gitnexus 1.4.9 → 1.5.0

package/dist/server/api.js

@@ -11,15 +11,23 @@ import express from 'express';
 import cors from 'cors';
 import path from 'path';
 import fs from 'fs/promises';
-import { loadMeta, listRegisteredRepos } from '../storage/repo-manager.js';
-import { executeQuery, closeLbug, withLbugDb } from '../core/lbug/lbug-adapter.js';
-import { NODE_TABLES } from '../core/lbug/schema.js';
+import { createRequire } from 'node:module';
+import { loadMeta, listRegisteredRepos, getStoragePath } from '../storage/repo-manager.js';
+import { executeQuery, executePrepared, executeWithReusedStatement, closeLbug, withLbugDb, } from '../core/lbug/lbug-adapter.js';
+import { isWriteQuery } from '../mcp/core/lbug-adapter.js';
+import { NODE_TABLES } from 'gitnexus-shared';
 import { searchFTSFromLbug } from '../core/search/bm25-index.js';
 import { hybridSearch } from '../core/search/hybrid-search.js';
 // Embedding imports are lazy (dynamic import) to avoid loading onnxruntime-node
 // at server startup — crashes on unsupported Node ABI versions (#89)
 import { LocalBackend } from '../mcp/local/local-backend.js';
 import { mountMCPEndpoints } from './mcp-http.js';
+import { fork } from 'child_process';
+import { fileURLToPath, pathToFileURL } from 'url';
+import { JobManager } from './analyze-job.js';
+import { extractRepoName, getCloneDir, cloneOrPull } from './git-clone.js';
+const _require = createRequire(import.meta.url);
+const pkg = _require('../../package.json');
 /**
  * Determine whether an HTTP Origin header value is allowed by CORS policy.
  *
@@ -42,13 +50,13 @@ export const isAllowedOrigin = (origin) => {
         // Non-browser requests (curl, server-to-server) have no Origin header
         return true;
     }
-    if (origin.startsWith('http://localhost:')
-        || origin === 'http://localhost'
-        || origin.startsWith('http://127.0.0.1:')
-        || origin === 'http://127.0.0.1'
-        || origin.startsWith('http://[::1]:')
-        || origin === 'http://[::1]'
-        || origin === 'https://gitnexus.vercel.app') {
+    if (origin.startsWith('http://localhost:') ||
+        origin === 'http://localhost' ||
+        origin.startsWith('http://127.0.0.1:') ||
+        origin === 'http://127.0.0.1' ||
+        origin.startsWith('http://[::1]:') ||
+        origin === 'http://[::1]' ||
+        origin === 'https://gitnexus.vercel.app') {
         return true;
     }
     // RFC 1918 private network ranges — allow any port on these hosts.
@@ -68,7 +76,7 @@ export const isAllowedOrigin = (origin) => {
     if (protocol !== 'http:' && protocol !== 'https:')
         return false;
     const octets = hostname.split('.').map(Number);
-    if (octets.length !== 4 || octets.some(o => !Number.isInteger(o) || o < 0 || o > 255)) {
+    if (octets.length !== 4 || octets.some((o) => !Number.isInteger(o) || o < 0 || o > 255)) {
         return false;
     }
     const [a, b] = octets;
@@ -83,13 +91,15 @@ export const isAllowedOrigin = (origin) => {
         return true;
     return false;
 };
-const buildGraph = async () => {
+const buildGraph = async (includeContent = false) => {
     const nodes = [];
     for (const table of NODE_TABLES) {
         try {
             let query = '';
             if (table === 'File') {
-                query = `MATCH (n:File) RETURN n.id AS id, n.name AS name, n.filePath AS filePath, n.content AS content`;
+                query = includeContent
+                    ? `MATCH (n:File) RETURN n.id AS id, n.name AS name, n.filePath AS filePath, n.content AS content`
+                    : `MATCH (n:File) RETURN n.id AS id, n.name AS name, n.filePath AS filePath`;
             }
             else if (table === 'Folder') {
                 query = `MATCH (n:Folder) RETURN n.id AS id, n.name AS name, n.filePath AS filePath`;
@@ -101,7 +111,9 @@ const buildGraph = async () => {
                 query = `MATCH (n:Process) RETURN n.id AS id, n.label AS label, n.heuristicLabel AS heuristicLabel, n.processType AS processType, n.stepCount AS stepCount, n.communities AS communities, n.entryPointId AS entryPointId, n.terminalId AS terminalId`;
             }
             else {
-                query = `MATCH (n:${table}) RETURN n.id AS id, n.name AS name, n.filePath AS filePath, n.startLine AS startLine, n.endLine AS endLine, n.content AS content`;
+                query = includeContent
+                    ? `MATCH (n:${table}) RETURN n.id AS id, n.name AS name, n.filePath AS filePath, n.startLine AS startLine, n.endLine AS endLine, n.content AS content`
+                    : `MATCH (n:${table}) RETURN n.id AS id, n.name AS name, n.filePath AS filePath, n.startLine AS startLine, n.endLine AS endLine`;
             }
             const rows = await executeQuery(query);
             for (const row of rows) {
@@ -113,7 +125,7 @@ const buildGraph = async () => {
                         filePath: row.filePath ?? row[2],
                         startLine: row.startLine,
                         endLine: row.endLine,
-                        content: row.content,
+                        content: includeContent ? row.content : undefined,
                         heuristicLabel: row.heuristicLabel,
                         cohesion: row.cohesion,
                         symbolCount: row.symbolCount,
@@ -145,6 +157,76 @@ const buildGraph = async () => {
     }
     return { nodes, relationships };
 };
+/**
+ * Mount an SSE progress endpoint for a JobManager.
+ * Handles: initial state, terminal events, heartbeat, event IDs, client disconnect.
+ */
+const mountSSEProgress = (app, routePath, jm) => {
+    app.get(routePath, (req, res) => {
+        const job = jm.getJob(req.params.jobId);
+        if (!job) {
+            res.status(404).json({ error: 'Job not found' });
+            return;
+        }
+        let eventId = 0;
+        res.writeHead(200, {
+            'Content-Type': 'text/event-stream',
+            'Cache-Control': 'no-cache',
+            Connection: 'keep-alive',
+            'X-Accel-Buffering': 'no',
+        });
+        // Send current state immediately
+        eventId++;
+        res.write(`id: ${eventId}\ndata: ${JSON.stringify(job.progress)}\n\n`);
+        // If already terminal, send event and close
+        if (job.status === 'complete' || job.status === 'failed') {
+            eventId++;
+            res.write(`id: ${eventId}\nevent: ${job.status}\ndata: ${JSON.stringify({
+                repoName: job.repoName,
+                error: job.error,
+            })}\n\n`);
+            res.end();
+            return;
+        }
+        // Heartbeat to detect zombie connections
+        const heartbeat = setInterval(() => {
+            try {
+                res.write(':heartbeat\n\n');
+            }
+            catch {
+                clearInterval(heartbeat);
+                unsubscribe();
+            }
+        }, 30_000);
+        // Subscribe to progress updates
+        const unsubscribe = jm.onProgress(job.id, (progress) => {
+            try {
+                eventId++;
+                if (progress.phase === 'complete' || progress.phase === 'failed') {
+                    const eventJob = jm.getJob(req.params.jobId);
+                    res.write(`id: ${eventId}\nevent: ${progress.phase}\ndata: ${JSON.stringify({
+                        repoName: eventJob?.repoName,
+                        error: eventJob?.error,
+                    })}\n\n`);
+                    clearInterval(heartbeat);
+                    res.end();
+                    unsubscribe();
+                }
+                else {
+                    res.write(`id: ${eventId}\ndata: ${JSON.stringify(progress)}\n\n`);
+                }
+            }
+            catch {
+                clearInterval(heartbeat);
+                unsubscribe();
+            }
+        });
+        req.on('close', () => {
+            clearInterval(heartbeat);
+            unsubscribe();
+        });
+    });
+};
 const statusFromError = (err) => {
     const msg = String(err?.message ?? '');
     if (msg.includes('No indexed repositories') || msg.includes('not found'))
@@ -164,6 +246,7 @@ const requestedRepo = (req) => {
 };
 export const createServer = async (port, host = '127.0.0.1') => {
     const app = express();
+    app.disable('x-powered-by');
     // CORS: allow localhost, private/LAN networks, and the deployed site.
     // Non-browser requests (curl, server-to-server) have no origin and are allowed.
     app.use(cors({
@@ -174,29 +257,81 @@ export const createServer = async (port, host = '127.0.0.1') => {
             else {
                 callback(new Error('Not allowed by CORS'));
             }
-        }
+        },
     }));
     app.use(express.json({ limit: '10mb' }));
     // Initialize MCP backend (multi-repo, shared across all MCP sessions)
     const backend = new LocalBackend();
     await backend.init();
     const cleanupMcp = mountMCPEndpoints(app, backend);
+    const jobManager = new JobManager();
+    // Shared repo lock — prevents concurrent analyze + embed on the same repo path,
+    // which would corrupt LadybugDB (analyze calls closeLbug + initLbug while embed has queries in flight).
+    const activeRepoPaths = new Set();
+    const acquireRepoLock = (repoPath) => {
+        if (activeRepoPaths.has(repoPath)) {
+            return `Another job is already active for this repository`;
+        }
+        activeRepoPaths.add(repoPath);
+        return null;
+    };
+    const releaseRepoLock = (repoPath) => {
+        activeRepoPaths.delete(repoPath);
+    };
     // Helper: resolve a repo by name from the global registry, or default to first
     const resolveRepo = async (repoName) => {
         const repos = await listRegisteredRepos();
         if (repos.length === 0)
             return null;
         if (repoName)
-            return repos.find(r => r.name === repoName) || null;
+            return repos.find((r) => r.name === repoName) || null;
         return repos[0]; // default to first
     };
+    // SSE heartbeat — clients connect to detect server liveness instantly.
+    // When the server shuts down, the TCP connection drops and the client's
+    // EventSource fires onerror immediately (no polling delay).
+    app.get('/api/heartbeat', (_req, res) => {
+        // Use res.set() instead of res.writeHead() to preserve CORS headers from middleware
+        res.set({
+            'Content-Type': 'text/event-stream',
+            'Cache-Control': 'no-cache',
+            Connection: 'keep-alive',
+        });
+        res.flushHeaders();
+        // Send initial ping so the client knows it connected
+        res.write(':ok\n\n');
+        // Keep-alive ping every 15s to prevent proxy/firewall timeout
+        const interval = setInterval(() => res.write(':ping\n\n'), 15_000);
+        _req.on('close', () => clearInterval(interval));
+    });
+    // Server info: version and launch context (npx / global / local dev)
+    app.get('/api/info', (_req, res) => {
+        const execPath = process.env.npm_execpath ?? '';
+        const argv0 = process.argv[1] ?? '';
+        let launchContext;
+        if (execPath.includes('npx') ||
+            argv0.includes('_npx') ||
+            process.env.npm_config_prefix?.includes('_npx')) {
+            launchContext = 'npx';
+        }
+        else if (argv0.includes('node_modules')) {
+            launchContext = 'local';
+        }
+        else {
+            launchContext = 'global';
+        }
+        res.json({ version: pkg.version, launchContext, nodeVersion: process.version });
+    });
     // List all registered repos
     app.get('/api/repos', async (_req, res) => {
         try {
             const repos = await listRegisteredRepos();
-            res.json(repos.map(r => ({
-                name: r.name, path: r.path, indexedAt: r.indexedAt,
-                lastCommit: r.lastCommit, stats: r.stats,
+            res.json(repos.map((r) => ({
+                name: r.name,
+                path: r.path,
+                indexedAt: r.indexedAt,
+                lastCommit: r.lastCommit,
+                stats: r.stats,
             })));
         }
         catch (err) {
@@ -223,6 +358,61 @@ export const createServer = async (port, host = '127.0.0.1') => {
             res.status(500).json({ error: err.message || 'Failed to get repo info' });
         }
     });
+    // Delete a repo — removes index, clone dir (if any), and unregisters it
+    app.delete('/api/repo', async (req, res) => {
+        try {
+            const repoName = requestedRepo(req);
+            if (!repoName) {
+                res.status(400).json({ error: 'Missing repo name' });
+                return;
+            }
+            const entry = await resolveRepo(repoName);
+            if (!entry) {
+                res.status(404).json({ error: 'Repository not found' });
+                return;
+            }
+            // Acquire repo lock — prevents deleting while analyze/embed is in flight
+            const lockKey = getStoragePath(entry.path);
+            const lockErr = acquireRepoLock(lockKey);
+            if (lockErr) {
+                res.status(409).json({ error: lockErr });
+                return;
+            }
+            try {
+                // Close any open LadybugDB handle before deleting files
+                try {
+                    await closeLbug();
+                }
+                catch { }
+                // 1. Delete the .gitnexus index/storage directory
+                const storagePath = getStoragePath(entry.path);
+                await fs.rm(storagePath, { recursive: true, force: true }).catch(() => { });
+                // 2. Delete the cloned repo dir if it lives under ~/.gitnexus/repos/
+                const cloneDir = getCloneDir(entry.name);
+                try {
+                    const stat = await fs.stat(cloneDir);
+                    if (stat.isDirectory()) {
+                        await fs.rm(cloneDir, { recursive: true, force: true });
+                    }
+                }
+                catch {
+                    /* clone dir may not exist (local repos) */
+                }
+                // 3. Unregister from the global registry
+                const { unregisterRepo } = await import('../storage/repo-manager.js');
+                await unregisterRepo(entry.path);
+                // 4. Reinitialize backend to reflect the removal
+                await backend.init().catch(() => { });
+                res.json({ deleted: entry.name });
+            }
+            finally {
+                releaseRepoLock(lockKey);
+            }
+        }
+        catch (err) {
+            res.status(500).json({ error: err.message || 'Failed to delete repo' });
+        }
+    });
     // Get full graph
     app.get('/api/graph', async (req, res) => {
         try {
@@ -232,7 +422,8 @@ export const createServer = async (port, host = '127.0.0.1') => {
                 return;
             }
             const lbugPath = path.join(entry.storagePath, 'lbug');
-            const graph = await withLbugDb(lbugPath, async () => buildGraph());
+            const includeContent = req.query.includeContent === 'true';
+            const graph = await withLbugDb(lbugPath, async () => buildGraph(includeContent));
             res.json(graph);
         }
         catch (err) {
@@ -247,6 +438,10 @@ export const createServer = async (port, host = '127.0.0.1') => {
                 res.status(400).json({ error: 'Missing "cypher" in request body' });
                 return;
             }
+            if (isWriteQuery(cypher)) {
+                res.status(403).json({ error: 'Write queries are not allowed via the HTTP API' });
+                return;
+            }
             const entry = await resolveRepo(requestedRepo(req));
             if (!entry) {
                 res.status(404).json({ error: 'Repository not found' });
@@ -260,7 +455,7 @@ export const createServer = async (port, host = '127.0.0.1') => {
             res.status(500).json({ error: err.message || 'Query failed' });
         }
     });
-    // Search
+    // Search (supports mode: 'hybrid' | 'semantic' | 'bm25', and optional enrichment)
     app.post('/api/search', async (req, res) => {
         try {
             const query = (req.body.query ?? '').trim();
@@ -278,14 +473,108 @@ export const createServer = async (port, host = '127.0.0.1') => {
             const limit = Number.isFinite(parsedLimit)
                 ? Math.max(1, Math.min(100, Math.trunc(parsedLimit)))
                 : 10;
+            const mode = req.body.mode ?? 'hybrid';
+            const enrich = req.body.enrich !== false; // default true
             const results = await withLbugDb(lbugPath, async () => {
-                const { isEmbedderReady } = await import('../core/embeddings/embedder.js');
-                if (isEmbedderReady()) {
-                    const { semanticSearch } = await import('../core/embeddings/embedding-pipeline.js');
-                    return hybridSearch(query, limit, executeQuery, semanticSearch);
+                let searchResults;
+                if (mode === 'semantic') {
+                    const { isEmbedderReady } = await import('../core/embeddings/embedder.js');
+                    if (!isEmbedderReady()) {
+                        return [];
+                    }
+                    const { semanticSearch: semSearch } = await import('../core/embeddings/embedding-pipeline.js');
+                    searchResults = await semSearch(executeQuery, query, limit);
+                    // Normalize semantic results to HybridSearchResult shape
+                    searchResults = searchResults.map((r, i) => ({
+                        ...r,
+                        score: r.score ?? 1 - (r.distance ?? 0),
+                        rank: i + 1,
+                        sources: ['semantic'],
+                    }));
                 }
-                // FTS-only fallback when embeddings aren't loaded
-                return searchFTSFromLbug(query, limit);
+                else if (mode === 'bm25') {
+                    searchResults = await searchFTSFromLbug(query, limit);
+                    searchResults = searchResults.map((r, i) => ({
+                        ...r,
+                        rank: i + 1,
+                        sources: ['bm25'],
+                    }));
+                }
+                else {
+                    // hybrid (default)
+                    const { isEmbedderReady } = await import('../core/embeddings/embedder.js');
+                    if (isEmbedderReady()) {
+                        const { semanticSearch: semSearch } = await import('../core/embeddings/embedding-pipeline.js');
+                        searchResults = await hybridSearch(query, limit, executeQuery, semSearch);
+                    }
+                    else {
+                        searchResults = await searchFTSFromLbug(query, limit);
+                    }
+                }
+                if (!enrich)
+                    return searchResults;
+                // Server-side enrichment: add connections, cluster, processes per result
+                // Uses parameterized queries to prevent Cypher injection via nodeId
+                const validLabel = (label) => NODE_TABLES.includes(label);
+                const enriched = await Promise.all(searchResults.slice(0, limit).map(async (r) => {
+                    const nodeId = r.nodeId || r.id || '';
+                    const nodeLabel = nodeId.split(':')[0];
+                    const enrichment = {};
+                    if (!nodeId || !validLabel(nodeLabel))
+                        return { ...r, ...enrichment };
+                    // Run connections, cluster, and process queries in parallel
+                    // Label is validated against NODE_TABLES (compile-time safe identifiers);
+                    // nodeId uses $nid parameter binding to prevent injection
+                    const [connRes, clusterRes, procRes] = await Promise.all([
+                        executePrepared(`
+              MATCH (n:${nodeLabel} {id: $nid})
+              OPTIONAL MATCH (n)-[r1:CodeRelation]->(dst)
+              OPTIONAL MATCH (src)-[r2:CodeRelation]->(n)
+              RETURN
+                collect(DISTINCT {name: dst.name, type: r1.type, confidence: r1.confidence}) AS outgoing,
+                collect(DISTINCT {name: src.name, type: r2.type, confidence: r2.confidence}) AS incoming
+              LIMIT 1
+            `, { nid: nodeId }).catch(() => []),
+                        executePrepared(`
+              MATCH (n:${nodeLabel} {id: $nid})
+              MATCH (n)-[:CodeRelation {type: 'MEMBER_OF'}]->(c:Community)
+              RETURN c.label AS label, c.description AS description
+              LIMIT 1
+            `, { nid: nodeId }).catch(() => []),
+                        executePrepared(`
+              MATCH (n:${nodeLabel} {id: $nid})
+              MATCH (n)-[rel:CodeRelation {type: 'STEP_IN_PROCESS'}]->(p:Process)
+              RETURN p.id AS id, p.label AS label, rel.step AS step, p.stepCount AS stepCount
+              ORDER BY rel.step
+            `, { nid: nodeId }).catch(() => []),
+                    ]);
+                    if (connRes.length > 0) {
+                        const row = connRes[0];
+                        const outgoing = (Array.isArray(row) ? row[0] : row.outgoing || [])
+                            .filter((c) => c?.name)
+                            .slice(0, 5);
+                        const incoming = (Array.isArray(row) ? row[1] : row.incoming || [])
+                            .filter((c) => c?.name)
+                            .slice(0, 5);
+                        enrichment.connections = { outgoing, incoming };
+                    }
+                    if (clusterRes.length > 0) {
+                        const row = clusterRes[0];
+                        enrichment.cluster = Array.isArray(row) ? row[0] : row.label;
+                    }
+                    if (procRes.length > 0) {
+                        enrichment.processes = procRes
+                            .map((row) => ({
+                            id: Array.isArray(row) ? row[0] : row.id,
+                            label: Array.isArray(row) ? row[1] : row.label,
+                            step: Array.isArray(row) ? row[2] : row.step,
+                            stepCount: Array.isArray(row) ? row[3] : row.stepCount,
+                        }))
+                            .filter((p) => p.id && p.label);
+                    }
+                    return { ...r, ...enrichment };
+                }));
+                return enriched;
             });
             res.json({ results });
         }
@@ -313,8 +602,27 @@ export const createServer = async (port, host = '127.0.0.1') => {
                 res.status(403).json({ error: 'Path traversal denied' });
                 return;
             }
-            const content = await fs.readFile(fullPath, 'utf-8');
-            res.json({ content });
+            const raw = await fs.readFile(fullPath, 'utf-8');
+            // Optional line-range support: ?startLine=10&endLine=50
+            // Returns only the requested slice (0-indexed), plus metadata.
+            const startLine = req.query.startLine !== undefined ? Number(req.query.startLine) : undefined;
+            const endLine = req.query.endLine !== undefined ? Number(req.query.endLine) : undefined;
+            if (startLine !== undefined && Number.isFinite(startLine)) {
+                const lines = raw.split('\n');
+                const start = Math.max(0, startLine);
+                const end = endLine !== undefined && Number.isFinite(endLine)
+                    ? Math.min(lines.length, endLine + 1)
+                    : lines.length;
+                res.json({
+                    content: lines.slice(start, end).join('\n'),
+                    startLine: start,
+                    endLine: end - 1,
+                    totalLines: lines.length,
+                });
+            }
+            else {
+                res.json({ content: raw, totalLines: raw.split('\n').length });
+            }
         }
         catch (err) {
             if (err.code === 'ENOENT') {
@@ -325,6 +633,75 @@ export const createServer = async (port, host = '127.0.0.1') => {
             }
         }
     });
+    // Grep — regex search across file contents in the indexed repo
+    // Uses filesystem-based search for memory efficiency (never loads all files into memory)
+    app.get('/api/grep', async (req, res) => {
+        try {
+            const entry = await resolveRepo(requestedRepo(req));
+            if (!entry) {
+                res.status(404).json({ error: 'Repository not found' });
+                return;
+            }
+            const pattern = req.query.pattern;
+            if (!pattern) {
+                res.status(400).json({ error: 'Missing "pattern" query parameter' });
+                return;
+            }
+            // ReDoS protection: reject overly long or dangerous patterns
+            if (pattern.length > 200) {
+                res.status(400).json({ error: 'Pattern too long (max 200 characters)' });
+                return;
+            }
+            // Validate regex syntax
+            let regex;
+            try {
+                regex = new RegExp(pattern, 'gim');
+            }
+            catch {
+                res.status(400).json({ error: 'Invalid regex pattern' });
+                return;
+            }
+            const parsedLimit = Number(req.query.limit ?? 50);
+            const limit = Number.isFinite(parsedLimit)
+                ? Math.max(1, Math.min(200, Math.trunc(parsedLimit)))
+                : 50;
+            const results = [];
+            const repoRoot = path.resolve(entry.path);
+            // Get file paths from the graph (lightweight — no content loaded)
+            const lbugPath = path.join(entry.storagePath, 'lbug');
+            const fileRows = await withLbugDb(lbugPath, () => executeQuery(`MATCH (n:File) WHERE n.content IS NOT NULL RETURN n.filePath AS filePath`));
+            // Search files on disk one at a time (constant memory)
+            for (const row of fileRows) {
+                if (results.length >= limit)
+                    break;
+                const filePath = row.filePath || '';
+                const fullPath = path.resolve(repoRoot, filePath);
+                // Path traversal guard
+                if (!fullPath.startsWith(repoRoot + path.sep) && fullPath !== repoRoot)
+                    continue;
+                let content;
+                try {
+                    content = await fs.readFile(fullPath, 'utf-8');
+                }
+                catch {
+                    continue; // File may have been deleted since indexing
+                }
+                const lines = content.split('\n');
+                for (let i = 0; i < lines.length; i++) {
+                    if (results.length >= limit)
+                        break;
+                    if (regex.test(lines[i])) {
+                        results.push({ filePath, line: i + 1, text: lines[i].trim().slice(0, 200) });
+                    }
+                    regex.lastIndex = 0;
+                }
+            }
+            res.json({ results });
+        }
+        catch (err) {
+            res.status(500).json({ error: err.message || 'Grep failed' });
+        }
+    });
     // List all processes
     app.get('/api/processes', async (req, res) => {
         try {
@@ -351,7 +728,9 @@ export const createServer = async (port, host = '127.0.0.1') => {
             res.json(result);
         }
         catch (err) {
-            res.status(statusFromError(err)).json({ error: err.message || 'Failed to query process detail' });
+            res
+                .status(statusFromError(err))
+                .json({ error: err.message || 'Failed to query process detail' });
         }
     });
     // List all clusters
@@ -380,25 +759,397 @@ export const createServer = async (port, host = '127.0.0.1') => {
             res.json(result);
         }
         catch (err) {
-            res.status(statusFromError(err)).json({ error: err.message || 'Failed to query cluster detail' });
+            res
+                .status(statusFromError(err))
+                .json({ error: err.message || 'Failed to query cluster detail' });
         }
     });
+    // ── Analyze API ──────────────────────────────────────────────────────
+    // POST /api/analyze — start a new analysis job
+    app.post('/api/analyze', async (req, res) => {
+        try {
+            const { url: repoUrl, path: repoLocalPath, force, embeddings } = req.body;
+            // Input type validation
+            if (repoUrl !== undefined && typeof repoUrl !== 'string') {
+                res.status(400).json({ error: '"url" must be a string' });
+                return;
+            }
+            if (repoLocalPath !== undefined && typeof repoLocalPath !== 'string') {
+                res.status(400).json({ error: '"path" must be a string' });
+                return;
+            }
+            if (!repoUrl && !repoLocalPath) {
+                res.status(400).json({ error: 'Provide "url" (git URL) or "path" (local path)' });
+                return;
+            }
+            // Path validation: require absolute path, reject traversal (e.g. /tmp/../etc/passwd)
+            if (repoLocalPath) {
+                if (!path.isAbsolute(repoLocalPath)) {
+                    res.status(400).json({ error: '"path" must be an absolute path' });
+                    return;
+                }
+                if (path.normalize(repoLocalPath) !== path.resolve(repoLocalPath)) {
+                    res.status(400).json({ error: '"path" must not contain traversal sequences' });
+                    return;
+                }
+            }
+            const job = jobManager.createJob({ repoUrl, repoPath: repoLocalPath });
+            // If job was already running (dedup), just return its id
+            if (job.status !== 'queued') {
+                res.status(202).json({ jobId: job.id, status: job.status });
+                return;
+            }
+            // Mark as active synchronously to prevent race with concurrent requests
+            jobManager.updateJob(job.id, { status: 'cloning' });
+            // Start async work — don't await
+            (async () => {
+                let targetPath = repoLocalPath;
+                try {
+                    // Clone if URL provided
+                    if (repoUrl && !repoLocalPath) {
+                        const repoName = extractRepoName(repoUrl);
+                        targetPath = getCloneDir(repoName);
+                        jobManager.updateJob(job.id, {
+                            status: 'cloning',
+                            repoName,
+                            progress: { phase: 'cloning', percent: 0, message: `Cloning ${repoUrl}...` },
+                        });
+                        await cloneOrPull(repoUrl, targetPath, (progress) => {
+                            jobManager.updateJob(job.id, {
+                                progress: { phase: progress.phase, percent: 5, message: progress.message },
+                            });
+                        });
+                    }
+                    if (!targetPath) {
+                        throw new Error('No target path resolved');
+                    }
+                    // Acquire shared repo lock (keyed on storagePath to match embed handler)
+                    const analyzeLockKey = getStoragePath(targetPath);
+                    const lockErr = acquireRepoLock(analyzeLockKey);
+                    if (lockErr) {
+                        jobManager.updateJob(job.id, { status: 'failed', error: lockErr });
+                        return;
+                    }
+                    jobManager.updateJob(job.id, { repoPath: targetPath, status: 'analyzing' });
+                    // ── Worker fork with auto-retry ──────────────────────────────
+                    //
+                    // Forks a child process with 8GB heap. If the worker crashes
+                    // (OOM, native addon segfault, etc.), it retries up to
+                    // MAX_WORKER_RETRIES times with exponential backoff before
+                    // marking the job as permanently failed.
+                    //
+                    // In dev mode (tsx), registers the tsx ESM hook via a file://
+                    // URL so the child can compile TypeScript on-the-fly.
+                    const MAX_WORKER_RETRIES = 2;
+                    const callerPath = fileURLToPath(import.meta.url);
+                    const isDev = callerPath.endsWith('.ts');
+                    const workerFile = isDev ? 'analyze-worker.ts' : 'analyze-worker.js';
+                    const workerPath = path.join(path.dirname(callerPath), workerFile);
+                    const tsxHookArgs = isDev
+                        ? ['--import', pathToFileURL(_require.resolve('tsx/esm')).href]
+                        : [];
+                    const forkWorker = () => {
+                        const currentJob = jobManager.getJob(job.id);
+                        if (!currentJob || currentJob.status === 'complete' || currentJob.status === 'failed')
+                            return;
+                        const child = fork(workerPath, [], {
+                            execArgv: [...tsxHookArgs, '--max-old-space-size=8192'],
+                            stdio: ['ignore', 'pipe', 'pipe', 'ipc'],
+                        });
+                        // Capture stderr for crash diagnostics
+                        let stderrChunks = '';
+                        child.stderr?.on('data', (chunk) => {
+                            stderrChunks += chunk.toString();
+                            if (stderrChunks.length > 4096)
+                                stderrChunks = stderrChunks.slice(-4096);
+                        });
+                        child.on('message', (msg) => {
+                            if (msg.type === 'progress') {
+                                jobManager.updateJob(job.id, {
+                                    status: 'analyzing',
+                                    progress: { phase: msg.phase, percent: msg.percent, message: msg.message },
+                                });
+                            }
+                            else if (msg.type === 'complete') {
+                                releaseRepoLock(analyzeLockKey);
+                                // Reinitialize backend BEFORE marking complete — ensures the new
+                                // repo is queryable when the client receives the SSE complete event.
+                                backend
+                                    .init()
+                                    .then(() => {
+                                    jobManager.updateJob(job.id, {
+                                        status: 'complete',
+                                        repoName: msg.result.repoName,
+                                    });
+                                })
+                                    .catch((err) => {
+                                    console.error('backend.init() failed after analyze:', err);
+                                    jobManager.updateJob(job.id, {
+                                        status: 'failed',
+                                        error: 'Server failed to reload after analysis. Try again.',
+                                    });
+                                });
+                            }
+                            else if (msg.type === 'error') {
+                                releaseRepoLock(analyzeLockKey);
+                                jobManager.updateJob(job.id, {
+                                    status: 'failed',
+                                    error: msg.message,
+                                });
+                            }
+                        });
+                        child.on('error', (err) => {
+                            releaseRepoLock(analyzeLockKey);
+                            jobManager.updateJob(job.id, {
+                                status: 'failed',
+                                error: `Worker process error: ${err.message}`,
+                            });
+                        });
+                        child.on('exit', (code) => {
+                            const j = jobManager.getJob(job.id);
+                            if (!j || j.status === 'complete' || j.status === 'failed')
+                                return;
+                            // Worker crashed — attempt retry if under the limit
+                            if (j.retryCount < MAX_WORKER_RETRIES) {
+                                j.retryCount++;
+                                const delay = 1000 * Math.pow(2, j.retryCount - 1); // 1s, 2s
+                                const lastErr = stderrChunks.trim().split('\n').pop() || '';
+                                console.warn(`Analyze worker crashed (code ${code}), retry ${j.retryCount}/${MAX_WORKER_RETRIES} in ${delay}ms` +
+                                    (lastErr ? `: ${lastErr}` : ''));
+                                jobManager.updateJob(job.id, {
+                                    status: 'analyzing',
+                                    progress: {
+                                        phase: 'retrying',
+                                        percent: j.progress.percent,
+                                        message: `Worker crashed, retrying (${j.retryCount}/${MAX_WORKER_RETRIES})...`,
+                                    },
+                                });
+                                stderrChunks = '';
+                                setTimeout(forkWorker, delay);
+                            }
+                            else {
+                                // Exhausted retries — permanent failure
+                                releaseRepoLock(analyzeLockKey);
+                                jobManager.updateJob(job.id, {
+                                    status: 'failed',
+                                    error: `Worker crashed ${MAX_WORKER_RETRIES + 1} times (code ${code})${stderrChunks ? ': ' + stderrChunks.trim().split('\n').pop() : ''}`,
+                                });
+                            }
+                        });
+                        // Register child for cancellation + timeout tracking
+                        jobManager.registerChild(job.id, child);
+                        // Send start command to child
+                        child.send({
+                            type: 'start',
+                            repoPath: targetPath,
+                            options: { force: !!force, embeddings: !!embeddings },
+                        });
+                    };
+                    forkWorker();
+                }
+                catch (err) {
+                    if (targetPath)
+                        releaseRepoLock(getStoragePath(targetPath));
+                    jobManager.updateJob(job.id, {
+                        status: 'failed',
+                        error: err.message || 'Analysis failed',
+                    });
+                }
+            })();
+            res.status(202).json({ jobId: job.id, status: job.status });
+        }
+        catch (err) {
+            if (err.message?.includes('already in progress')) {
+                res.status(409).json({ error: err.message });
+            }
+            else {
+                res.status(500).json({ error: err.message || 'Failed to start analysis' });
+            }
+        }
+    });
+    // GET /api/analyze/:jobId — poll job status
+    app.get('/api/analyze/:jobId', (req, res) => {
+        const job = jobManager.getJob(req.params.jobId);
+        if (!job) {
+            res.status(404).json({ error: 'Job not found' });
+            return;
+        }
+        res.json({
+            id: job.id,
+            status: job.status,
+            repoUrl: job.repoUrl,
+            repoPath: job.repoPath,
+            repoName: job.repoName,
+            progress: job.progress,
+            error: job.error,
+            startedAt: job.startedAt,
+            completedAt: job.completedAt,
+        });
+    });
+    // GET /api/analyze/:jobId/progress — SSE stream (shared helper)
+    mountSSEProgress(app, '/api/analyze/:jobId/progress', jobManager);
+    // DELETE /api/analyze/:jobId — cancel a running analysis job
+    app.delete('/api/analyze/:jobId', (req, res) => {
+        const job = jobManager.getJob(req.params.jobId);
+        if (!job) {
+            res.status(404).json({ error: 'Job not found' });
+            return;
+        }
+        if (job.status === 'complete' || job.status === 'failed') {
+            res.status(400).json({ error: `Job already ${job.status}` });
+            return;
+        }
+        jobManager.cancelJob(req.params.jobId, 'Cancelled by user');
+        res.json({ id: job.id, status: 'failed', error: 'Cancelled by user' });
+    });
+    // ── Embedding endpoints ────────────────────────────────────────────
+    const embedJobManager = new JobManager();
+    // POST /api/embed — trigger server-side embedding generation
+    app.post('/api/embed', async (req, res) => {
+        try {
+            const entry = await resolveRepo(requestedRepo(req));
+            if (!entry) {
+                res.status(404).json({ error: 'Repository not found' });
+                return;
+            }
+            // Check shared repo lock — prevent concurrent analyze + embed on same repo
+            const repoLockPath = entry.storagePath;
+            const lockErr = acquireRepoLock(repoLockPath);
+            if (lockErr) {
+                res.status(409).json({ error: lockErr });
+                return;
+            }
+            const job = embedJobManager.createJob({ repoPath: entry.storagePath });
+            embedJobManager.updateJob(job.id, {
+                repoName: entry.name,
+                status: 'analyzing',
+                progress: { phase: 'analyzing', percent: 0, message: 'Starting embedding generation...' },
+            });
+            // 30-minute timeout for embedding jobs (same as analyze jobs)
+            const EMBED_TIMEOUT_MS = 30 * 60 * 1000;
+            const embedTimeout = setTimeout(() => {
+                const current = embedJobManager.getJob(job.id);
+                if (current && current.status !== 'complete' && current.status !== 'failed') {
+                    releaseRepoLock(repoLockPath);
+                    embedJobManager.updateJob(job.id, {
+                        status: 'failed',
+                        error: 'Embedding timed out (30 minute limit)',
+                    });
+                }
+            }, EMBED_TIMEOUT_MS);
+            // Run embedding pipeline asynchronously
+            (async () => {
+                try {
+                    const lbugPath = path.join(entry.storagePath, 'lbug');
+                    await withLbugDb(lbugPath, async () => {
+                        const { runEmbeddingPipeline } = await import('../core/embeddings/embedding-pipeline.js');
+                        await runEmbeddingPipeline(executeQuery, executeWithReusedStatement, (p) => {
+                            embedJobManager.updateJob(job.id, {
+                                progress: {
+                                    phase: p.phase === 'ready' ? 'complete' : p.phase === 'error' ? 'failed' : p.phase,
+                                    percent: p.percent,
+                                    message: p.phase === 'loading-model'
+                                        ? 'Loading embedding model...'
+                                        : p.phase === 'embedding'
+                                            ? `Embedding nodes (${p.percent}%)...`
+                                            : p.phase === 'indexing'
+                                                ? 'Creating vector index...'
+                                                : p.phase === 'ready'
+                                                    ? 'Embeddings complete'
+                                                    : `${p.phase} (${p.percent}%)`,
+                                },
+                            });
+                        });
+                    });
+                    clearTimeout(embedTimeout);
+                    releaseRepoLock(repoLockPath);
+                    // Don't overwrite 'failed' if the job was cancelled while the pipeline was running
+                    const current = embedJobManager.getJob(job.id);
+                    if (!current || current.status !== 'failed') {
+                        embedJobManager.updateJob(job.id, { status: 'complete' });
+                    }
+                }
+                catch (err) {
+                    clearTimeout(embedTimeout);
+                    releaseRepoLock(repoLockPath);
+                    const current = embedJobManager.getJob(job.id);
+                    if (!current || current.status !== 'failed') {
+                        embedJobManager.updateJob(job.id, {
+                            status: 'failed',
+                            error: err.message || 'Embedding generation failed',
+                        });
+                    }
+                }
+            })();
+            res.status(202).json({ jobId: job.id, status: 'analyzing' });
+        }
+        catch (err) {
+            if (err.message?.includes('already in progress')) {
+                res.status(409).json({ error: err.message });
+            }
+            else {
+                res.status(500).json({ error: err.message || 'Failed to start embedding generation' });
+            }
+        }
+    });
+    // GET /api/embed/:jobId — poll embedding job status
+    app.get('/api/embed/:jobId', (req, res) => {
+        const job = embedJobManager.getJob(req.params.jobId);
+        if (!job) {
+            res.status(404).json({ error: 'Job not found' });
+            return;
+        }
+        res.json({
+            id: job.id,
+            status: job.status,
+            repoName: job.repoName,
+            progress: job.progress,
+            error: job.error,
+            startedAt: job.startedAt,
+            completedAt: job.completedAt,
+        });
+    });
+    // GET /api/embed/:jobId/progress — SSE stream (shared helper)
+    mountSSEProgress(app, '/api/embed/:jobId/progress', embedJobManager);
+    // DELETE /api/embed/:jobId — cancel embedding job
+    app.delete('/api/embed/:jobId', (req, res) => {
+        const job = embedJobManager.getJob(req.params.jobId);
+        if (!job) {
+            res.status(404).json({ error: 'Job not found' });
+            return;
+        }
+        if (job.status === 'complete' || job.status === 'failed') {
+            res.status(400).json({ error: `Job already ${job.status}` });
+            return;
+        }
+        embedJobManager.cancelJob(req.params.jobId, 'Cancelled by user');
+        res.json({ id: job.id, status: 'failed', error: 'Cancelled by user' });
+    });
     // Global error handler — catch anything the route handlers miss
     app.use((err, _req, res, _next) => {
         console.error('Unhandled error:', err);
         res.status(500).json({ error: 'Internal server error' });
     });
-    const server = app.listen(port, host, () => {
-        console.log(`GitNexus server running on http://${host}:${port}`);
+    // Wrap listen in a promise so errors (EADDRINUSE, EACCES, etc.) propagate
+    // to the caller instead of crashing with an unhandled 'error' event.
+    await new Promise((resolve, reject) => {
+        const server = app.listen(port, host, () => {
+            console.log(`GitNexus server running on http://${host}:${port}`);
+            resolve();
+        });
+        server.on('error', (err) => reject(err));
+        // Graceful shutdown — close Express + LadybugDB cleanly
+        const shutdown = async () => {
+            console.log('\nShutting down...');
+            server.close();
+            jobManager.dispose();
+            embedJobManager.dispose();
+            await cleanupMcp();
+            await closeLbug();
+            await backend.disconnect();
+            process.exit(0);
+        };
+        process.once('SIGINT', shutdown);
+        process.once('SIGTERM', shutdown);
     });
-    // Graceful shutdown — close Express + LadybugDB cleanly
-    const shutdown = async () => {
-        server.close();
-        await cleanupMcp();
-        await closeLbug();
-        await backend.disconnect();
-        process.exit(0);
-    };
-    process.once('SIGINT', shutdown);
-    process.once('SIGTERM', shutdown);
 };