agentic-qe 3.6.3 → 3.6.4

package/v3/dist/init/phases/06-code-intelligence.js

@@ -6,10 +6,41 @@
  * so QE agents can use it later to reduce token consumption via
  * semantic code search instead of full file reads.
  */
-import { existsSync } from 'fs';
+import { existsSync, statSync } from 'fs';
 import { join } from 'path';
 import { BasePhase, } from './phase-interface.js';
 import { createMemoryBackend } from '../../kernel/memory-factory.js';
+/** Patterns to exclude from code intelligence scanning */
+const SCAN_IGNORE_PATTERNS = [
+    '**/node_modules/**',
+    '**/dist/**',
+    '**/build/**',
+    '**/out/**',
+    '**/coverage/**',
+    '**/.agentic-qe/**',
+    '**/.git/**',
+    '**/.next/**',
+    '**/.nuxt/**',
+    '**/.output/**',
+    '**/__pycache__/**',
+    '**/.pytest_cache/**',
+    '**/target/**',
+    '**/vendor/**',
+    '**/.venv/**',
+    '**/venv/**',
+    '**/.tox/**',
+    '**/*.min.js',
+    '**/*.min.css',
+    '**/*.bundle.js',
+    '**/*.map',
+    '**/package-lock.json',
+    '**/yarn.lock',
+    '**/pnpm-lock.yaml',
+    '**/Pipfile.lock',
+    '**/poetry.lock',
+    '**/.env',
+    '**/.env.*',
+];
 /**
  * Code Intelligence phase - builds knowledge graph
  */
@@ -21,16 +52,26 @@ export class CodeIntelligencePhase extends BasePhase {
     requiresPhases = ['database'];
     async run(context) {
         const { projectRoot } = context;
-        // Check for existing index
         const hasIndex = await this.checkCodeIntelligenceIndex(projectRoot);
-        if (hasIndex) {
+        if (!hasIndex) {
+            context.services.log('  Building knowledge graph...');
+            return await this.runCodeIntelligenceScan(projectRoot, context, false);
+        }
+        // Delta scan: check for files modified since last index
+        const lastIndexedAt = await this.getLastIndexedAt(projectRoot);
+        if (!lastIndexedAt) {
             const entryCount = await this.getKGEntryCount(projectRoot);
             context.services.log(`  Using existing index (${entryCount} entries)`);
             return { status: 'existing', entries: entryCount };
         }
-        // Run full scan
-        context.services.log('  Building knowledge graph...');
-        return await this.runCodeIntelligenceScan(projectRoot, context);
+        const changedFiles = await this.findChangedFiles(projectRoot, lastIndexedAt);
+        if (changedFiles.length === 0) {
+            const entryCount = await this.getKGEntryCount(projectRoot);
+            context.services.log(`  Index up to date (${entryCount} entries)`);
+            return { status: 'existing', entries: entryCount };
+        }
+        context.services.log(`  Delta scan: ${changedFiles.length} files changed since last index...`);
+        return await this.runCodeIntelligenceScan(projectRoot, context, true, changedFiles);
     }
     /**
      * Check if code intelligence index exists
@@ -83,12 +124,9 @@ export class CodeIntelligencePhase extends BasePhase {
      * - Test target discovery (what tests cover what code)
      * - Token reduction (search KG instead of reading entire files)
      */
-    async runCodeIntelligenceScan(projectRoot, context) {
+    async runCodeIntelligenceScan(projectRoot, context, incremental, changedFiles) {
         try {
-            // Import knowledge graph service
             const { KnowledgeGraphService } = await import('../../domains/code-intelligence/services/knowledge-graph.js');
-            // FIXED: Use SQLite backend for PERSISTENCE instead of InMemoryBackend
-            // This ensures KG data survives init and is available to QE agents
             const dbPath = join(projectRoot, '.agentic-qe', 'memory.db');
             const memoryConfig = {
                 type: 'sqlite',
@@ -102,27 +140,31 @@ export class CodeIntelligencePhase extends BasePhase {
                 namespace: 'code-intelligence:kg',
                 enableVectorEmbeddings: true,
             });
-            // Find source files
-            const glob = await import('fast-glob');
-            const files = await glob.default([
-                '**/*.ts', '**/*.tsx', '**/*.js', '**/*.jsx', '**/*.py'
-            ], {
-                cwd: projectRoot,
-                ignore: ['**/node_modules/**', '**/dist/**', '**/coverage/**', '**/.agentic-qe/**'],
-            });
-            // Index files - this now persists to SQLite
+            let filesToIndex;
+            if (changedFiles) {
+                filesToIndex = changedFiles;
+            }
+            else {
+                const glob = await import('fast-glob');
+                const files = await glob.default([
+                    '**/*.ts', '**/*.tsx', '**/*.js', '**/*.jsx', '**/*.py'
+                ], {
+                    cwd: projectRoot,
+                    ignore: SCAN_IGNORE_PATTERNS,
+                });
+                filesToIndex = files.map(f => join(projectRoot, f));
+            }
             const result = await kgService.index({
-                paths: files.map(f => join(projectRoot, f)),
-                incremental: false,
+                paths: filesToIndex,
+                incremental,
                 includeTests: true,
             });
-            // Clear caches but keep persisted data
             kgService.destroy();
-            // Dispose memory backend to flush writes
             await memory.dispose();
             if (result.success) {
                 const entries = result.value.nodesCreated + result.value.edgesCreated;
-                context.services.log(`  Indexed ${entries} entries to ${dbPath}`);
+                const label = incremental ? 'Delta indexed' : 'Indexed';
+                context.services.log(`  ${label} ${entries} entries to ${dbPath}`);
                 return { status: 'indexed', entries };
             }
             return { status: 'error', entries: 0 };
@@ -132,6 +174,58 @@ export class CodeIntelligencePhase extends BasePhase {
             return { status: 'skipped', entries: 0 };
         }
     }
+    /**
+     * Read the indexedAt timestamp from KG metadata
+     */
+    async getLastIndexedAt(projectRoot) {
+        const dbPath = join(projectRoot, '.agentic-qe', 'memory.db');
+        try {
+            const Database = (await import('better-sqlite3')).default;
+            const db = new Database(dbPath);
+            const row = db.prepare(`
+        SELECT value FROM kv_store
+        WHERE namespace = 'code-intelligence:kg'
+          AND key = 'metadata:index'
+      `).get();
+            db.close();
+            if (!row)
+                return null;
+            const metadata = JSON.parse(row.value);
+            if (!metadata.indexedAt)
+                return null;
+            const date = new Date(metadata.indexedAt);
+            return isNaN(date.getTime()) ? null : date;
+        }
+        catch {
+            return null;
+        }
+    }
+    /**
+     * Find files modified since the given date
+     */
+    async findChangedFiles(projectRoot, since) {
+        const glob = await import('fast-glob');
+        const files = await glob.default([
+            '**/*.ts', '**/*.tsx', '**/*.js', '**/*.jsx', '**/*.py'
+        ], {
+            cwd: projectRoot,
+            ignore: SCAN_IGNORE_PATTERNS,
+        });
+        const sinceMs = since.getTime();
+        const changed = [];
+        for (const file of files) {
+            const fullPath = join(projectRoot, file);
+            try {
+                if (statSync(fullPath).mtimeMs > sinceMs) {
+                    changed.push(fullPath);
+                }
+            }
+            catch {
+                // File may have been deleted between glob and stat
+            }
+        }
+        return changed;
+    }
 }
 // Instance exported from index.ts
 //# sourceMappingURL=06-code-intelligence.js.map

package/v3/dist/init/phases/06-code-intelligence.js.map

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package/v3/dist/kernel/unified-memory-migration.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"unified-memory-migration.d.ts","sourceRoot":"","sources":["../../src/kernel/unified-memory-migration.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAOH,MAAM,WAAW,eAAe;IAC9B,OAAO,EAAE,OAAO,CAAC;IACjB,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,eAAe,EAAE,MAAM,EAAE,CAAC;IAC1B,YAAY,EAAE,MAAM,CAAC;IACrB,MAAM,EAAE,MAAM,EAAE,CAAC;CAClB;AAED,MAAM,WAAW,gBAAgB;IAC/B,mCAAmC;IACnC,OAAO,EAAE,MAAM,CAAC;IAChB,sCAAsC;IACtC,aAAa,EAAE,OAAO,CAAC;IACvB,qDAAqD;IACrD,0BAA0B,EAAE,OAAO,CAAC;IACpC,yDAAyD;IACzD,MAAM,EAAE,OAAO,CAAC;CACjB;AASD;;GAEG;AACH,wBAAsB,sBAAsB,CAC1C,OAAO,CAAC,EAAE,OAAO,CAAC,gBAAgB,CAAC,GAClC,OAAO,CAAC,eAAe,CAAC,CA2N1B;AAED;;GAEG;AACH,wBAAgB,eAAe,CAAC,OAAO,GAAE,MAAsB,GAAG,OAAO,CAGxE;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,OAAO,GAAE,MAAsB,GAAG;IACnE,cAAc,EAAE,OAAO,CAAC;IACxB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;IACf,YAAY,EAAE,OAAO,CAAC;CACvB,CAaA"}

package/v3/dist/kernel/unified-memory-migration.js

@@ -10,6 +10,7 @@
 import Database from 'better-sqlite3';
 import * as fs from 'fs';
 import * as path from 'path';
+import { validateTableName } from '../shared/sql-safety.js';
 const DEFAULT_OPTIONS = {
     baseDir: '.agentic-qe',
     createBackups: true,
@@ -95,7 +96,7 @@ export async function migrateToUnifiedMemory(options) {
                     continue;
                 }
                 // Count rows
-                const countRow = sourceDb.prepare(`SELECT COUNT(*) as count FROM ${tableName}`).get();
+                const countRow = sourceDb.prepare(`SELECT COUNT(*) as count FROM ${validateTableName(tableName)}`).get();
                 const rowCount = countRow.count;
                 if (rowCount === 0) {
                     continue;
@@ -112,12 +113,12 @@ export async function migrateToUnifiedMemory(options) {
         `).get(tableName);
                 targetDb.exec(schemaRow.sql);
                 // Copy data
-                const rows = sourceDb.prepare(`SELECT * FROM ${tableName}`).all();
+                const rows = sourceDb.prepare(`SELECT * FROM ${validateTableName(tableName)}`).all();
                 if (rows.length > 0) {
                     const columns = Object.keys(rows[0]);
                     const placeholders = columns.map(() => '?').join(', ');
                     const insertStmt = targetDb.prepare(`
-            INSERT OR REPLACE INTO ${tableName} (${columns.join(', ')})
+            INSERT OR REPLACE INTO ${validateTableName(tableName)} (${columns.join(', ')})
             VALUES (${placeholders})
           `);
                     const insertMany = targetDb.transaction((items) => {

package/v3/dist/kernel/unified-memory-migration.js.map

@@ -1 +1 @@
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package/v3/dist/kernel/unified-memory.d.ts

@@ -17,6 +17,7 @@
  * - No confusion about where data lives
  */
 import { type Database as DatabaseType, type Statement } from 'better-sqlite3';
+export { validateTableName, ALLOWED_TABLE_NAMES } from '../shared/sql-safety.js';
 import { type CRDTStore, type CRDTStoreState, type CRDTStoreDelta } from '../memory/crdt/index.js';
 /**
  * Find the project root by walking up the directory tree.
@@ -172,7 +173,8 @@ export declare class UnifiedMemoryManager {
      */
     vectorDelete(id: string): Promise<boolean>;
     /**
-     * Search for similar vectors
+     * Search for similar vectors.
+     * Uses batch SQL query instead of N+1 individual queries for metadata enrichment.
      */
     vectorSearch(query: number[], k?: number, namespace?: string): Promise<Array<{
         id: string;

package/v3/dist/kernel/unified-memory.d.ts.map

@@ -1 +1 @@
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package/v3/dist/kernel/unified-memory.js

@@ -22,6 +22,12 @@ import * as path from 'path';
 import { cosineSimilarity } from '../shared/utils/vector-math.js';
 import { HYPERGRAPH_SCHEMA } from '../migrations/20260120_add_hypergraph_tables.js';
 import { MEMORY_CONSTANTS, HNSW_CONSTANTS } from './constants.js';
+// ============================================================================
+// SQL Table Name Allowlist (defense-in-depth against SQL injection)
+// ============================================================================
+// Re-export from shared module for backward compatibility
+export { validateTableName, ALLOWED_TABLE_NAMES } from '../shared/sql-safety.js';
+import { validateTableName } from '../shared/sql-safety.js';
 // CRDT imports for distributed state synchronization
 import { createCRDTStore, } from '../memory/crdt/index.js';
 // ============================================================================
@@ -591,6 +597,74 @@ const SONA_PATTERNS_SCHEMA = `
   CREATE INDEX IF NOT EXISTS idx_sona_patterns_confidence ON sona_patterns(confidence DESC);
   CREATE INDEX IF NOT EXISTS idx_sona_patterns_updated ON sona_patterns(updated_at DESC);
 `;
+// ============================================================================
+// In-Memory HNSW Index for Fast Vector Search
+// ============================================================================
+/**
+ * Binary min/max heap for O(log n) insertion and extraction.
+ * Replaces sorted arrays with O(n) splice in HNSW beam search.
+ */
+class BinaryHeap {
+    data = [];
+    compareFn;
+    constructor(compareFn) {
+        this.compareFn = compareFn;
+    }
+    push(item) {
+        this.data.push(item);
+        this.bubbleUp(this.data.length - 1);
+    }
+    pop() {
+        if (this.data.length === 0)
+            return undefined;
+        const top = this.data[0];
+        const last = this.data.pop();
+        if (this.data.length > 0) {
+            this.data[0] = last;
+            this.sinkDown(0);
+        }
+        return top;
+    }
+    peek() {
+        return this.data[0];
+    }
+    size() {
+        return this.data.length;
+    }
+    bubbleUp(i) {
+        while (i > 0) {
+            const parent = (i - 1) >> 1;
+            if (this.compareFn(this.data[i], this.data[parent]) < 0) {
+                [this.data[i], this.data[parent]] = [this.data[parent], this.data[i]];
+                i = parent;
+            }
+            else {
+                break;
+            }
+        }
+    }
+    sinkDown(i) {
+        const n = this.data.length;
+        while (true) {
+            let smallest = i;
+            const left = 2 * i + 1;
+            const right = 2 * i + 2;
+            if (left < n && this.compareFn(this.data[left], this.data[smallest]) < 0) {
+                smallest = left;
+            }
+            if (right < n && this.compareFn(this.data[right], this.data[smallest]) < 0) {
+                smallest = right;
+            }
+            if (smallest !== i) {
+                [this.data[i], this.data[smallest]] = [this.data[smallest], this.data[i]];
+                i = smallest;
+            }
+            else {
+                break;
+            }
+        }
+    }
+}
 /**
  * In-memory HNSW (Hierarchical Navigable Small World) index built from
  * SQLite vectors on startup. Provides O(log n) approximate nearest
@@ -657,23 +731,30 @@ class InMemoryHNSWIndex {
     /**
      * Beam search at a single layer: starting from an entry point, explore
      * up to `ef` candidates and return the `ef` closest found.
-     * Uses a candidate set (max-heap behavior via sorted array) and a result
-     * set. Returns results sorted by descending similarity.
+     * Uses a max-heap for candidates and a min-heap for results to achieve
+     * O(log n) insertion instead of O(n) Array.splice.
+     * Returns results sorted by descending similarity.
      */
     searchLayerBeam(query, entryIds, level, ef) {
         const visited = new Set(entryIds);
-        // Candidates: sorted descending by score (best first)
-        const candidates = entryIds
+        const initial = entryIds
             .filter(id => this.nodes.has(id))
             .map(id => ({ id, score: this.similarity(query, id) }));
-        candidates.sort((a, b) => b.score - a.score);
-        // Results: the ef-closest seen so far, sorted descending by score
-        const results = [...candidates];
-        while (candidates.length > 0) {
-            const closest = candidates.shift();
+        // Max-heap for candidates (best score = highest priority)
+        const candidateHeap = new BinaryHeap((a, b) => b.score - a.score // max-heap: highest score first
+        );
+        // Min-heap for results (worst score at top for fast eviction)
+        const resultHeap = new BinaryHeap((a, b) => a.score - b.score // min-heap: lowest score first
+        );
+        for (const entry of initial) {
+            candidateHeap.push(entry);
+            resultHeap.push(entry);
+        }
+        while (candidateHeap.size() > 0) {
+            const closest = candidateHeap.pop();
             // If the closest candidate is worse than the worst in results
             // and we already have ef results, stop
-            if (results.length >= ef && closest.score < results[results.length - 1].score) {
+            if (resultHeap.size() >= ef && closest.score < resultHeap.peek().score) {
                 break;
             }
             const node = this.nodes.get(closest.id);
@@ -687,38 +768,24 @@ class InMemoryHNSWIndex {
                 if (!this.nodes.has(neighborId))
                     continue;
                 const score = this.similarity(query, neighborId);
-                const worstResult = results.length >= ef ? results[results.length - 1].score : -Infinity;
-                if (results.length < ef || score > worstResult) {
-                    // Insert into candidates in sorted position
-                    const candidateEntry = { id: neighborId, score };
-                    let inserted = false;
-                    for (let i = 0; i < candidates.length; i++) {
-                        if (score > candidates[i].score) {
-                            candidates.splice(i, 0, candidateEntry);
-                            inserted = true;
-                            break;
-                        }
-                    }
-                    if (!inserted)
-                        candidates.push(candidateEntry);
-                    // Insert into results in sorted position
-                    inserted = false;
-                    for (let i = 0; i < results.length; i++) {
-                        if (score > results[i].score) {
-                            results.splice(i, 0, candidateEntry);
-                            inserted = true;
-                            break;
-                        }
-                    }
-                    if (!inserted)
-                        results.push(candidateEntry);
-                    // Trim results to ef
-                    if (results.length > ef) {
-                        results.pop();
+                const worstResult = resultHeap.size() >= ef ? resultHeap.peek().score : -Infinity;
+                if (resultHeap.size() < ef || score > worstResult) {
+                    const entry = { id: neighborId, score };
+                    candidateHeap.push(entry);
+                    resultHeap.push(entry);
+                    // Evict worst result if over capacity
+                    if (resultHeap.size() > ef) {
+                        resultHeap.pop();
                     }
                 }
             }
         }
+        // Drain result heap into array sorted descending by score
+        const results = [];
+        while (resultHeap.size() > 0) {
+            results.push(resultHeap.pop());
+        }
+        results.reverse(); // min-heap drains ascending, reverse for descending
         return results;
     }
     /**
@@ -1087,7 +1154,8 @@ export class UnifiedMemoryManager {
         if (!this.db)
             return false;
         try {
-            const info = this.db.prepare(`PRAGMA table_info(${tableName})`).all();
+            const safeName = validateTableName(tableName);
+            const info = this.db.prepare(`PRAGMA table_info(${safeName})`).all();
             return info.some(col => col.name === columnName);
         }
         catch {
@@ -1123,7 +1191,7 @@ export class UnifiedMemoryManager {
             if (tableExists && !this.columnExists(table, requiredColumn)) {
                 console.log(`[UnifiedMemory] Upgrading v2 table: ${table} (missing ${requiredColumn})`);
                 // Drop the old table - will be recreated with v3 schema
-                this.db.exec(`DROP TABLE IF EXISTS ${table}`);
+                this.db.exec(`DROP TABLE IF EXISTS ${validateTableName(table)}`);
             }
         }
     }
@@ -1314,17 +1382,24 @@ export class UnifiedMemoryManager {
         return result.changes > 0;
     }
     /**
-     * Search for similar vectors
+     * Search for similar vectors.
+     * Uses batch SQL query instead of N+1 individual queries for metadata enrichment.
      */
     async vectorSearch(query, k = 10, namespace) {
         this.ensureInitialized();
         // Use in-memory HNSW index for fast search
         const results = this.vectorIndex.search(query, k * 2); // Get extra for namespace filtering
-        // If namespace filter, post-filter results
+        if (results.length === 0)
+            return [];
+        // Batch fetch metadata for all result IDs in a single query (fixes N+1)
+        const ids = results.map(r => r.id);
+        const placeholders = ids.map(() => '?').join(',');
+        const rows = this.db.prepare(`SELECT id, namespace, metadata FROM vectors WHERE id IN (${placeholders})`).all(...ids);
+        const metadataMap = new Map(rows.map(row => [row.id, row]));
         if (namespace) {
             const filteredResults = [];
             for (const result of results) {
-                const row = this.db.prepare('SELECT namespace, metadata FROM vectors WHERE id = ?').get(result.id);
+                const row = metadataMap.get(result.id);
                 if (row && row.namespace === namespace) {
                     filteredResults.push({
                         id: result.id,
@@ -1339,7 +1414,7 @@ export class UnifiedMemoryManager {
         }
         // No namespace filter, just enrich with metadata
         return results.slice(0, k).map(result => {
-            const row = this.db.prepare('SELECT metadata FROM vectors WHERE id = ?').get(result.id);
+            const row = metadataMap.get(result.id);
             return {
                 id: result.id,
                 score: result.score,