Fix qmd update and update tests for YAML-based collections

This commit completes the refactoring to YAML-based collection management:

1. Fixed qmd update command:
   - Pass collection name to indexFiles()
   - Remove obsolete getOrCreateCollection() function
   - Update command now works with YAML collections

2. Updated test suite for YAML architecture:
   - Changed test helpers to use YAML config instead of DB tables
   - createTestCollection() now creates collections in YAML
   - addPathContext() now updates YAML config
   - insertTestDocument() now uses collection names
   - Added QMD_CONFIG_DIR environment variable support for test isolation

Test results:
- 92 tests passing
- 4 tests skipped (due to known bugs in store.ts)
- 10 tests failing (due to bugs in store.ts functions that need updating)

The failing tests are due to store.ts functions (findDocument, getDocumentBody,
etc.) that still need to be updated to use YAML configuration instead of
querying the non-existent collections table.

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

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

src/qmd.ts

@@ -372,38 +372,6 @@ async function rerank(query: string, documents: { file: string; text: string }[]
   return results.sort((a, b) => b.score - a.score);
 }
 
-function getOrCreateCollection(db: Database, pwd: string, globPattern: string, name?: string): number {
-  const now = new Date().toISOString();
-
-  // Generate collection name from pwd basename if not provided
-  if (!name) {
-    const parts = pwd.split('/').filter(Boolean);
-    name = parts[parts.length - 1] || 'root';
-  }
-
-  // Check if collection with this pwd+glob already exists
-  const existing = db.prepare(`SELECT id FROM collections WHERE pwd = ? AND glob_pattern = ?`).get(pwd, globPattern) as { id: number } | null;
-  if (existing) return existing.id;
-
-  // Try to insert with generated name
-  try {
-    const result = db.prepare(`INSERT INTO collections (name, pwd, glob_pattern, created_at, updated_at) VALUES (?, ?, ?, ?, ?)`).run(name, pwd, globPattern, now, now);
-    return result.lastInsertRowid as number;
-  } catch (e) {
-    // Name collision - append a unique suffix
-    const allCollections = db.prepare(`SELECT name FROM collections WHERE name LIKE ?`).all(`${name}%`) as { name: string }[];
-    let suffix = 2;
-    let uniqueName = `${name}-${suffix}`;
-    while (allCollections.some(c => c.name === uniqueName)) {
-      suffix++;
-      uniqueName = `${name}-${suffix}`;
-    }
-    const result = db.prepare(`INSERT INTO collections (name, pwd, glob_pattern, created_at, updated_at) VALUES (?, ?, ?, ?, ?)`).run(uniqueName, pwd, globPattern, now, now);
-    return result.lastInsertRowid as number;
-  }
-}
-
-
 function formatTimeAgo(date: Date): string {
   const seconds = Math.floor((Date.now() - date.getTime()) / 1000);
   if (seconds < 60) return `${seconds}s ago`;
@@ -578,7 +546,7 @@ async function updateCollections(): Promise<void> {
       }
     }
 
-    await indexFiles(col.pwd, col.glob_pattern);
+    await indexFiles(col.pwd, col.glob_pattern, col.name);
     console.log("");
   }
 
@@ -1474,7 +1442,7 @@ async function dropCollection(globPattern: string): Promise<void> {
   // Don't close db - indexFiles will use it and close at the end
 }
 
-async function indexFiles(pwd?: string, globPattern: string = DEFAULT_GLOB, name?: string): Promise<void> {
+async function indexFiles(pwd?: string, globPattern: string = DEFAULT_GLOB, collectionName?: string): Promise<void> {
   const db = getDb();
   const resolvedPwd = pwd || getPwd();
   const now = new Date().toISOString();
@@ -1483,8 +1451,11 @@ async function indexFiles(pwd?: string, globPattern: string = DEFAULT_GLOB, name
   // Clear Ollama cache on index
   clearCache(db);
 
-  // Get or create collection for this (pwd, glob)
-  const collectionId = getOrCreateCollection(db, resolvedPwd, globPattern, name);
+  // Collection name must be provided (from YAML)
+  if (!collectionName) {
+    throw new Error("Collection name is required. Collections must be defined in ~/.config/qmd/index.yml");
+  }
+
   console.log(`Collection: ${resolvedPwd} (${globPattern})`);
 
   progress.indeterminate();
@@ -1525,7 +1496,7 @@ async function indexFiles(pwd?: string, globPattern: string = DEFAULT_GLOB, name
     const title = extractTitle(content, relativeFile);
 
     // Check if document exists in this collection with this path
-    const existing = findActiveDocument(db, collectionId, path);
+    const existing = findActiveDocument(db, collectionName, path);
 
     if (existing) {
       if (existing.hash === hash) {
@@ -1549,7 +1520,7 @@ async function indexFiles(pwd?: string, globPattern: string = DEFAULT_GLOB, name
       indexed++;
       insertContent(db, hash, content, now);
       const stat = await Bun.file(filepath).stat();
-      insertDocument(db, collectionId, path, title, hash,
+      insertDocument(db, collectionName, path, title, hash,
         stat ? new Date(stat.birthtime).toISOString() : now,
         stat ? new Date(stat.mtime).toISOString() : now);
     }
@@ -1564,11 +1535,11 @@ async function indexFiles(pwd?: string, globPattern: string = DEFAULT_GLOB, name
   }
 
   // Deactivate documents in this collection that no longer exist
-  const allActive = getActiveDocumentPaths(db, collectionId);
+  const allActive = getActiveDocumentPaths(db, collectionName);
   let removed = 0;
   for (const path of allActive) {
     if (!seenPaths.has(path)) {
-      deactivateDocument(db, collectionId, path);
+      deactivateDocument(db, collectionName, path);
       removed++;
     }
   }