@@ -1,18 +1,18 @@
 {
   "name": "ruvector",
-  "version": "0.3.3",
-  "description": "Self-learning vector database for Node.js — hybrid search, Graph RAG, FlashAttention-3, HNSW, 50+ attention mechanisms",
+  "version": "0.3.4",
+  "description": "Self-learning vector database for Node.js — native HNSW, ONNX embeddings, GNN, attention, SONA routing, and an MCP server for agents",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
   "bin": {
     "ruvector": "bin/cli.js"
   },
   "scripts": {
-    "build": "tsc && node -e \"require('fs').cpSync('src/core/onnx','dist/core/onnx',{recursive:true})\"",
+    "build": "tsc && node -e \"require('fs').cpSync('src/core/onnx','dist/core/onnx',{recursive:true,filter:(f)=>!/\\.(db|rvf|lock)$/.test(f)})\"",
     "verify-dist": "node scripts/verify-dist.js",
     "prepack": "npm run build && npm run verify-dist",
     "prepublishOnly": "npm run build && npm run verify-dist",
-    "test": "node test/integration.js && node test/graph-modularity.js && node test/backend-fallback.js && node test/mincut-wasm.js && node test/metaharness-sdk.js && node test/metaharness-optional-deps.js && node test/cli-commands.js && node test/metaharness-cli.js && node test/db-workflow.js && node test/mcp-stdio.js && node test/metaharness-mcp.js && node test/sigterm-cleanup.js && node test/mcp-policy.js && node test/mcp-command-security.js && node test/mcp-handshake.js && node test/mcp-intel-durability.js && node test/startup-budget.js"
+    "test": "node test/integration.js && node test/graph-modularity.js && node test/backend-fallback.js && node test/mincut-wasm.js && node test/metaharness-sdk.js && node test/metaharness-optional-deps.js && node test/cli-commands.js && node test/metaharness-cli.js && node test/db-workflow.js && node test/mcp-stdio.js && node test/metaharness-mcp.js && node test/sigterm-cleanup.js && node test/mcp-policy.js && node test/mcp-command-security.js && node test/mcp-exploit-regression.js && node test/mcp-handshake.js && node test/mcp-intel-durability.js && node test/startup-budget.js"
   },
   "keywords": [
     "vector",
@@ -48,12 +48,7 @@
     "shared-intelligence",
     "mcp",
     "edge-computing",
-    "graph-rag",
     "hnsw",
-    "hybrid-search",
-    "colbert",
-    "turboquant",
-    "mamba",
     "pi-brain",
     "identity",
     "pi-key",
 
@@ -48,4 +48,27 @@ if (missing.length > 0) {
   process.exit(1);
 }
 
+// Local runtime artifacts (vector stores, RVF files, scan reports) must never
+// ride along in the tarball: `files` whitelists bin/ and dist/, so .npmignore
+// does not filter them.
+const STRAY = /\.(db|rvf|lock)$|(^|\/)\.claude(\/|$)/;
+const stray = [];
+for (const dir of ['bin', 'dist', 'wasm']) {
+  const walk = (rel) => {
+    const abs = path.join(pkgRoot, rel);
+    if (!fs.existsSync(abs)) return;
+    for (const ent of fs.readdirSync(abs, { withFileTypes: true })) {
+      const child = path.posix.join(rel, ent.name);
+      if (STRAY.test(child)) stray.push(child);
+      else if (ent.isDirectory()) walk(child);
+    }
+  };
+  walk(dir);
+}
+if (stray.length > 0) {
+  console.error(`verify-dist: ${stray.length} stray runtime artifact(s) would be published:`);
+  for (const rel of stray) console.error(`  - ${rel}`);
+  process.exit(1);
+}
+
 console.log(`verify-dist: ${unique.length} dist path(s) present.`);
@@ -364,9 +364,9 @@ export class MoEAttention {
     const attention = getAttentionModule();
     this.inner = new attention.MoEAttention({
       dim: config.dim,
-      num_experts: config.numExperts,
-      top_k: config.topK,
-      expert_capacity: config.expertCapacity ?? 1.25,
+      numExperts: config.numExperts,
+      topK: config.topK,
+      expertCapacity: config.expertCapacity ?? 1.25,
     });
     this.config = config;
   }
@@ -544,7 +544,7 @@ export class EdgeFeaturedAttention {
 
   constructor(dim: number, edgeDim: number = 16) {
     const attention = getAttentionModule();
-    this.inner = new attention.EdgeFeaturedAttention(dim, edgeDim);
+    this.inner = new attention.EdgeFeaturedAttention({ nodeDim: dim, edgeDim, numHeads: 1 });
     this.dim = dim;
     this.edgeDim = edgeDim;
   }
 
@@ -8,7 +8,20 @@
  * - Review prioritization
  */
 
-import { execSync } from 'child_process';
+import { execFileSync } from 'child_process';
+
+const GIT_OPTS = { encoding: 'utf8' as const, maxBuffer: 10 * 1024 * 1024, stdio: ['ignore', 'pipe', 'ignore'] as any };
+
+/**
+ * Validate a git revision supplied by a caller (CLI flag or MCP tool arg).
+ * Revisions are passed as argv (never through a shell) and must not look like options.
+ */
+export function assertSafeGitRef(ref: string): string {
+  if (typeof ref !== 'string' || !/^[0-9A-Za-z._\/~^@{}:-]{1,200}$/.test(ref) || ref.startsWith('-')) {
+    throw new Error(`Invalid git revision: ${JSON.stringify(ref)}`);
+  }
+  return ref;
+}
 import { embed, embedBatch, isReady, initOnnxEmbedder } from './onnx-embedder';
 
 export interface DiffHunk {
@@ -211,10 +224,7 @@ export async function analyzeFileDiff(file: string, diff: string, message: strin
  */
 export function getCommitDiff(commitHash: string = 'HEAD'): string {
   try {
-    return execSync(`git show ${commitHash} --format="" 2>/dev/null`, {
-      encoding: 'utf8',
-      maxBuffer: 10 * 1024 * 1024,
-    });
+    return execFileSync('git', ['show', '--format=', assertSafeGitRef(commitHash), '--'], GIT_OPTS) as string;
   } catch {
     return '';
   }
@@ -225,10 +235,7 @@ export function getCommitDiff(commitHash: string = 'HEAD'): string {
  */
 export function getStagedDiff(): string {
   try {
-    return execSync('git diff --cached 2>/dev/null', {
-      encoding: 'utf8',
-      maxBuffer: 10 * 1024 * 1024,
-    });
+    return execFileSync('git', ['diff', '--cached'], GIT_OPTS) as string;
   } catch {
     return '';
   }
@@ -239,10 +246,7 @@ export function getStagedDiff(): string {
  */
 export function getUnstagedDiff(): string {
   try {
-    return execSync('git diff 2>/dev/null', {
-      encoding: 'utf8',
-      maxBuffer: 10 * 1024 * 1024,
-    });
+    return execFileSync('git', ['diff'], GIT_OPTS) as string;
   } catch {
     return '';
   }
@@ -252,14 +256,13 @@ export function getUnstagedDiff(): string {
  * Analyze a commit
  */
 export async function analyzeCommit(commitHash: string = 'HEAD'): Promise<CommitAnalysis> {
+  assertSafeGitRef(commitHash);
   const diff = getCommitDiff(commitHash);
 
   // Get commit metadata
   let message = '', author = '', date = '';
   try {
-    const info = execSync(`git log -1 --format="%s|%an|%aI" ${commitHash} 2>/dev/null`, {
-      encoding: 'utf8',
-    }).trim();
+    const info = (execFileSync('git', ['log', '-1', '--format=%s|%an|%aI', commitHash, '--'], GIT_OPTS) as string).trim();
     [message, author, date] = info.split('|');
   } catch {}
 
@@ -327,9 +330,8 @@ export async function findSimilarCommits(
   // Get recent commits
   let commits: string[] = [];
   try {
-    commits = execSync(`git log -${recentCommits} --format="%H" 2>/dev/null`, {
-      encoding: 'utf8',
-    }).trim().split('\n');
+    const n = Math.max(1, Math.min(10000, Math.floor(Number(recentCommits)) || 50));
+    commits = (execFileSync('git', ['log', `-${n}`, '--format=%H'], GIT_OPTS) as string).trim().split('\n');
   } catch {
     return [];
   }
 
@@ -11,6 +11,7 @@
  * Replaces the simple Q-learning approach with real ML-powered intelligence.
  */
 
+import * as path from 'path';
 import { FastAgentDB, Episode, Trajectory, EpisodeSearchResult } from './agentdb-fast';
 import { SonaEngine, SonaConfig, LearnedPattern, SonaStats, isSonaAvailable } from './sona-wrapper';
 import { OnnxEmbedder, OnnxEmbedderConfig, isOnnxAvailable, initOnnxEmbedder, getEmbedderProvenance, getEmbeddingSpaceIdentity, getEmbeddingSpaceId, embedBulk, shutdownParallelEmbedder } from './onnx-embedder';
@@ -312,11 +313,19 @@ export class IntelligenceEngine {
   }
 
   private async initVectorDb(): Promise<void> {
+    // Without an explicit storagePath the native VectorDb defaults to
+    // ./ruvector.db, which dropped a multi-MB file into the user's project on
+    // the first semantic hook. The index is rebuilt from the JSON store in every
+    // (short-lived) hook process anyway, so brute-force cosine over memories is
+    // both cheaper and file-free; an HNSW index is used only when a storage
+    // location is configured.
+    if (!this.config.storagePath) return;
     try {
       const VDB = getVectorDB();
       this.vectorDb = new VDB({
         dimensions: this.config.embeddingDim,
         distanceMetric: 'Cosine',
+        storagePath: path.join(this.config.storagePath, 'engine-vectors.db'),
       });
     } catch {
       // VectorDB not available, use fallback
 
@@ -148,6 +148,16 @@ export class LearningEngine {
    * Configure algorithm for a specific task type
    */
   configure(task: TaskType, config: Partial<LearningConfig>): void {
+    if (config.algorithm !== undefined &&
+        !LearningEngine.getAlgorithms().some(a => a.algorithm === config.algorithm)) {
+      throw new Error(`Unknown learning algorithm: ${config.algorithm}`);
+    }
+    for (const key of ['learningRate', 'discountFactor', 'epsilon'] as const) {
+      const v = config[key];
+      if (v !== undefined && !(Number.isFinite(v) && v >= 0 && v <= 1)) {
+        throw new Error(`${key} must be a number in [0, 1], got ${v}`);
+      }
+    }
     const existing = this.configs.get(task) || TASK_ALGORITHM_MAP[task] || DEFAULT_TASK_CONFIG;
     this.configs.set(task, { ...existing, ...config });
   }
@@ -163,6 +173,9 @@ export class LearningEngine {
    * Update Q-value using the appropriate algorithm
    */
   update(task: TaskType, experience: Experience): number {
+    if (!Number.isFinite(experience.reward)) {
+      throw new Error(`reward must be a finite number, got ${experience.reward}`);
+    }
     const config = this.getConfig(task);
     let delta = 0;
 
@@ -201,6 +214,8 @@ export class LearningEngine {
       case 'dqn':
         delta = this.dqnUpdate(experience, config);
         break;
+      default:
+        throw new Error(`Unknown learning algorithm: ${config.algorithm}`);
     }
 
     // Update stats
@@ -212,23 +227,30 @@ export class LearningEngine {
   /**
    * Get best action for a state
    */
-  getBestAction(task: TaskType, state: string, actions: string[]): { action: string; confidence: number } {
+  getBestAction(
+    task: TaskType,
+    state: string,
+    actions: string[],
+    options: { explore?: boolean } = {}
+  ): { action: string; confidence: number; explored?: boolean } {
     const config = this.getConfig(task);
 
-    // Epsilon-greedy exploration
-    if (Math.random() < config.epsilon) {
+    // Epsilon-greedy exploration (opt-in: recommendations shown to users are greedy)
+    if (options.explore && Math.random() < config.epsilon) {
       const randomAction = actions[Math.floor(Math.random() * actions.length)];
-      return { action: randomAction, confidence: 0.5 };
+      return { action: randomAction, confidence: 0.5, explored: true };
     }
 
     let bestAction = actions[0];
     let bestValue = -Infinity;
     let values: number[] = [];
 
     const qTable = this.getQTable(state);
+    // Double Q-learning writes to either table at random; act on their sum.
+    const qTable2 = config.algorithm === 'double-q' ? this.getQTable2(state) : null;
 
     for (const action of actions) {
-      const value = qTable.get(action) || 0;
+      const value = (qTable.get(action) || 0) + (qTable2 ? qTable2.get(action) || 0 : 0);
       values.push(value);
       if (value > bestValue) {
         bestValue = value;
@@ -501,7 +523,7 @@ export class LearningEngine {
 
       // Weight by normalized return
       const normalizedReturn = returns[i] / (Math.abs(returns[0]) + 1);
-      const target = currentQ + α * normalizedReturn * exp.reward;
+      const target = currentQ + α * normalizedReturn;
       const delta = target - currentQ;
 
       qTable.set(exp.action, target);
 
@@ -486,11 +486,11 @@ export class ExtendedWorkerPool {
       }
 
       async function gitBlame(files) {
-        const { execSync } = require('child_process');
+        const { execFileSync } = require('child_process');
         const results = [];
         for (const file of files) {
           try {
-            const output = execSync(\`git blame --line-porcelain "\${file}" 2>/dev/null\`, { encoding: 'utf8', maxBuffer: 10 * 1024 * 1024 });
+            const output = execFileSync('git', ['blame', '--line-porcelain', '--', String(file)], { encoding: 'utf8', maxBuffer: 10 * 1024 * 1024, stdio: ['ignore', 'pipe', 'ignore'] });
             const lines = [];
             let currentLine = {};
             for (const line of output.split('\\n')) {
@@ -511,13 +511,13 @@ export class ExtendedWorkerPool {
       }
 
       async function gitChurn(files, since) {
-        const { execSync } = require('child_process');
+        const { execFileSync } = require('child_process');
         const results = [];
-        const sinceArg = since ? \`--since="\${since}"\` : '--since="30 days ago"';
+        const sinceArg = '--since=' + (since ? String(since) : '30 days ago');
 
         for (const file of files) {
           try {
-            const log = execSync(\`git log \${sinceArg} --format="%H|%an|%aI" --numstat -- "\${file}" 2>/dev/null\`, { encoding: 'utf8' });
+            const log = execFileSync('git', ['log', sinceArg, '--format=%H|%an|%aI', '--numstat', '--', String(file)], { encoding: 'utf8', stdio: ['ignore', 'pipe', 'ignore'] });
             let additions = 0, deletions = 0, commits = 0;
             const authors = new Set();
             let lastModified = '';
 
@@ -455,6 +455,8 @@ export class TensorCompress {
     this.compressTimer = setInterval(() => {
       this.recompressAll();
     }, this.config.compressIntervalMs);
+    // Background maintenance must not keep the host process alive.
+    (this.compressTimer as any)?.unref?.();
   }
 
   /**
Original file line number	Diff line number	Diff line change
`@@ -455,6 +455,8 @@ export class TensorCompress {`
`455`	`455`	`this.compressTimer = setInterval(() => {`
`456`	`456`	`this.recompressAll();`
`457`	`457`	`}, this.config.compressIntervalMs);`
	`458`	`+ // Background maintenance must not keep the host process alive.`
	`459`	`+ (this.compressTimer as any)?.unref?.();`
`458`	`460`	`}`
`459`	`461`
`460`	`462`	`/**`