gitnexus 1.1.3 → 1.1.5

package/dist/cli/ai-context.d.ts

@@ -10,6 +10,7 @@ interface RepoStats {
     nodes?: number;
     edges?: number;
     communities?: number;
+    clusters?: number;
     processes?: number;
 }
 /**

package/dist/cli/ai-context.js

@@ -17,6 +17,7 @@ const GITNEXUS_END_MARKER = '<!-- gitnexus:end -->';
  * Generate the full GitNexus context content (resources-first approach)
  */
 function generateGitNexusContent(projectName, stats) {
+    const clusterCount = stats.clusters || stats.communities || 0;
     return `${GITNEXUS_START_MARKER}
 # GitNexus MCP
 
@@ -29,9 +30,11 @@ This project is indexed as **${projectName}** by GitNexus, providing AI agents w
 | Files | ${stats.files || 0} |
 | Symbols | ${stats.nodes || 0} |
 | Relationships | ${stats.edges || 0} |
-| Communities | ${stats.communities || 0} |
+| Clusters | ${clusterCount} |
 | Processes | ${stats.processes || 0} |
 
+> **Staleness:** If the index is out of date, run \`gitnexus_analyze({repo: "${projectName}"})\` to refresh. The \`gitnexus://repo/${projectName}/context\` resource will warn you when the index is stale.
+
 ## Quick Start
 
 \`\`\`
@@ -63,6 +66,7 @@ This project is indexed as **${projectName}** by GitNexus, providing AI agents w
 | \`explore\` | Deep dive on symbol/cluster/process | Detailed investigation |
 | \`impact\` | Blast radius analysis | Before making changes |
 | \`cypher\` | Raw graph queries | Complex analysis |
+| \`analyze\` | Re-index repository | When index is stale or after major code changes |
 
 > **Multi-repo:** When multiple repos are indexed, pass \`repo: "${projectName}"\` to target this project.
 
@@ -71,17 +75,17 @@ This project is indexed as **${projectName}** by GitNexus, providing AI agents w
 ### Exploring the Codebase
 \`\`\`
 READ gitnexus://repos                            → Discover repos
-READ gitnexus://repo/${projectName}/context       → Stats and overview
-READ gitnexus://repo/${projectName}/clusters      → Find relevant cluster
-READ gitnexus://repo/${projectName}/cluster/Auth  → Explore Auth cluster
-gitnexus_explore({name: "validateUser", type: "symbol", repo: "${projectName}"})
+READ gitnexus://repo/${projectName}/context       → Stats and overview (check for staleness)
+READ gitnexus://repo/${projectName}/clusters      → Find relevant cluster by name
+READ gitnexus://repo/${projectName}/cluster/{name} → See members of that cluster
+gitnexus_explore({name: "<symbol_name>", type: "symbol", repo: "${projectName}"})
 \`\`\`
 
 ### Planning a Change
 \`\`\`
-gitnexus_impact({target: "UserService", direction: "upstream", repo: "${projectName}"})
-READ gitnexus://repo/${projectName}/processes     → Check affected flows
-gitnexus_explore({name: "LoginFlow", type: "process", repo: "${projectName}"})
+gitnexus_search({query: "<what you want to change>", repo: "${projectName}"})
+gitnexus_impact({target: "<symbol_name>", direction: "upstream", repo: "${projectName}"})
+READ gitnexus://repo/${projectName}/processes     → Check affected execution flows
 \`\`\`
 
 ## Graph Schema

package/dist/cli/analyze.js

@@ -70,6 +70,7 @@ export const analyzeCommand = async (inputPath, options) => {
         await createFTSIndex('Function', 'function_fts', ['name', 'content']);
         await createFTSIndex('Class', 'class_fts', ['name', 'content']);
         await createFTSIndex('Method', 'method_fts', ['name', 'content']);
+        await createFTSIndex('Interface', 'interface_fts', ['name', 'content']);
     }
     catch (e) {
         // FTS index creation may fail if tables are empty (no data for that type)
@@ -103,11 +104,23 @@ export const analyzeCommand = async (inputPath, options) => {
     await addToGitignore(repoPath);
     // Generate AI context files
     const projectName = path.basename(repoPath);
+    // Compute aggregated cluster count (grouped by heuristicLabel, >=5 symbols)
+    // This matches the aggregation logic in local-backend.ts for tool output consistency.
+    let aggregatedClusterCount = 0;
+    if (pipelineResult.communityResult?.communities) {
+        const groups = new Map();
+        for (const c of pipelineResult.communityResult.communities) {
+            const label = c.heuristicLabel || c.label || 'Unknown';
+            groups.set(label, (groups.get(label) || 0) + c.symbolCount);
+        }
+        aggregatedClusterCount = Array.from(groups.values()).filter(count => count >= 5).length;
+    }
     const aiContext = await generateAIContextFiles(repoPath, storagePath, projectName, {
         files: pipelineResult.fileContents.size,
         nodes: stats.nodes,
         edges: stats.edges,
         communities: pipelineResult.communityResult?.stats.totalCommunities,
+        clusters: aggregatedClusterCount,
         processes: pipelineResult.processResult?.stats.totalProcesses,
     });
     // Close database

package/dist/cli/mcp.js

@@ -8,35 +8,7 @@
 import { startMCPServer } from '../mcp/server.js';
 import { LocalBackend } from '../mcp/local/local-backend.js';
 import { listRegisteredRepos } from '../storage/repo-manager.js';
-/**
- * Protect MCP stdio protocol from library stdout pollution.
- *
- * Libraries like @huggingface/transformers, ONNX Runtime, and kuzu may
- * write progress bars, warnings, or init messages to stdout.
- * MCP uses stdout exclusively for JSON-RPC — any foreign output corrupts
- * the protocol and causes Cursor to kill the connection.
- *
- * This intercept redirects all non-JSON-RPC stdout writes to stderr.
- */
-function installStdoutGuard() {
-    const origWrite = process.stdout.write.bind(process.stdout);
-    process.stdout.write = ((chunk, encodingOrCb, cb) => {
-        const text = typeof chunk === 'string'
-            ? chunk
-            : Buffer.isBuffer(chunk)
-                ? chunk.toString('utf-8')
-                : '';
-        // MCP SDK messages always contain "jsonrpc" — let them through
-        if (text.includes('"jsonrpc"')) {
-            return origWrite(chunk, encodingOrCb, cb);
-        }
-        // Redirect everything else to stderr (library noise)
-        return process.stderr.write(chunk, encodingOrCb, cb);
-    });
-}
 export const mcpCommand = async () => {
-    // Must be first — before any library can pollute stdout
-    installStdoutGuard();
     // Load all registered repos
     const entries = await listRegisteredRepos({ validate: true });
     if (entries.length === 0) {

package/dist/core/ingestion/process-processor.js

@@ -121,10 +121,16 @@ export const processProcesses = async (knowledgeGraph, memberships, onProgress,
         },
     };
 };
+/**
+ * Minimum edge confidence for process tracing.
+ * Filters out ambiguous fuzzy-global matches (0.3) that cause
+ * traces to jump across unrelated code areas.
+ */
+const MIN_TRACE_CONFIDENCE = 0.5;
 const buildCallsGraph = (graph) => {
     const adj = new Map();
     graph.relationships.forEach(rel => {
-        if (rel.type === 'CALLS') {
+        if (rel.type === 'CALLS' && rel.confidence >= MIN_TRACE_CONFIDENCE) {
             if (!adj.has(rel.sourceId)) {
                 adj.set(rel.sourceId, []);
             }
@@ -136,7 +142,7 @@ const buildCallsGraph = (graph) => {
 const buildReverseCallsGraph = (graph) => {
     const adj = new Map();
     graph.relationships.forEach(rel => {
-        if (rel.type === 'CALLS') {
+        if (rel.type === 'CALLS' && rel.confidence >= MIN_TRACE_CONFIDENCE) {
             if (!adj.has(rel.targetId)) {
                 adj.set(rel.targetId, []);
             }

package/dist/core/search/bm25-index.js

@@ -44,25 +44,27 @@ async function queryFTSViaExecutor(executor, tableName, indexName, query, limit)
  * @returns Ranked search results from FTS indexes
  */
 export const searchFTSFromKuzu = async (query, limit = 20, repoId) => {
-    let fileResults, functionResults, classResults, methodResults;
+    let fileResults, functionResults, classResults, methodResults, interfaceResults;
     if (repoId) {
         // Use MCP connection pool via dynamic import
         const { executeQuery } = await import('../../mcp/core/kuzu-adapter.js');
         const executor = (cypher) => executeQuery(repoId, cypher);
-        [fileResults, functionResults, classResults, methodResults] = await Promise.all([
+        [fileResults, functionResults, classResults, methodResults, interfaceResults] = await Promise.all([
             queryFTSViaExecutor(executor, 'File', 'file_fts', query, limit),
             queryFTSViaExecutor(executor, 'Function', 'function_fts', query, limit),
             queryFTSViaExecutor(executor, 'Class', 'class_fts', query, limit),
             queryFTSViaExecutor(executor, 'Method', 'method_fts', query, limit),
+            queryFTSViaExecutor(executor, 'Interface', 'interface_fts', query, limit),
         ]);
     }
     else {
         // Use core kuzu adapter (CLI / pipeline context)
-        [fileResults, functionResults, classResults, methodResults] = await Promise.all([
+        [fileResults, functionResults, classResults, methodResults, interfaceResults] = await Promise.all([
             queryFTS('File', 'file_fts', query, limit, false).catch(() => []),
             queryFTS('Function', 'function_fts', query, limit, false).catch(() => []),
             queryFTS('Class', 'class_fts', query, limit, false).catch(() => []),
             queryFTS('Method', 'method_fts', query, limit, false).catch(() => []),
+            queryFTS('Interface', 'interface_fts', query, limit, false).catch(() => []),
         ]);
     }
     // Merge results by filePath, summing scores for same file
@@ -82,6 +84,7 @@ export const searchFTSFromKuzu = async (query, limit = 20, repoId) => {
     addResults(functionResults);
     addResults(classResults);
     addResults(methodResults);
+    addResults(interfaceResults);
     // Sort by score descending and add rank
     const sorted = Array.from(merged.values())
         .sort((a, b) => b.score - a.score)

package/dist/mcp/core/embedder.js

@@ -31,10 +31,19 @@ export const initEmbedder = async () => {
             const devicesToTry = ['webgpu', 'cpu'];
             for (const device of devicesToTry) {
                 try {
-                    embedderInstance = await pipeline('feature-extraction', MODEL_ID, {
-                        device: device,
-                        dtype: 'fp32',
-                    });
+                    // Silence stdout during model load — ONNX Runtime and transformers.js
+                    // may write progress/init messages to stdout which corrupts MCP stdio protocol.
+                    const origWrite = process.stdout.write;
+                    process.stdout.write = (() => true);
+                    try {
+                        embedderInstance = await pipeline('feature-extraction', MODEL_ID, {
+                            device: device,
+                            dtype: 'fp32',
+                        });
+                    }
+                    finally {
+                        process.stdout.write = origWrite;
+                    }
                     console.error(`GitNexus: Embedding model loaded (${device})`);
                     return embedderInstance;
                 }

package/dist/mcp/core/kuzu-adapter.js

@@ -82,8 +82,19 @@ export const initKuzu = async (repoId, dbPath) => {
         throw new Error(`KuzuDB not found at ${dbPath}. Run: gitnexus analyze`);
     }
     evictLRU();
-    const db = new kuzu.Database(dbPath);
-    const conn = new kuzu.Connection(db);
+    // Silence stdout during KuzuDB init — native module may write to stdout
+    // which corrupts the MCP stdio protocol.
+    const origWrite = process.stdout.write;
+    process.stdout.write = (() => true);
+    let db;
+    let conn;
+    try {
+        db = new kuzu.Database(dbPath);
+        conn = new kuzu.Connection(db);
+    }
+    finally {
+        process.stdout.write = origWrite;
+    }
     pool.set(repoId, { db, conn, lastUsed: Date.now(), dbPath });
     ensureIdleTimer();
 };

package/dist/mcp/local/local-backend.js

@@ -123,7 +123,8 @@ export class LocalBackend {
     }
     // ─── Lazy KuzuDB Init ────────────────────────────────────────────
     async ensureInitialized(repoId) {
-        if (this.initializedRepos.has(repoId))
+        // Always check the actual pool — the idle timer may have evicted the connection
+        if (this.initializedRepos.has(repoId) && isKuzuReady(repoId))
             return;
         const handle = this.repos.get(repoId);
         if (!handle)
@@ -192,11 +193,13 @@ export class LocalBackend {
             this.semanticSearch(repo, query, limit * 2),
         ]);
         // Merge and deduplicate results using reciprocal rank fusion
+        // Key by nodeId (symbol-level) so semantic precision is preserved.
+        // Fall back to filePath for File-level results that lack a nodeId.
         const scoreMap = new Map();
         // BM25 results
         for (let i = 0; i < bm25Results.length; i++) {
             const result = bm25Results[i];
-            const key = result.filePath;
+            const key = result.nodeId || result.filePath;
             const rrfScore = 1 / (60 + i);
             const existing = scoreMap.get(key);
             if (existing) {
@@ -210,7 +213,7 @@ export class LocalBackend {
         // Semantic results
         for (let i = 0; i < semanticResults.length; i++) {
             const result = semanticResults[i];
-            const key = result.filePath;
+            const key = result.nodeId || result.filePath;
             const rrfScore = 1 / (60 + i);
             const existing = scoreMap.get(key);
             if (existing) {
@@ -282,11 +285,11 @@ export class LocalBackend {
         const bm25Results = await searchFTSFromKuzu(query, limit, repo.id);
         const results = [];
         for (const bm25Result of bm25Results) {
-            const fileName = bm25Result.filePath.split('/').pop() || bm25Result.filePath;
+            const fullPath = bm25Result.filePath;
             try {
                 const symbolQuery = `
           MATCH (n) 
-          WHERE n.filePath CONTAINS '${fileName.replace(/'/g, "''")}'
+          WHERE n.filePath = '${fullPath.replace(/'/g, "''")}'
           RETURN n.id AS id, n.name AS name, labels(n)[0] AS type, n.filePath AS filePath, n.startLine AS startLine, n.endLine AS endLine
           LIMIT 3
         `;
@@ -305,6 +308,7 @@ export class LocalBackend {
                     }
                 }
                 else {
+                    const fileName = fullPath.split('/').pop() || fullPath;
                     results.push({
                         name: fileName,
                         type: 'File',
@@ -314,6 +318,7 @@ export class LocalBackend {
                 }
             }
             catch {
+                const fileName = fullPath.split('/').pop() || fullPath;
                 results.push({
                     name: fileName,
                     type: 'File',

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gitnexus",
-  "version": "1.1.3",
+  "version": "1.1.5",
   "description": "Graph-powered code intelligence for AI agents. Index any codebase, query via MCP or CLI.",
   "author": "Abhigyan Patwari",
   "license": "PolyForm-Noncommercial-1.0.0",