agentic-qe 3.15.14 → 3.15.16

package/dist/feedback/test-outcome-tracker.js

@@ -142,12 +142,15 @@ export class TestOutcomeTracker {
     /**
      * Persist a single outcome to DB (write-through)
      */
-    persistOutcome(outcome) {
+    async persistOutcome(outcome) {
         if (!this.db)
             return;
         try {
-            const database = this.db.getDatabase();
-            database.prepare(`
+            const memory = this.db;
+            const database = memory.getDatabase();
+            // #1283: queued, so a locked memory.db does not freeze the MCP server's
+            // event loop while the tool call that recorded this test outcome waits.
+            await memory.writeWhenUnlocked(() => database.prepare(`
         INSERT OR REPLACE INTO test_outcomes (
           id, test_id, test_name, generated_by, pattern_id,
           framework, language, domain, passed, error_message,
@@ -156,10 +159,10 @@ export class TestOutcomeTracker {
           maintainability_score, complexity, lines_of_code,
           assertion_count, file_path, source_file_path, metadata_json
         ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
-      `).run(outcome.id, outcome.testId, outcome.testName, outcome.generatedBy, outcome.patternId || null, outcome.framework, outcome.language, outcome.domain, outcome.passed ? 1 : 0, outcome.errorMessage || null, outcome.coverage.lines, outcome.coverage.branches, outcome.coverage.functions, outcome.mutationScore ?? null, outcome.executionTimeMs, outcome.flaky ? 1 : 0, outcome.flakinessScore ?? null, outcome.maintainabilityScore, outcome.complexity ?? null, outcome.linesOfCode ?? null, outcome.assertionCount ?? null, outcome.filePath || null, outcome.sourceFilePath || null, outcome.metadata ? JSON.stringify(outcome.metadata) : null);
+      `).run(outcome.id, outcome.testId, outcome.testName, outcome.generatedBy, outcome.patternId || null, outcome.framework, outcome.language, outcome.domain, outcome.passed ? 1 : 0, outcome.errorMessage || null, outcome.coverage.lines, outcome.coverage.branches, outcome.coverage.functions, outcome.mutationScore ?? null, outcome.executionTimeMs, outcome.flaky ? 1 : 0, outcome.flakinessScore ?? null, outcome.maintainabilityScore, outcome.complexity ?? null, outcome.linesOfCode ?? null, outcome.assertionCount ?? null, outcome.filePath || null, outcome.sourceFilePath || null, outcome.metadata ? JSON.stringify(outcome.metadata) : null));
             this.persistCount++;
             if (this.persistCount % TestOutcomeTracker.RETENTION_CLEANUP_INTERVAL === 0) {
-                this.enforceRetention(database);
+                await this.enforceRetention(memory);
             }
         }
         catch (error) {
@@ -169,14 +172,15 @@ export class TestOutcomeTracker {
     /**
      * Delete oldest rows beyond retention limit
      */
-    enforceRetention(database) {
+    async enforceRetention(memory) {
         try {
+            const database = memory.getDatabase();
             const maxRows = this.config.maxOutcomesInMemory * 2; // Keep 2x in-memory limit in DB
-            database.prepare(`
+            await memory.writeWhenUnlocked(() => database.prepare(`
         DELETE FROM test_outcomes WHERE id NOT IN (
           SELECT id FROM test_outcomes ORDER BY created_at DESC LIMIT ?
         )
-      `).run(maxRows);
+      `).run(maxRows));
         }
         catch (error) {
             console.warn('[TestOutcomeTracker] Retention cleanup failed:', toErrorMessage(error));
@@ -188,7 +192,7 @@ export class TestOutcomeTracker {
     async track(outcome) {
         // 1. Store outcome
         this.store.add(outcome);
-        this.persistOutcome(outcome);
+        await this.persistOutcome(outcome);
         // 2. Update pattern metrics if pattern was used
         if (outcome.patternId) {
             this.updatePatternMetrics(outcome);

package/dist/governance/witness-chain.d.ts

@@ -245,6 +245,11 @@ export declare class WitnessChain {
 export interface IWitnessChainPersistence {
     /** Store a receipt in SQLite. Called after each appendWitness(). */
     insertReceipt(receipt: WitnessReceipt): void;
+    /**
+     * Store a receipt without blocking on a locked database (#1283). When
+     * present, appendWitness() uses it instead of insertReceipt().
+     */
+    insertReceiptWhenUnlocked?(receipt: WitnessReceipt): Promise<void>;
     /** Load all receipts from SQLite, ordered by chainIndex. */
     loadAllReceipts(): WitnessReceipt[];
     /** Get the total count of persisted receipts. */

package/dist/governance/witness-chain.js

@@ -18,6 +18,7 @@
 import { createHash, randomUUID } from 'crypto';
 import { LoggerFactory } from '../logging/index.js';
 import { getRuVectorFeatureFlags } from '../integrations/ruvector/feature-flags.js';
+import { writeWhenUnlockedOn } from '../shared/sqlite-write-queue.js';
 const logger = LoggerFactory.create('witness-chain');
 // ============================================================================
 // SPRT Accumulator
@@ -387,14 +388,25 @@ export class PersistentWitnessChain extends WitnessChain {
      */
     appendWitness(decision) {
         const receipt = super.appendWitness(decision);
-        try {
-            this.persistence.insertReceipt(receipt);
-        }
-        catch (err) {
+        const warn = (err) => {
             logger.warn('Failed to persist witness receipt to SQLite', {
                 chainIndex: receipt.chainIndex,
                 error: err instanceof Error ? err.message : String(err),
             });
+        };
+        try {
+            // #1283: queue the insert when the backend can, so a locked memory.db
+            // does not freeze the MCP server's event loop. The receipt is already in
+            // the in-memory chain, which is what callers read.
+            if (this.persistence.insertReceiptWhenUnlocked) {
+                this.persistence.insertReceiptWhenUnlocked(receipt).catch(warn);
+            }
+            else {
+                this.persistence.insertReceipt(receipt);
+            }
+        }
+        catch (err) {
+            warn(err);
         }
         return receipt;
     }
@@ -440,9 +452,13 @@ export function createWitnessChainSQLitePersistence(db) {
     const countStmt = db.prepare(`
     SELECT COUNT(*) as cnt FROM witness_chain_receipts
   `);
+    const insertReceipt = (receipt) => {
+        insertStmt.run(receipt.id, receipt.chainIndex, receipt.timestamp, receipt.previousHash, receipt.hash, receipt.decision.type, receipt.decision.decision, JSON.stringify(receipt.decision.context), receipt.decision.evidence ?? null);
+    };
     return {
-        insertReceipt(receipt) {
-            insertStmt.run(receipt.id, receipt.chainIndex, receipt.timestamp, receipt.previousHash, receipt.hash, receipt.decision.type, receipt.decision.decision, JSON.stringify(receipt.decision.context), receipt.decision.evidence ?? null);
+        insertReceipt,
+        insertReceiptWhenUnlocked(receipt) {
+            return writeWhenUnlockedOn(db, () => insertReceipt(receipt));
         },
         loadAllReceipts() {
             const rows = loadAllStmt.all();

package/dist/init/init-wizard-hooks.d.ts

@@ -21,7 +21,7 @@ export declare function configureHooks(projectRoot: string, config: AQEInitConfi
 /**
  * Configure MCP server.
  * Creates .mcp.json (root level) with AQE v3 MCP server configuration.
- * Uses npx to run the MCP server without requiring global installation.
+ * Runs the installed `aqe-mcp` binary, matching the phase-based installer.
  *
  * #922: skipped when the agentic-qe-fleet Claude Code plugin is enabled (it
  * already provides the AQE MCP server) unless `force` is set (--with-mcp).

package/dist/init/init-wizard-hooks.js

@@ -13,6 +13,7 @@ import { existsSync, mkdirSync, writeFileSync, readFileSync, copyFileSync } from
 import { join, dirname } from 'path';
 import { safeJsonParse } from '../shared/safe-json.js';
 import { aqePluginMcpSkipMessage, detectAqeFleetPlugin } from './claude-plugin-detection.js';
+import { removeUntrustedAqeMcpServers, scrubUntrustedAqeMcpFile } from './settings-merge.js';
 import { mergeHooksSmart, generateAqeEnvVars, generateV3SettingsSections, applyV3Sections, mergeAqeEnv, backupSettingsFile, } from './settings-merge.js';
 // ============================================================================
 // Hook Configuration
@@ -240,7 +241,7 @@ async function installCrossPhaseMemoryHooks(projectRoot) {
     // If no asset found, create minimal config
     const minimalConfig = `# Cross-Phase Memory Hooks Configuration
 # Generated by aqe init
-# See: https://github.com/anthropics/agentic-qe/docs/cross-phase-memory.md
+# See: https://github.com/proffesor-for-testing/agentic-qe/blob/main/docs/architecture/CROSS-PHASE-MEMORY-IMPLEMENTATION.md
 
 version: "1.0"
 enabled: true
@@ -272,7 +273,7 @@ routing:
 /**
  * Configure MCP server.
  * Creates .mcp.json (root level) with AQE v3 MCP server configuration.
- * Uses npx to run the MCP server without requiring global installation.
+ * Runs the installed `aqe-mcp` binary, matching the phase-based installer.
  *
  * #922: skipped when the agentic-qe-fleet Claude Code plugin is enabled (it
  * already provides the AQE MCP server) unless `force` is set (--with-mcp).
@@ -280,6 +281,7 @@ routing:
 export async function configureMCP(projectRoot, options = {}) {
     if (!options.force && detectAqeFleetPlugin(projectRoot).enabled) {
         console.log(aqePluginMcpSkipMessage(projectRoot));
+        scrubUntrustedAqeMcpFile(join(projectRoot, '.mcp.json'));
         return false;
     }
     const mcpPath = join(projectRoot, '.mcp.json');
@@ -297,13 +299,10 @@ export async function configureMCP(projectRoot, options = {}) {
         mcpConfig.mcpServers = {};
     }
     const servers = mcpConfig.mcpServers;
+    removeUntrustedAqeMcpServers(servers);
     servers['agentic-qe'] = {
-        command: 'npx',
-        args: [
-            '@anthropics/agentic-qe',
-            'mcp',
-            'start'
-        ],
+        command: 'aqe-mcp',
+        args: [],
         env: {
             AQE_LEARNING_ENABLED: 'true',
             AQE_VERBOSE: 'false',

package/dist/init/phases/08-mcp.js

@@ -16,6 +16,7 @@ import { writeFileIfChanged } from '../idempotent-write.js';
 import { join } from 'path';
 import { safeJsonParse } from '../../shared/safe-json.js';
 import { aqePluginMcpSkipMessage, detectAqeFleetPlugin, } from '../claude-plugin-detection.js';
+import { removeUntrustedAqeMcpServers, scrubUntrustedAqeMcpFile } from '../settings-merge.js';
 import { BasePhase, } from './phase-interface.js';
 /**
  * MCP phase - configures MCP server
@@ -56,6 +57,7 @@ export class MCPPhase extends BasePhase {
             const plugin = this.detectPlugin(projectRoot);
             if (plugin.enabled) {
                 context.services.log(aqePluginMcpSkipMessage(projectRoot));
+                reportUntrustedMcpRemoval(context, scrubUntrustedAqeMcpFile(join(projectRoot, '.mcp.json')));
                 return {
                     configured: false,
                     mcpPath: '',
@@ -107,6 +109,7 @@ export class MCPPhase extends BasePhase {
             rootMcpConfig.mcpServers = {};
         }
         const rootServers = rootMcpConfig.mcpServers;
+        reportUntrustedMcpRemoval(context, removeUntrustedAqeMcpServers(rootServers));
         rootServers['agentic-qe'] = aqeServerConfig;
         // #778: no rewrite (mtime churn) when the merged config is unchanged.
         writeFileIfChanged(rootMcpPath, JSON.stringify(rootMcpConfig, null, 2));
@@ -128,5 +131,11 @@ export class MCPPhase extends BasePhase {
         };
     }
 }
+/** GHSA-chjc-8q37-52fg: say which stale server entries init removed. */
+function reportUntrustedMcpRemoval(context, removed) {
+    if (removed.length > 0) {
+        context.services.log(`  MCP: removed server entry launching @anthropics/agentic-qe: ${removed.join(', ')}`);
+    }
+}
 // Instance exported from index.ts
 //# sourceMappingURL=08-mcp.js.map

package/dist/init/settings-merge.d.ts

@@ -59,12 +59,25 @@ export declare function generateAqeEnvVars(config: AQEInitConfig, options?: {
  * "Agentic QE v3" banner). Anything else is treated as user-owned and preserved.
  */
 export declare function isAqeStatusLine(statusLine: unknown): boolean;
+/** Drop allow-list entries that pre-approve the untrusted package. */
+export declare function removeUntrustedAqePermissions(allow: string[]): string[];
+/**
+ * Remove MCP servers that launch the untrusted package.
+ * Mutates `servers` and returns the removed server names.
+ */
+export declare function removeUntrustedAqeMcpServers(servers: Record<string, unknown>): string[];
+/**
+ * Remove untrusted-package servers from an existing `.mcp.json`, leaving the
+ * rest of the file alone. Used where init does not write its own entry.
+ */
+export declare function scrubUntrustedAqeMcpFile(mcpPath: string): string[];
 /**
  * Apply the generated v3 settings sections onto an existing settings object
  * WITHOUT clobbering configuration the user already set:
  *
  * - `_aqePermissions`: union-merge into `permissions.allow`, preserving the
  *   user's existing allow/deny entries (#362).
+ *   Entries naming the untrusted package are dropped (GHSA-chjc-8q37-52fg).
  * - `statusLine`: generic Claude Code setting — only written when absent or when
  *   the existing one is AQE's own (so a user's custom status line is preserved).
  * - `includeCoAuthoredBy`: generic Claude Code setting — only written when the

package/dist/init/settings-merge.js

@@ -186,12 +186,60 @@ function deepMergeOwned(target, source) {
 function isPlainObject(value) {
     return typeof value === 'object' && value !== null && !Array.isArray(value);
 }
+/**
+ * A package name earlier AQE versions wrote into `permissions.allow` and
+ * `.mcp.json` (GHSA-chjc-8q37-52fg). AQE does not publish or control it, so
+ * init removes any entry naming it instead of leaving a standing grant.
+ */
+const UNTRUSTED_AQE_PACKAGE = /@anthropics\/agentic-qe\b/i;
+/** Drop allow-list entries that pre-approve the untrusted package. */
+export function removeUntrustedAqePermissions(allow) {
+    return allow.filter((entry) => typeof entry !== 'string' || !UNTRUSTED_AQE_PACKAGE.test(entry));
+}
+/**
+ * Remove MCP servers that launch the untrusted package.
+ * Mutates `servers` and returns the removed server names.
+ */
+export function removeUntrustedAqeMcpServers(servers) {
+    const removed = [];
+    for (const [name, server] of Object.entries(servers)) {
+        const { command, args } = (isPlainObject(server) ? server : {});
+        const parts = [command, ...(Array.isArray(args) ? args : [])];
+        if (parts.some((part) => typeof part === 'string' && UNTRUSTED_AQE_PACKAGE.test(part))) {
+            delete servers[name];
+            removed.push(name);
+        }
+    }
+    return removed;
+}
+/**
+ * Remove untrusted-package servers from an existing `.mcp.json`, leaving the
+ * rest of the file alone. Used where init does not write its own entry.
+ */
+export function scrubUntrustedAqeMcpFile(mcpPath) {
+    if (!existsSync(mcpPath))
+        return [];
+    let config;
+    try {
+        config = JSON.parse(readFileSync(mcpPath, 'utf-8'));
+    }
+    catch {
+        return [];
+    }
+    if (!isPlainObject(config) || !isPlainObject(config.mcpServers))
+        return [];
+    const removed = removeUntrustedAqeMcpServers(config.mcpServers);
+    if (removed.length > 0)
+        writeFileSync(mcpPath, JSON.stringify(config, null, 2), 'utf-8');
+    return removed;
+}
 /**
  * Apply the generated v3 settings sections onto an existing settings object
  * WITHOUT clobbering configuration the user already set:
  *
  * - `_aqePermissions`: union-merge into `permissions.allow`, preserving the
  *   user's existing allow/deny entries (#362).
+ *   Entries naming the untrusted package are dropped (GHSA-chjc-8q37-52fg).
  * - `statusLine`: generic Claude Code setting — only written when absent or when
  *   the existing one is AQE's own (so a user's custom status line is preserved).
  * - `includeCoAuthoredBy`: generic Claude Code setting — only written when the
@@ -205,7 +253,7 @@ export function applyV3Sections(settings, sections, options = {}) {
     for (const [key, value] of Object.entries(sections)) {
         if (key === '_aqePermissions') {
             const existingPerms = settings.permissions || {};
-            const existingAllow = existingPerms.allow || [];
+            const existingAllow = removeUntrustedAqePermissions(existingPerms.allow || []);
             const merged = [...new Set([...existingAllow, ...value])];
             settings.permissions = { ...existingPerms, allow: merged };
         }
@@ -261,7 +309,6 @@ export function generateV3SettingsSections(config, projectRoot, options = {}) {
         // permissions are union-merged in 07-hooks.ts — not set here to avoid overwriting user entries (#362)
         _aqePermissions: [
             'Bash(npx agentic-qe:*)',
-            'Bash(npx @anthropics/agentic-qe:*)',
             'mcp__agentic-qe__*',
         ],
         includeCoAuthoredBy: true,