gitnexus 1.2.7 → 1.2.8

package/dist/cli/analyze.js

@@ -8,7 +8,7 @@ import cliProgress from 'cli-progress';
 import { runPipelineFromRepo } from '../core/ingestion/pipeline.js';
 import { initKuzu, loadGraphToKuzu, getKuzuStats, executeQuery, executeWithReusedStatement, closeKuzu, createFTSIndex, loadCachedEmbeddings } from '../core/kuzu/kuzu-adapter.js';
 import { runEmbeddingPipeline } from '../core/embeddings/embedding-pipeline.js';
-import { disposeEmbedder } from '../core/embeddings/embedder.js';
+// disposeEmbedder intentionally not called — ONNX Runtime segfaults on cleanup (see #38)
 import { getStoragePaths, saveMeta, loadMeta, addToGitignore, registerRepo, getGlobalRegistryPath } from '../storage/repo-manager.js';
 import { getCurrentCommit, isGitRepo, getGitRoot } from '../storage/git.js';
 import { generateAIContextFiles } from './ai-context.js';
@@ -70,11 +70,29 @@ export const analyzeCommand = async (inputPath, options) => {
         stopOnComplete: false,
     }, cliProgress.Presets.shades_grey);
     bar.start(100, 0, { phase: 'Initializing...' });
+    // Route all console output through bar.log() so the bar doesn't stamp itself
+    // multiple times when other code writes to stdout/stderr mid-render.
+    const origLog = console.log.bind(console);
+    const origWarn = console.warn.bind(console);
+    const origError = console.error.bind(console);
+    const barLog = (...args) => bar.log(args.map(a => (typeof a === 'string' ? a : String(a))).join(' '));
+    console.log = barLog;
+    console.warn = barLog;
+    console.error = barLog;
+    // Show elapsed seconds for phases that run longer than 3s
+    let lastPhaseLabel = 'Initializing...';
+    let phaseStart = Date.now();
+    const elapsedTimer = setInterval(() => {
+        const elapsed = Math.round((Date.now() - phaseStart) / 1000);
+        if (elapsed >= 3) {
+            bar.update({ phase: `${lastPhaseLabel} (${elapsed}s)` });
+        }
+    }, 1000);
     const t0Global = Date.now();
     // ── Cache embeddings from existing index before rebuild ────────────
     let cachedEmbeddingNodeIds = new Set();
     let cachedEmbeddings = [];
-    if (existingMeta && !options?.force) {
+    if (options?.embeddings && existingMeta && !options?.force) {
         try {
             bar.update(0, { phase: 'Caching embeddings...' });
             await initKuzu(kuzuPath);
@@ -94,10 +112,16 @@ export const analyzeCommand = async (inputPath, options) => {
     const pipelineResult = await runPipelineFromRepo(repoPath, (progress) => {
         const phaseLabel = PHASE_LABELS[progress.phase] || progress.phase;
         const scaled = Math.round(progress.percent * 0.6);
+        if (phaseLabel !== lastPhaseLabel) {
+            lastPhaseLabel = phaseLabel;
+            phaseStart = Date.now();
+        }
         bar.update(scaled, { phase: phaseLabel });
     });
     // ── Phase 2: KuzuDB (60–85%) ──────────────────────────────────────
-    bar.update(60, { phase: 'Loading into KuzuDB...' });
+    lastPhaseLabel = 'Loading into KuzuDB...';
+    phaseStart = Date.now();
+    bar.update(60, { phase: lastPhaseLabel });
     await closeKuzu();
     const kuzuFiles = [kuzuPath, `${kuzuPath}.wal`, `${kuzuPath}.lock`];
     for (const f of kuzuFiles) {
@@ -117,7 +141,9 @@ export const analyzeCommand = async (inputPath, options) => {
     const kuzuTime = ((Date.now() - t0Kuzu) / 1000).toFixed(1);
     const kuzuWarnings = kuzuResult.warnings;
     // ── Phase 3: FTS (85–90%) ─────────────────────────────────────────
-    bar.update(85, { phase: 'Creating search indexes...' });
+    lastPhaseLabel = 'Creating search indexes...';
+    phaseStart = Date.now();
+    bar.update(85, { phase: lastPhaseLabel });
     const t0Fts = Date.now();
     try {
         await createFTSIndex('File', 'file_fts', ['name', 'content']);
@@ -146,22 +172,28 @@ export const analyzeCommand = async (inputPath, options) => {
     // ── Phase 4: Embeddings (90–98%) ──────────────────────────────────
     const stats = await getKuzuStats();
     let embeddingTime = '0.0';
-    let embeddingSkipped = false;
-    let embeddingSkipReason = '';
-    if (options?.skipEmbeddings) {
-        embeddingSkipped = true;
-        embeddingSkipReason = 'skipped (--skip-embeddings)';
-    }
-    else if (stats.nodes > EMBEDDING_NODE_LIMIT) {
-        embeddingSkipped = true;
-        embeddingSkipReason = `skipped (${stats.nodes.toLocaleString()} nodes > ${EMBEDDING_NODE_LIMIT.toLocaleString()} limit)`;
+    let embeddingSkipped = true;
+    let embeddingSkipReason = 'off (use --embeddings to enable)';
+    if (options?.embeddings) {
+        if (stats.nodes > EMBEDDING_NODE_LIMIT) {
+            embeddingSkipReason = `skipped (${stats.nodes.toLocaleString()} nodes > ${EMBEDDING_NODE_LIMIT.toLocaleString()} limit)`;
+        }
+        else {
+            embeddingSkipped = false;
+        }
     }
     if (!embeddingSkipped) {
-        bar.update(90, { phase: 'Loading embedding model...' });
+        lastPhaseLabel = 'Loading embedding model...';
+        phaseStart = Date.now();
+        bar.update(90, { phase: lastPhaseLabel });
         const t0Emb = Date.now();
         await runEmbeddingPipeline(executeQuery, executeWithReusedStatement, (progress) => {
             const scaled = 90 + Math.round((progress.percent / 100) * 8);
             const label = progress.phase === 'loading-model' ? 'Loading embedding model...' : `Embedding ${progress.nodesProcessed || 0}/${progress.totalNodes || '?'}`;
+            if (label !== lastPhaseLabel) {
+                lastPhaseLabel = label;
+                phaseStart = Date.now();
+            }
             bar.update(scaled, { phase: label });
         }, {}, cachedEmbeddingNodeIds.size > 0 ? cachedEmbeddingNodeIds : undefined);
         embeddingTime = ((Date.now() - t0Emb) / 1000).toFixed(1);
@@ -203,8 +235,14 @@ export const analyzeCommand = async (inputPath, options) => {
         processes: pipelineResult.processResult?.stats.totalProcesses,
     });
     await closeKuzu();
-    await disposeEmbedder();
+    // Note: we intentionally do NOT call disposeEmbedder() here.
+    // ONNX Runtime's native cleanup segfaults on macOS and some Linux configs.
+    // Since the process exits immediately after, Node.js reclaims everything.
     const totalTime = ((Date.now() - t0Global) / 1000).toFixed(1);
+    clearInterval(elapsedTimer);
+    console.log = origLog;
+    console.warn = origWarn;
+    console.error = origError;
     bar.update(100, { phase: 'Done' });
     bar.stop();
     // ── Summary ───────────────────────────────────────────────────────
@@ -233,4 +271,10 @@ export const analyzeCommand = async (inputPath, options) => {
         console.log('\n  Tip: Run `gitnexus setup` to configure MCP for your editor.');
     }
     console.log('');
+    // ONNX Runtime registers native atexit hooks that segfault during process
+    // shutdown on macOS (#38) and some Linux configs (#40). Force-exit to
+    // bypass them when embeddings were loaded.
+    if (!embeddingSkipped) {
+        process.exit(0);
+    }
 };

package/dist/cli/index.js

@@ -24,7 +24,7 @@ program
     .command('analyze [path]')
     .description('Index a repository (full analysis)')
     .option('-f, --force', 'Force full re-index even if up to date')
-    .option('--skip-embeddings', 'Skip embedding generation (faster)')
+    .option('--embeddings', 'Enable embedding generation for semantic search (off by default)')
     .action(analyzeCommand);
 program
     .command('serve')

package/dist/core/augmentation/engine.js

@@ -98,11 +98,11 @@ export async function augment(pattern, cwd) {
         for (const result of bm25Results.slice(0, 5)) {
             const escaped = result.filePath.replace(/'/g, "''");
             try {
-                const symbols = await executeQuery(repoId, `
-          MATCH (n) WHERE n.filePath = '${escaped}'
-          AND n.name CONTAINS '${pattern.replace(/'/g, "''").split(/\s+/)[0]}'
-          RETURN n.id AS id, n.name AS name, labels(n)[0] AS type, n.filePath AS filePath
-          LIMIT 3
+                const symbols = await executeQuery(repoId, `
+          MATCH (n) WHERE n.filePath = '${escaped}'
+          AND n.name CONTAINS '${pattern.replace(/'/g, "''").split(/\s+/)[0]}'
+          RETURN n.id AS id, n.name AS name, labels(n)[0] AS type, n.filePath AS filePath
+          LIMIT 3
         `);
                 for (const sym of symbols) {
                     symbolMatches.push({
@@ -130,10 +130,10 @@ export async function augment(pattern, cwd) {
             // Callers
             let callers = [];
             try {
-                const rows = await executeQuery(repoId, `
-          MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(n {id: '${escaped}'})
-          RETURN caller.name AS name
-          LIMIT 3
+                const rows = await executeQuery(repoId, `
+          MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(n {id: '${escaped}'})
+          RETURN caller.name AS name
+          LIMIT 3
         `);
                 callers = rows.map((r) => r.name || r[0]).filter(Boolean);
             }
@@ -141,10 +141,10 @@ export async function augment(pattern, cwd) {
             // Callees
             let callees = [];
             try {
-                const rows = await executeQuery(repoId, `
-          MATCH (n {id: '${escaped}'})-[:CodeRelation {type: 'CALLS'}]->(callee)
-          RETURN callee.name AS name
-          LIMIT 3
+                const rows = await executeQuery(repoId, `
+          MATCH (n {id: '${escaped}'})-[:CodeRelation {type: 'CALLS'}]->(callee)
+          RETURN callee.name AS name
+          LIMIT 3
         `);
                 callees = rows.map((r) => r.name || r[0]).filter(Boolean);
             }
@@ -152,9 +152,9 @@ export async function augment(pattern, cwd) {
             // Processes
             let processes = [];
             try {
-                const rows = await executeQuery(repoId, `
-          MATCH (n {id: '${escaped}'})-[r:CodeRelation {type: 'STEP_IN_PROCESS'}]->(p:Process)
-          RETURN p.heuristicLabel AS label, r.step AS step, p.stepCount AS stepCount
+                const rows = await executeQuery(repoId, `
+          MATCH (n {id: '${escaped}'})-[r:CodeRelation {type: 'STEP_IN_PROCESS'}]->(p:Process)
+          RETURN p.heuristicLabel AS label, r.step AS step, p.stepCount AS stepCount
         `);
                 processes = rows.map((r) => {
                     const label = r.label || r[0];
@@ -167,10 +167,10 @@ export async function augment(pattern, cwd) {
             // Cluster cohesion (internal ranking signal)
             let cohesion = 0;
             try {
-                const rows = await executeQuery(repoId, `
-          MATCH (n {id: '${escaped}'})-[:CodeRelation {type: 'MEMBER_OF'}]->(c:Community)
-          RETURN c.cohesion AS cohesion
-          LIMIT 1
+                const rows = await executeQuery(repoId, `
+          MATCH (n {id: '${escaped}'})-[:CodeRelation {type: 'MEMBER_OF'}]->(c:Community)
+          RETURN c.cohesion AS cohesion
+          LIMIT 1
         `);
                 if (rows.length > 0) {
                     cohesion = (rows[0].cohesion ?? rows[0][0]) || 0;

package/dist/core/embeddings/embedder.js

@@ -89,6 +89,7 @@ export const initEmbedder = async (onProgress, config = {}, forceDevice) => {
                         device: device,
                         dtype: 'fp32',
                         progress_callback: progressCallback,
+                        session_options: { logSeverityLevel: 3 },
                     });
                     currentDevice = device;
                     if (isDev) {

package/dist/core/embeddings/embedding-pipeline.js

@@ -24,19 +24,19 @@ const queryEmbeddableNodes = async (executeQuery) => {
             let query;
             if (label === 'File') {
                 // File nodes don't have startLine/endLine
-                query = `
-          MATCH (n:File)
-          RETURN n.id AS id, n.name AS name, 'File' AS label, 
-                 n.filePath AS filePath, n.content AS content
+                query = `
+          MATCH (n:File)
+          RETURN n.id AS id, n.name AS name, 'File' AS label, 
+                 n.filePath AS filePath, n.content AS content
         `;
             }
             else {
                 // Code elements have startLine/endLine
-                query = `
-          MATCH (n:${label})
-          RETURN n.id AS id, n.name AS name, '${label}' AS label, 
-                 n.filePath AS filePath, n.content AS content,
-                 n.startLine AS startLine, n.endLine AS endLine
+                query = `
+          MATCH (n:${label})
+          RETURN n.id AS id, n.name AS name, '${label}' AS label, 
+                 n.filePath AS filePath, n.content AS content,
+                 n.startLine AS startLine, n.endLine AS endLine
         `;
             }
             const rows = await executeQuery(query);
@@ -77,8 +77,8 @@ const batchInsertEmbeddings = async (executeWithReusedStatement, updates) => {
  * Now indexes the separate CodeEmbedding table
  */
 const createVectorIndex = async (executeQuery) => {
-    const cypher = `
-    CALL CREATE_VECTOR_INDEX('CodeEmbedding', 'code_embedding_idx', 'embedding', metric := 'cosine')
+    const cypher = `
+    CALL CREATE_VECTOR_INDEX('CodeEmbedding', 'code_embedding_idx', 'embedding', metric := 'cosine')
   `;
     try {
         await executeQuery(cypher);
@@ -240,14 +240,14 @@ export const semanticSearch = async (executeQuery, query, k = 10, maxDistance =
     const queryVec = embeddingToArray(queryEmbedding);
     const queryVecStr = `[${queryVec.join(',')}]`;
     // Query the vector index on CodeEmbedding to get nodeIds and distances
-    const vectorQuery = `
-    CALL QUERY_VECTOR_INDEX('CodeEmbedding', 'code_embedding_idx', 
-      CAST(${queryVecStr} AS FLOAT[384]), ${k})
-    YIELD node AS emb, distance
-    WITH emb, distance
-    WHERE distance < ${maxDistance}
-    RETURN emb.nodeId AS nodeId, distance
-    ORDER BY distance
+    const vectorQuery = `
+    CALL QUERY_VECTOR_INDEX('CodeEmbedding', 'code_embedding_idx', 
+      CAST(${queryVecStr} AS FLOAT[384]), ${k})
+    YIELD node AS emb, distance
+    WITH emb, distance
+    WHERE distance < ${maxDistance}
+    RETURN emb.nodeId AS nodeId, distance
+    ORDER BY distance
   `;
     const embResults = await executeQuery(vectorQuery);
     if (embResults.length === 0) {
@@ -266,16 +266,16 @@ export const semanticSearch = async (executeQuery, query, k = 10, maxDistance =
         try {
             let nodeQuery;
             if (label === 'File') {
-                nodeQuery = `
-          MATCH (n:File {id: '${nodeId.replace(/'/g, "''")}'}) 
-          RETURN n.name AS name, n.filePath AS filePath
+                nodeQuery = `
+          MATCH (n:File {id: '${nodeId.replace(/'/g, "''")}'}) 
+          RETURN n.name AS name, n.filePath AS filePath
         `;
             }
             else {
-                nodeQuery = `
-          MATCH (n:${label} {id: '${nodeId.replace(/'/g, "''")}'}) 
-          RETURN n.name AS name, n.filePath AS filePath, 
-                 n.startLine AS startLine, n.endLine AS endLine
+                nodeQuery = `
+          MATCH (n:${label} {id: '${nodeId.replace(/'/g, "''")}'}) 
+          RETURN n.name AS name, n.filePath AS filePath, 
+                 n.startLine AS startLine, n.endLine AS endLine
         `;
             }
             const nodeRows = await executeQuery(nodeQuery);

package/dist/core/ingestion/cluster-enricher.js

@@ -13,12 +13,12 @@ const buildEnrichmentPrompt = (members, heuristicLabel) => {
     const memberList = limitedMembers
         .map(m => `${m.name} (${m.type})`)
         .join(', ');
-    return `Analyze this code cluster and provide a semantic name and short description.
-
-Heuristic: "${heuristicLabel}"
-Members: ${memberList}${members.length > 20 ? ` (+${members.length - 20} more)` : ''}
-
-Reply with JSON only:
+    return `Analyze this code cluster and provide a semantic name and short description.
+
+Heuristic: "${heuristicLabel}"
+Members: ${memberList}${members.length > 20 ? ` (+${members.length - 20} more)` : ''}
+
+Reply with JSON only:
 {"name": "2-4 word semantic name", "description": "One sentence describing purpose"}`;
 };
 // ============================================================================
@@ -115,18 +115,18 @@ export const enrichClustersBatch = async (communities, memberMap, llmClient, bat
             const memberList = limitedMembers
                 .map(m => `${m.name} (${m.type})`)
                 .join(', ');
-            return `Cluster ${idx + 1} (id: ${community.id}):
-Heuristic: "${community.heuristicLabel}"
+            return `Cluster ${idx + 1} (id: ${community.id}):
+Heuristic: "${community.heuristicLabel}"
 Members: ${memberList}`;
         }).join('\n\n');
-        const prompt = `Analyze these code clusters and generate semantic names, keywords, and descriptions.
-
-${batchPrompt}
-
-Output JSON array:
-[
-  {"id": "comm_X", "name": "...", "keywords": [...], "description": "..."},
-  ...
+        const prompt = `Analyze these code clusters and generate semantic names, keywords, and descriptions.
+
+${batchPrompt}
+
+Output JSON array:
+[
+  {"id": "comm_X", "name": "...", "keywords": [...], "description": "..."},
+  ...
 ]`;
         try {
             const response = await llmClient.generate(prompt);