@graphmemory/server 1.1.0 → 1.3.0

package/dist/api/tools/tasks/search-tasks.js

@@ -5,15 +5,16 @@ const zod_1 = require("zod");
 function register(server, mgr) {
     server.registerTool('search_tasks', {
         description: 'Semantic search over the task graph. ' +
-            'Finds the most relevant tasks using vector similarity, then expands results ' +
+            'Supports three modes: hybrid (default, BM25 + vector), vector, keyword. ' +
+            'Finds the most relevant tasks, then expands results ' +
             'by traversing relations between tasks (graph walk). ' +
             'Returns an array sorted by relevance score (0–1), each with: ' +
             'id, title, description, status, priority, tags, score.',
         inputSchema: {
             query: zod_1.z.string().describe('Natural language search query'),
-            topK: zod_1.z.number().optional().describe('How many top similar tasks to use as seeds (default 5)'),
-            bfsDepth: zod_1.z.number().optional().describe('How many hops to follow relations from each seed (default 1; 0 = no expansion)'),
-            maxResults: zod_1.z.number().optional().describe('Maximum number of results to return (default 20)'),
+            topK: zod_1.z.number().min(1).max(500).optional().describe('How many top similar tasks to use as seeds (default 5)'),
+            bfsDepth: zod_1.z.number().min(0).max(10).optional().describe('How many hops to follow relations from each seed (default 1; 0 = no expansion)'),
+            maxResults: zod_1.z.number().min(1).max(500).optional().describe('Maximum number of results to return (default 20)'),
             minScore: zod_1.z.number().min(0).max(1).optional().describe('Minimum relevance score 0–1 (default 0.5)'),
             bfsDecay: zod_1.z.number().min(0).max(1).optional().describe('Score multiplier per hop (default 0.8)'),
             searchMode: zod_1.z.enum(['hybrid', 'vector', 'keyword']).optional().describe('Search mode: hybrid (default, BM25 + vector), vector (embedding only), keyword (BM25 only)'),

package/dist/cli/index.js

@@ -13,55 +13,22 @@ const multi_config_1 = require("../lib/multi-config");
 const jwt_1 = require("../lib/jwt");
 const project_manager_1 = require("../lib/project-manager");
 const embedder_1 = require("../lib/embedder");
-const docs_1 = require("../graphs/docs");
-const code_1 = require("../graphs/code");
-const knowledge_1 = require("../graphs/knowledge");
-const file_index_1 = require("../graphs/file-index");
-const task_1 = require("../graphs/task");
-const skill_1 = require("../graphs/skill");
 const index_1 = require("../api/index");
-const indexer_1 = require("../cli/indexer");
-const watcher_1 = require("../lib/watcher");
 const program = new commander_1.Command();
 program
     .name('graphmemory')
     .description('MCP server for semantic graph memory from markdown docs and source code')
-    .version('1.1.0');
+    .version('1.3.0');
 const parseIntArg = (v) => parseInt(v, 10);
 // ---------------------------------------------------------------------------
-// Helper: resolve a single project from YAML config + --project flag
+// Helper: load config from file, or fall back to default (cwd as single project)
 // ---------------------------------------------------------------------------
-function resolveProject(configPath, projectId) {
-    const mc = (0, multi_config_1.loadMultiConfig)(configPath);
-    const ids = Array.from(mc.projects.keys());
-    if (ids.length === 0) {
-        process.stderr.write('[cli] No projects defined in config\n');
-        process.exit(1);
-    }
-    const id = projectId ?? ids[0];
-    const project = mc.projects.get(id);
-    if (!project) {
-        process.stderr.write(`[cli] Project "${id}" not found in config. Available: ${ids.join(', ')}\n`);
-        process.exit(1);
+function loadConfigOrDefault(configPath) {
+    if (fs_1.default.existsSync(configPath)) {
+        return (0, multi_config_1.loadMultiConfig)(configPath);
     }
-    return { id, project, server: mc.server };
-}
-async function loadAllModels(projectId, config, modelsDir) {
-    for (const gn of multi_config_1.GRAPH_NAMES) {
-        if (!config.graphConfigs[gn].enabled)
-            continue;
-        await (0, embedder_1.loadModel)(config.graphConfigs[gn].model, config.graphConfigs[gn].embedding, modelsDir, `${projectId}:${gn}`);
-    }
-}
-function buildEmbedFns(projectId) {
-    const pair = (gn) => ({
-        document: (q) => (0, embedder_1.embed)(q, '', `${projectId}:${gn}`),
-        query: (q) => (0, embedder_1.embedQuery)(q, `${projectId}:${gn}`),
-    });
-    return {
-        docs: pair('docs'), code: pair('code'), knowledge: pair('knowledge'),
-        tasks: pair('tasks'), files: pair('files'), skills: pair('skills'),
-    };
+    process.stderr.write(`[cli] Config "${configPath}" not found, using current directory as project\n`);
+    return (0, multi_config_1.defaultConfig)(process.cwd());
 }
 // ---------------------------------------------------------------------------
 // Command: index — scan one project and exit
@@ -74,7 +41,7 @@ program
     .option('--reindex', 'Discard persisted graphs and re-index from scratch')
     .action((opts) => {
     (async () => {
-        const mc = (0, multi_config_1.loadMultiConfig)(opts.config);
+        const mc = loadConfigOrDefault(opts.config);
         const reindex = !!opts.reindex;
         if (reindex)
             process.stderr.write('[index] Re-indexing from scratch\n');
@@ -139,172 +106,6 @@ program
     });
 });
 // ---------------------------------------------------------------------------
-// Command: mcp — single-project stdio mode
-// ---------------------------------------------------------------------------
-program
-    .command('mcp')
-    .description('Index one project (or workspace), keep watching for changes, and start MCP server on stdio')
-    .option('--config <path>', 'Path to graph-memory.yaml', 'graph-memory.yaml')
-    .option('--project <id>', 'Project ID (defaults to first project)')
-    .option('--workspace <id>', 'Workspace ID (loads all workspace projects with shared graphs)')
-    .option('--reindex', 'Discard persisted graphs and re-index from scratch')
-    .action(async (opts) => {
-    // Workspace mode: load all projects in the workspace with shared graphs
-    if (opts.workspace) {
-        const mc = (0, multi_config_1.loadMultiConfig)(opts.config);
-        const wsConfig = mc.workspaces.get(opts.workspace);
-        if (!wsConfig) {
-            process.stderr.write(`[mcp] Workspace "${opts.workspace}" not found in config. Available: ${Array.from(mc.workspaces.keys()).join(', ')}\n`);
-            process.exit(1);
-        }
-        const fresh = !!opts.reindex;
-        if (fresh)
-            process.stderr.write(`[mcp] Re-indexing workspace "${opts.workspace}" from scratch\n`);
-        const manager = new project_manager_1.ProjectManager(mc.server);
-        await manager.addWorkspace(opts.workspace, wsConfig, fresh);
-        for (const projId of wsConfig.projects) {
-            const projConfig = mc.projects.get(projId);
-            if (!projConfig) {
-                process.stderr.write(`[mcp] Project "${projId}" referenced by workspace not found\n`);
-                process.exit(1);
-            }
-            await manager.addProject(projId, projConfig, fresh, opts.workspace);
-        }
-        // Use specified project (or first) for stdio server
-        const targetId = opts.project ?? wsConfig.projects[0];
-        if (!wsConfig.projects.includes(targetId)) {
-            process.stderr.write(`[mcp] Project "${targetId}" is not part of workspace "${opts.workspace}"\n`);
-            process.exit(1);
-        }
-        const instance = manager.getProject(targetId);
-        const sessionCtx = {
-            projectId: targetId,
-            workspaceId: opts.workspace,
-            workspaceProjects: wsConfig.projects,
-        };
-        await (0, index_1.startStdioServer)(instance.docGraph, instance.codeGraph, instance.knowledgeGraph, instance.fileIndexGraph, instance.taskGraph, instance.embedFns, instance.config.projectDir, instance.skillGraph, sessionCtx);
-        // Load models and index in background
-        (async () => {
-            await manager.loadWorkspaceModels(opts.workspace);
-            for (const projId of wsConfig.projects) {
-                await manager.loadModels(projId);
-                await manager.startIndexing(projId);
-            }
-            await manager.startWorkspaceMirror(opts.workspace);
-            process.stderr.write(`[mcp] Workspace "${opts.workspace}" fully indexed\n`);
-        })().catch((err) => {
-            process.stderr.write(`[mcp] Workspace indexer error: ${err}\n`);
-        });
-        let shuttingDown = false;
-        async function shutdown() {
-            if (shuttingDown) {
-                process.stderr.write('[mcp] Force exit\n');
-                process.exit(1);
-            }
-            shuttingDown = true;
-            process.stderr.write('[mcp] Shutting down...\n');
-            const forceTimer = setTimeout(() => { process.stderr.write('[mcp] Shutdown timeout, force exit\n'); process.exit(1); }, 5000);
-            try {
-                await manager.shutdown();
-            }
-            catch { /* ignore */ }
-            clearTimeout(forceTimer);
-            // Let event loop drain naturally — avoids ONNX global thread pool destructor crash on macOS
-        }
-        process.on('SIGINT', () => { void shutdown(); });
-        process.on('SIGTERM', () => { void shutdown(); });
-        return;
-    }
-    const { id, project, server } = resolveProject(opts.config, opts.project);
-    const projectDir = path_1.default.resolve(project.projectDir);
-    const fresh = !!opts.reindex;
-    if (fresh)
-        process.stderr.write(`[mcp] Re-indexing project "${id}" from scratch\n`);
-    const gc = project.graphConfigs;
-    // Load persisted graphs (or create fresh ones if reindexing / model changed) and start MCP server immediately
-    const docGraph = gc.docs.enabled ? (0, docs_1.loadGraph)(project.graphMemory, fresh, (0, multi_config_1.embeddingFingerprint)(gc.docs.model)) : undefined;
-    const codeGraph = gc.code.enabled ? (0, code_1.loadCodeGraph)(project.graphMemory, fresh, (0, multi_config_1.embeddingFingerprint)(gc.code.model)) : undefined;
-    const knowledgeGraph = gc.knowledge.enabled ? (0, knowledge_1.loadKnowledgeGraph)(project.graphMemory, fresh, (0, multi_config_1.embeddingFingerprint)(gc.knowledge.model)) : undefined;
-    const fileIndexGraph = gc.files.enabled ? (0, file_index_1.loadFileIndexGraph)(project.graphMemory, fresh, (0, multi_config_1.embeddingFingerprint)(gc.files.model)) : undefined;
-    const taskGraph = gc.tasks.enabled ? (0, task_1.loadTaskGraph)(project.graphMemory, fresh, (0, multi_config_1.embeddingFingerprint)(gc.tasks.model)) : undefined;
-    const skillGraph = gc.skills.enabled ? (0, skill_1.loadSkillGraph)(project.graphMemory, fresh, (0, multi_config_1.embeddingFingerprint)(gc.skills.model)) : undefined;
-    const embedFns = buildEmbedFns(id);
-    const sessionCtx = { projectId: id };
-    await (0, index_1.startStdioServer)(docGraph, codeGraph, knowledgeGraph, fileIndexGraph, taskGraph, embedFns, project.projectDir, skillGraph, sessionCtx);
-    // Load models and start watcher in the background
-    let watcher;
-    let indexer;
-    async function startIndexing() {
-        await loadAllModels(id, project, server.modelsDir);
-        indexer = (0, indexer_1.createProjectIndexer)(docGraph, codeGraph, {
-            projectId: id,
-            projectDir,
-            docsInclude: gc.docs.enabled ? gc.docs.include : undefined,
-            docsExclude: gc.docs.exclude,
-            codeInclude: gc.code.enabled ? gc.code.include : undefined,
-            codeExclude: gc.code.exclude,
-            filesExclude: gc.files.exclude,
-            chunkDepth: project.chunkDepth,
-            maxFileSize: project.maxFileSize,
-            docsModelName: `${id}:docs`,
-            codeModelName: `${id}:code`,
-            filesModelName: `${id}:files`,
-        }, knowledgeGraph, fileIndexGraph, taskGraph, skillGraph);
-        watcher = indexer.watch();
-        await watcher.whenReady;
-        await indexer.drain();
-        if (docGraph) {
-            (0, docs_1.saveGraph)(docGraph, project.graphMemory, (0, multi_config_1.embeddingFingerprint)(gc.docs.model));
-            process.stderr.write(`[mcp] Docs indexed. ${docGraph.order} nodes, ${docGraph.size} edges.\n`);
-        }
-        if (codeGraph) {
-            (0, code_1.saveCodeGraph)(codeGraph, project.graphMemory, (0, multi_config_1.embeddingFingerprint)(gc.code.model));
-            process.stderr.write(`[mcp] Code indexed. ${codeGraph.order} nodes, ${codeGraph.size} edges.\n`);
-        }
-        if (fileIndexGraph) {
-            (0, file_index_1.saveFileIndexGraph)(fileIndexGraph, project.graphMemory, (0, multi_config_1.embeddingFingerprint)(gc.files.model));
-            process.stderr.write(`[mcp] File index done. ${fileIndexGraph.order} nodes, ${fileIndexGraph.size} edges.\n`);
-        }
-    }
-    startIndexing().catch((err) => {
-        process.stderr.write(`[mcp] Indexer error: ${err}\n`);
-    });
-    let shuttingDown = false;
-    async function shutdown() {
-        if (shuttingDown) {
-            process.stderr.write('[mcp] Force exit\n');
-            process.exit(1);
-        }
-        shuttingDown = true;
-        process.stderr.write('[mcp] Shutting down...\n');
-        const forceTimer = setTimeout(() => {
-            process.stderr.write('[mcp] Shutdown timeout, force exit\n');
-            process.exit(1);
-        }, 5000);
-        try {
-            if (watcher)
-                await watcher.close();
-            if (indexer)
-                await indexer.drain();
-            if (docGraph)
-                (0, docs_1.saveGraph)(docGraph, project.graphMemory, (0, multi_config_1.embeddingFingerprint)(gc.docs.model));
-            if (codeGraph)
-                (0, code_1.saveCodeGraph)(codeGraph, project.graphMemory, (0, multi_config_1.embeddingFingerprint)(gc.code.model));
-            if (knowledgeGraph)
-                (0, knowledge_1.saveKnowledgeGraph)(knowledgeGraph, project.graphMemory, (0, multi_config_1.embeddingFingerprint)(gc.knowledge.model));
-            if (fileIndexGraph)
-                (0, file_index_1.saveFileIndexGraph)(fileIndexGraph, project.graphMemory, (0, multi_config_1.embeddingFingerprint)(gc.files.model));
-            if (taskGraph)
-                (0, task_1.saveTaskGraph)(taskGraph, project.graphMemory, (0, multi_config_1.embeddingFingerprint)(gc.tasks.model));
-        }
-        catch { /* ignore */ }
-        clearTimeout(forceTimer);
-        // Let event loop drain naturally — avoids ONNX global thread pool destructor crash on macOS
-    }
-    process.on('SIGINT', () => { void shutdown(); });
-    process.on('SIGTERM', () => { void shutdown(); });
-});
-// ---------------------------------------------------------------------------
 // Command: serve — multi-project HTTP mode
 // ---------------------------------------------------------------------------
 program
@@ -315,7 +116,7 @@ program
     .option('--port <n>', 'HTTP server port', parseIntArg)
     .option('--reindex', 'Discard persisted graphs and re-index from scratch')
     .action(async (opts) => {
-    const mc = (0, multi_config_1.loadMultiConfig)(opts.config);
+    const mc = loadConfigOrDefault(opts.config);
     const host = opts.host ?? mc.server.host;
     const port = opts.port ?? mc.server.port;
     const sessionTimeoutMs = mc.server.sessionTimeout * 1000;
@@ -345,7 +146,48 @@ program
     }
     // Embedding API model name (loaded in background with other models)
     const embeddingApiModelName = mc.server.embeddingApi?.enabled ? '__server__' : undefined;
-    // Start HTTP server immediately (before models are loaded)
+    // Load models and index all projects before starting HTTP
+    // Load embedding API model if enabled
+    if (embeddingApiModelName) {
+        try {
+            await (0, embedder_1.loadModel)(mc.server.model, mc.server.embedding, mc.server.modelsDir, embeddingApiModelName);
+            process.stderr.write(`[serve] Embedding API model ready\n`);
+        }
+        catch (err) {
+            process.stderr.write(`[serve] Failed to load embedding API model: ${err}\n`);
+        }
+    }
+    // Load workspace models
+    for (const wsId of manager.listWorkspaces()) {
+        try {
+            await manager.loadWorkspaceModels(wsId);
+        }
+        catch (err) {
+            process.stderr.write(`[serve] Failed to load workspace "${wsId}" models: ${err}\n`);
+        }
+    }
+    // Load project models and start indexing
+    for (const id of manager.listProjects()) {
+        try {
+            await manager.loadModels(id);
+            await manager.startIndexing(id);
+        }
+        catch (err) {
+            process.stderr.write(`[serve] Failed to initialize project "${id}": ${err}\n`);
+        }
+    }
+    // Start workspace mirror watchers (after all projects are indexed)
+    for (const wsId of manager.listWorkspaces()) {
+        try {
+            await manager.startWorkspaceMirror(wsId);
+        }
+        catch (err) {
+            process.stderr.write(`[serve] Failed to start workspace "${wsId}" mirror: ${err}\n`);
+        }
+    }
+    // Start auto-save
+    manager.startAutoSave();
+    // Start HTTP server (all models loaded, all projects indexed)
     const httpServer = await (0, index_1.startMultiProjectHttpServer)(host, port, sessionTimeoutMs, manager, {
         serverConfig: mc.server,
         users: mc.users,
@@ -357,104 +199,6 @@ program
         openSockets.add(socket);
         socket.on('close', () => openSockets.delete(socket));
     });
-    // Start auto-save
-    manager.startAutoSave();
-    // Load models and start indexing in background (workspaces first, then projects)
-    async function initProjects() {
-        // Load embedding API model if enabled
-        if (embeddingApiModelName) {
-            try {
-                await (0, embedder_1.loadModel)(mc.server.model, mc.server.embedding, mc.server.modelsDir, embeddingApiModelName);
-                process.stderr.write(`[serve] Embedding API model ready\n`);
-            }
-            catch (err) {
-                process.stderr.write(`[serve] Failed to load embedding API model: ${err}\n`);
-            }
-        }
-        // Load workspace models
-        for (const wsId of manager.listWorkspaces()) {
-            try {
-                await manager.loadWorkspaceModels(wsId);
-            }
-            catch (err) {
-                process.stderr.write(`[serve] Failed to load workspace "${wsId}" models: ${err}\n`);
-            }
-        }
-        // Load project models and start indexing
-        for (const id of manager.listProjects()) {
-            try {
-                await manager.loadModels(id);
-                await manager.startIndexing(id);
-            }
-            catch (err) {
-                process.stderr.write(`[serve] Failed to initialize project "${id}": ${err}\n`);
-            }
-        }
-        // Start workspace mirror watchers (after all projects are indexed)
-        for (const wsId of manager.listWorkspaces()) {
-            try {
-                await manager.startWorkspaceMirror(wsId);
-            }
-            catch (err) {
-                process.stderr.write(`[serve] Failed to start workspace "${wsId}" mirror: ${err}\n`);
-            }
-        }
-    }
-    initProjects().catch((err) => {
-        process.stderr.write(`[serve] Init error: ${err}\n`);
-    });
-    // Watch YAML config for hot-reload
-    let reloading = false;
-    const configWatcher = (0, watcher_1.startWatcher)(path_1.default.dirname(path_1.default.resolve(opts.config)), {
-        onAdd: () => { },
-        onChange: async (f) => {
-            if (path_1.default.resolve(f) !== path_1.default.resolve(opts.config))
-                return;
-            if (reloading)
-                return;
-            reloading = true;
-            try {
-                process.stderr.write('[serve] Config changed, reloading...\n');
-                const newMc = (0, multi_config_1.loadMultiConfig)(opts.config);
-                const currentIds = new Set(manager.listProjects());
-                const newIds = new Set(newMc.projects.keys());
-                // Remove projects no longer in config
-                for (const id of currentIds) {
-                    if (!newIds.has(id)) {
-                        await manager.removeProject(id);
-                    }
-                }
-                // Add new projects
-                for (const [id, config] of newMc.projects) {
-                    if (!currentIds.has(id)) {
-                        await manager.addProject(id, config);
-                        await manager.loadModels(id);
-                        await manager.startIndexing(id);
-                    }
-                }
-                // Re-add changed projects
-                for (const [id, config] of newMc.projects) {
-                    if (currentIds.has(id)) {
-                        const existing = manager.getProject(id);
-                        if (existing && JSON.stringify(existing.config) !== JSON.stringify(config)) {
-                            await manager.removeProject(id);
-                            await manager.addProject(id, config);
-                            await manager.loadModels(id);
-                            await manager.startIndexing(id);
-                        }
-                    }
-                }
-                process.stderr.write('[serve] Config reload complete\n');
-            }
-            catch (err) {
-                process.stderr.write(`[serve] Config reload error: ${err}\n`);
-            }
-            finally {
-                reloading = false;
-            }
-        },
-        onUnlink: () => { },
-    }, path_1.default.basename(opts.config));
     let shuttingDown = false;
     async function shutdown() {
         if (shuttingDown) {
@@ -475,7 +219,6 @@ program
                 socket.destroy();
             }
             openSockets.clear();
-            await configWatcher.close();
             await manager.shutdown();
         }
         catch { /* ignore */ }
@@ -572,13 +315,28 @@ usersCmd
             process.stderr.write('Passwords do not match\n');
             process.exit(1);
         }
+        // Validate inputs
+        if (/[\x00-\x1f\x7f]/.test(name)) {
+            process.stderr.write('Name contains invalid characters\n');
+            process.exit(1);
+        }
+        if (!/^[^\s@]+@[^\s@]+\.[^\s@]+$/.test(email)) {
+            process.stderr.write('Invalid email format\n');
+            process.exit(1);
+        }
+        if (password.length > 256) {
+            process.stderr.write('Password too long (max 256)\n');
+            process.exit(1);
+        }
         const pwHash = await (0, jwt_1.hashPassword)(password);
         const apiKey = `mgm-${crypto_1.default.randomBytes(24).toString('base64url')}`;
-        // Build YAML block for the new user
+        // Build YAML block for the new user — escape quotes to prevent YAML injection
+        const safeName = name.replace(/\\/g, '\\\\').replace(/"/g, '\\"');
+        const safeEmail = email.replace(/\\/g, '\\\\').replace(/"/g, '\\"');
         const userBlock = [
             `  ${id}:`,
-            `    name: "${name}"`,
-            `    email: "${email}"`,
+            `    name: "${safeName}"`,
+            `    email: "${safeEmail}"`,
             `    apiKey: "${apiKey}"`,
             `    passwordHash: "${pwHash}"`,
         ].join('\n');

package/dist/cli/indexer.js

@@ -19,31 +19,51 @@ const skill_1 = require("../graphs/skill");
 const file_index_1 = require("../graphs/file-index");
 function createProjectIndexer(docGraph, codeGraph, config, knowledgeGraph, fileIndexGraph, taskGraph, skillGraph) {
     // Three independent serial queues — docs, code, and file index.
-    let docsQueue = Promise.resolve();
-    let codeQueue = Promise.resolve();
-    let fileQueue = Promise.resolve();
-    // Error tracking
-    let docErrors = 0;
-    let codeErrors = 0;
-    let fileErrors = 0;
-    function enqueueDoc(fn) {
-        docsQueue = docsQueue.then(fn).catch((err) => {
-            docErrors++;
-            process.stderr.write(`[indexer] Doc error: ${err}\n`);
-        });
-    }
-    function enqueueCode(fn) {
-        codeQueue = codeQueue.then(fn).catch((err) => {
-            codeErrors++;
-            process.stderr.write(`[indexer] Code error: ${err}\n`);
-        });
-    }
-    function enqueueFile(fn) {
-        fileQueue = fileQueue.then(fn).catch((err) => {
-            fileErrors++;
-            process.stderr.write(`[indexer] File index error: ${err}\n`);
-        });
+    // Array-based to avoid promise chain memory accumulation during scan.
+    function createSerialQueue(label) {
+        const pending = [];
+        let running = false;
+        let errors = 0;
+        let idleResolve = null;
+        let idlePromise = Promise.resolve();
+        async function pump() {
+            running = true;
+            while (pending.length > 0) {
+                const fn = pending.shift();
+                try {
+                    await fn();
+                }
+                catch (err) {
+                    errors++;
+                    process.stderr.write(`[indexer] ${label} error: ${err}\n`);
+                }
+            }
+            running = false;
+            if (idleResolve) {
+                idleResolve();
+                idleResolve = null;
+            }
+        }
+        return {
+            enqueue(fn) {
+                pending.push(fn);
+                if (!running) {
+                    idlePromise = new Promise(r => { idleResolve = r; });
+                    void pump();
+                }
+            },
+            waitIdle() {
+                return (pending.length === 0 && !running) ? Promise.resolve() : idlePromise;
+            },
+            get errors() { return errors; },
+        };
     }
+    const docsQueue = createSerialQueue('Doc');
+    const codeQueue = createSerialQueue('Code');
+    const fileQueue = createSerialQueue('File index');
+    function enqueueDoc(fn) { docsQueue.enqueue(fn); }
+    function enqueueCode(fn) { codeQueue.enqueue(fn); }
+    function enqueueFile(fn) { fileQueue.enqueue(fn); }
     // ---------------------------------------------------------------------------
     // Per-file indexing
     // ---------------------------------------------------------------------------
@@ -126,7 +146,16 @@ function createProjectIndexer(docGraph, codeGraph, config, knowledgeGraph, fileI
         const parsed = await (0, code_1.parseCodeFile)(absolutePath, config.projectDir, mtime);
         // Batch-embed all symbols + file-level in one forward pass
         const batchInputs = parsed.nodes.map(({ attrs }) => ({ title: attrs.signature, content: attrs.docComment }));
-        batchInputs.push({ title: fileId, content: '' });
+        // File-level embedding: path + exported symbol names + import summary
+        const fileNode = parsed.nodes.find(n => n.attrs.kind === 'file');
+        const exportedNames = parsed.nodes
+            .filter(n => n.attrs.isExported && n.attrs.kind !== 'file')
+            .map(n => n.attrs.name);
+        const fileEmbedTitle = exportedNames.length > 0
+            ? `${fileId} ${exportedNames.join(' ')}`
+            : fileId;
+        const fileEmbedContent = fileNode?.attrs.body ?? ''; // body = importSummary for file nodes
+        batchInputs.push({ title: fileEmbedTitle, content: fileEmbedContent });
         const embeddings = await (0, embedder_1.embedBatch)(batchInputs, config.codeModelName);
         for (let i = 0; i < parsed.nodes.length; i++) {
             parsed.nodes[i].attrs.embedding = embeddings[i];
@@ -226,7 +255,7 @@ function createProjectIndexer(docGraph, codeGraph, config, knowledgeGraph, fileI
     function scan() {
         function walk(dir) {
             for (const entry of fs_1.default.readdirSync(dir, { withFileTypes: true })) {
-                if (entry.name.startsWith('.'))
+                if (entry.name.startsWith('.') || watcher_1.ALWAYS_IGNORED.has(entry.name))
                     continue;
                 const full = path_1.default.join(dir, entry.name);
                 if (entry.isDirectory()) {
@@ -252,7 +281,7 @@ function createProjectIndexer(docGraph, codeGraph, config, knowledgeGraph, fileI
         }, '**/*', allExcludePatterns.length > 0 ? allExcludePatterns : undefined);
     }
     async function drain() {
-        await Promise.all([docsQueue, codeQueue, fileQueue]);
+        await Promise.all([docsQueue.waitIdle(), codeQueue.waitIdle(), fileQueue.waitIdle()]);
         if (fileIndexGraph)
             (0, file_index_1.rebuildDirectoryStats)(fileIndexGraph);
         // Resolve cross-file edges that were deferred during indexing
@@ -265,10 +294,13 @@ function createProjectIndexer(docGraph, codeGraph, config, knowledgeGraph, fileI
             const codeImports = (0, code_2.resolvePendingImports)(codeGraph);
             if (codeImports > 0)
                 process.stderr.write(`[indexer] Resolved ${codeImports} deferred code import edge(s)\n`);
+            const codeEdges = (0, code_2.resolvePendingEdges)(codeGraph);
+            if (codeEdges > 0)
+                process.stderr.write(`[indexer] Resolved ${codeEdges} deferred code extends/implements edge(s)\n`);
         }
-        const totalErrors = docErrors + codeErrors + fileErrors;
+        const totalErrors = docsQueue.errors + codeQueue.errors + fileQueue.errors;
         if (totalErrors > 0) {
-            process.stderr.write(`[indexer] Completed with ${totalErrors} error(s): docs=${docErrors}, code=${codeErrors}, files=${fileErrors}\n`);
+            process.stderr.write(`[indexer] Completed with ${totalErrors} error(s): docs=${docsQueue.errors}, code=${codeQueue.errors}, files=${fileQueue.errors}\n`);
         }
     }
     return { scan, watch, drain };