Add git status and --pull flag to qmd update command

This commit adds git integration to the qmd update command:

1. Git repository detection: Checks for .git directory in each collection
2. Git status display: Shows short status for git repositories during update
3. --pull flag: Added optional --pull flag to execute git pull before reindexing
4. Error handling: Gracefully handles git errors without failing the update

When a collection is a git repository:
- Displays "Git repository detected"
- If --pull is specified, runs git pull and shows output (dimmed)
- Shows git status --short output (dimmed)
- If status is clean, shows "Git status: clean"

Usage:
  qmd update           # Update all collections, show git status
  qmd update --pull    # Pull changes first, then update

All git operations are non-blocking - failures are shown as warnings
but don't prevent the update from continuing.

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

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

.beads/issues.jsonl

@@ -1,4 +1,4 @@
-{"id":"qmd-0ic","title":"in qmd status, list all the additonal contexts under the collections that match","description":"","status":"in_progress","priority":2,"issue_type":"task","created_at":"2025-12-12T16:41:42.126194-05:00","updated_at":"2025-12-12T17:08:53.355395-05:00"}
+{"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-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-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"}]}

CLAUDE.md

@@ -18,7 +18,7 @@ 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
 qmd status                        # Show index status and collections
-qmd update                        # Re-index all collections
+qmd update [--pull]               # Re-index all collections (--pull: git pull first)
 qmd embed                         # Generate vector embeddings (requires Ollama)
 qmd search <query>                # BM25 full-text search
 qmd vsearch <query>               # Vector similarity search

src/qmd.ts

@@ -2439,12 +2439,13 @@ switch (cli.command) {
   case "context": {
     const subcommand = cli.args[0];
     if (!subcommand) {
-      console.error("Usage: qmd context <add|list|rm>");
+      console.error("Usage: qmd context <add|list|check|rm>");
       console.error("");
       console.error("Commands:");
       console.error("  qmd context add [path] \"text\"  - Add context (defaults to current dir)");
       console.error("  qmd context add / \"text\"       - Add global context to all collections");
       console.error("  qmd context list                - List all contexts");
+      console.error("  qmd context check               - Check for missing contexts");
       console.error("  qmd context rm <path>           - Remove context");
       process.exit(1);
     }
@@ -2488,6 +2489,11 @@ switch (cli.command) {
         break;
       }
 
+      case "check": {
+        contextCheck();
+        break;
+      }
+
       case "rm":
       case "remove": {
         if (cli.args.length < 2) {
@@ -2503,7 +2509,7 @@ switch (cli.command) {
 
       default:
         console.error(`Unknown subcommand: ${subcommand}`);
-        console.error("Available: add, list, rm");
+        console.error("Available: add, list, check, rm");
         process.exit(1);
     }
     break;

src/store.ts

@@ -602,6 +602,8 @@ export type Store = {
   getContextForPath: (collectionId: number, path: string) => string | null;
   getCollectionIdByName: (name: string) => number | null;
   getCollectionByName: (name: string) => { id: number; name: string; pwd: string; glob_pattern: string } | null;
+  getCollectionsWithoutContext: () => { id: number; name: string; pwd: string; doc_count: number }[];
+  getTopLevelPathsWithoutContext: (collectionId: number) => string[];
 
   // Virtual paths
   parseVirtualPath: typeof parseVirtualPath;
@@ -1422,6 +1424,72 @@ export function getAllCollections(db: Database): { id: number; name: string }[]
   return db.prepare(`SELECT id, name FROM collections`).all() as { id: number; name: string }[];
 }
 
+/**
+ * Check which collections don't have any context defined.
+ * Returns collections that have no context entries at all (not even root context).
+ */
+export function getCollectionsWithoutContext(db: Database): { id: number; name: string; pwd: string; doc_count: number }[] {
+  const collections = db.prepare(`
+    SELECT c.id, c.name, c.pwd, COUNT(d.id) as doc_count
+    FROM collections c
+    LEFT JOIN documents d ON d.collection_id = c.id AND d.active = 1
+    WHERE NOT EXISTS (
+      SELECT 1 FROM path_contexts pc WHERE pc.collection_id = c.id
+    )
+    GROUP BY c.id
+    ORDER BY c.name
+  `).all() as { id: number; name: string; pwd: string; doc_count: number }[];
+  return collections;
+}
+
+/**
+ * Get top-level directories in a collection that don't have context.
+ * Useful for suggesting where context might be needed.
+ */
+export function getTopLevelPathsWithoutContext(db: Database, collectionId: number): string[] {
+  // Get all paths in the collection
+  const paths = db.prepare(`
+    SELECT DISTINCT path FROM documents
+    WHERE collection_id = ? AND active = 1
+  `).all(collectionId) as { path: string }[];
+
+  // Get existing contexts for this collection
+  const contexts = db.prepare(`
+    SELECT path_prefix FROM path_contexts WHERE collection_id = ?
+  `).all(collectionId) as { path_prefix: string }[];
+
+  const contextPrefixes = new Set(contexts.map(c => c.path_prefix));
+
+  // Extract top-level directories (first path component)
+  const topLevelDirs = new Set<string>();
+  for (const { path } of paths) {
+    const parts = path.split('/').filter(Boolean);
+    if (parts.length > 1) {
+      topLevelDirs.add(parts[0]);
+    }
+  }
+
+  // Filter out directories that already have context (exact or parent)
+  const missing: string[] = [];
+  for (const dir of topLevelDirs) {
+    let hasContext = false;
+
+    // Check if this dir or any parent has context
+    for (const prefix of contextPrefixes) {
+      if (prefix === '' || prefix === dir || dir.startsWith(prefix + '/')) {
+        hasContext = true;
+        break;
+      }
+    }
+
+    if (!hasContext) {
+      missing.push(dir);
+    }
+  }
+
+  return missing.sort();
+}
+
 // =============================================================================
 // FTS Search
 // =============================================================================