qmd collection rename <old> <new> # Rename a collection
 qmd ls [collection[/path]]        # List collections or files in a collection
 qmd context add [path] "text"     # Add context for path (defaults to current dir)
 qmd context list                  # List all contexts
+qmd context check                 # Check for collections/paths missing context
 qmd context rm <path>             # Remove context
 qmd get <file>                    # Get document content (fuzzy matches if not found)
 qmd multi-get <pattern>           # Get multiple docs by glob or comma-separated list
@@ -66,6 +67,9 @@ qmd context add qmd://journals/2024 "Journal entries from 2024"
 # List all contexts
 qmd context list
 
+# Check for collections or paths without context
+qmd context check
+
 # Remove context
 qmd context rm qmd://journals/2024
 qmd context rm /  # Remove global context

src/qmd.ts

@@ -66,6 +66,8 @@ import {
   deleteGlobalContexts,
   listPathContexts,
   getAllCollections,
+  getCollectionsWithoutContext,
+  getTopLevelPathsWithoutContext,
   OLLAMA_URL,
   DEFAULT_EMBED_MODEL,
   DEFAULT_QUERY_MODEL,