agentic-qe 3.14.4 → 3.14.6

package/dist/init/idempotent-write.js

@@ -0,0 +1,160 @@
+/**
+ * Idempotent file writers for `aqe init` (#778).
+ *
+ * A repeat `aqe init` on an unchanged project must be a byte-stable
+ * convergence step: files whose content would not change are left alone (no
+ * rewrite, so the mtime is preserved too), and volatile fields such as
+ * generation timestamps are carried over from the existing file unless
+ * something else in that file actually changed.
+ */
+import { copyFileSync, existsSync, readFileSync, writeFileSync } from 'fs';
+import { safeJsonParse } from '../shared/safe-json.js';
+/**
+ * Write `content` to `path` only when the bytes on disk differ.
+ * @returns true when the file was written.
+ */
+export function writeFileIfChanged(path, content) {
+    const next = typeof content === 'string' ? Buffer.from(content, 'utf-8') : content;
+    try {
+        if (existsSync(path) && readFileSync(path).equals(next))
+            return false;
+    }
+    catch {
+        // Unreadable target — fall through and (re)write it.
+    }
+    if (typeof content === 'string')
+        writeFileSync(path, content, 'utf-8');
+    else
+        writeFileSync(path, content);
+    return true;
+}
+/**
+ * Copy `src` to `dest` only when `dest` is missing or its bytes differ.
+ * Uses copyFileSync for the actual copy so file-mode semantics are unchanged.
+ * @returns true when the file was copied.
+ */
+export function copyFileIfChanged(src, dest) {
+    try {
+        if (existsSync(dest) && readFileSync(dest).equals(readFileSync(src)))
+            return false;
+    }
+    catch {
+        // Unreadable target — fall through and copy.
+    }
+    copyFileSync(src, dest);
+    return true;
+}
+/**
+ * Write a text file whose content embeds a volatile line (e.g. a generation
+ * timestamp). When the existing file matches `content` on every line except
+ * the lines matching `volatileLine`, the file is left untouched.
+ * @returns true when the file was written.
+ */
+export function writeTextIfChangedIgnoring(path, content, volatileLine) {
+    try {
+        if (existsSync(path)) {
+            const strip = (text) => text.split('\n').filter((line) => !volatileLine.test(line)).join('\n');
+            if (strip(readFileSync(path, 'utf-8')) === strip(content))
+                return false;
+        }
+    }
+    catch {
+        // Unreadable target — fall through and write.
+    }
+    writeFileSync(path, content, 'utf-8');
+    return true;
+}
+/** The `*Generated by AQE v3 init on <ISO>*` footer of generated index docs. */
+export const GENERATED_ON_LINE = /^\*Generated by AQE v3 init on [^*]+\*$/;
+function isPlainObject(value) {
+    return typeof value === 'object' && value !== null && !Array.isArray(value);
+}
+/** JSON serialization with object keys sorted, for order-insensitive comparison. */
+export function canonicalJson(value) {
+    return JSON.stringify(value, (_key, v) => {
+        if (!isPlainObject(v))
+            return v;
+        const sorted = {};
+        for (const k of Object.keys(v).sort())
+            sorted[k] = v[k];
+        return sorted;
+    });
+}
+/** Deep structural equality of two JSON values, ignoring object key order. */
+export function jsonEquivalent(a, b) {
+    return canonicalJson(a) === canonicalJson(b);
+}
+function getPath(obj, path) {
+    let cur = obj;
+    for (const key of path) {
+        if (!isPlainObject(cur))
+            return undefined;
+        cur = cur[key];
+    }
+    return cur;
+}
+function setPath(obj, path, value) {
+    let cur = obj;
+    for (const key of path.slice(0, -1)) {
+        if (!isPlainObject(cur[key]))
+            return;
+        cur = cur[key];
+    }
+    const last = path[path.length - 1];
+    if (last in cur)
+        cur[last] = value;
+}
+/**
+ * Carry volatile fields (timestamps) over from `previous` into `next` when
+ * `next` is otherwise identical to `previous`.
+ *
+ * - Unchanged (apart from the volatile fields): `next` is mutated to hold the
+ *   previous values and `false` is returned — the caller should not write.
+ * - Changed, or no previous document: `next` keeps its fresh values and
+ *   `true` is returned — the caller should write.
+ */
+export function stabilizeVolatileFields(previous, next, volatilePaths) {
+    if (!isPlainObject(previous))
+        return true;
+    const candidate = JSON.parse(JSON.stringify(next));
+    for (const path of volatilePaths) {
+        const prevValue = getPath(previous, path);
+        if (prevValue !== undefined && getPath(candidate, path) !== undefined) {
+            setPath(candidate, path, prevValue);
+        }
+    }
+    if (!jsonEquivalent(previous, candidate))
+        return true;
+    for (const path of volatilePaths) {
+        const prevValue = getPath(previous, path);
+        if (prevValue !== undefined && getPath(next, path) !== undefined)
+            setPath(next, path, prevValue);
+    }
+    return false;
+}
+/** Read and parse a JSON file, or return undefined when missing/unparseable. */
+export function readJsonIfPresent(path) {
+    if (!existsSync(path))
+        return undefined;
+    try {
+        return safeJsonParse(readFileSync(path, 'utf-8'));
+    }
+    catch {
+        return undefined;
+    }
+}
+/**
+ * Write a generated JSON document (2-space indent) unless it is equivalent to
+ * the one already on disk, preserving the existing values of `volatilePaths`
+ * (e.g. `[['createdAt']]`) when nothing else changed.
+ * @returns true when the file was written.
+ */
+export function writeJsonIfChanged(path, doc, volatilePaths = []) {
+    const previous = readJsonIfPresent(path);
+    if (previous !== undefined && !stabilizeVolatileFields(previous, doc, volatilePaths)) {
+        return false;
+    }
+    writeFileSync(path, JSON.stringify(doc, null, 2), 'utf-8');
+    return true;
+}
+//# sourceMappingURL=idempotent-write.js.map

package/dist/init/orchestrator.js

@@ -158,6 +158,7 @@ export class ModularInitOrchestrator {
                 claudeMdGenerated: claudeMdResult?.data?.generated ?? false,
                 workersStarted: workersResult?.data?.workersConfigured ?? 0,
                 codexGuidance: assetsResult?.data?.codexGuidance,
+                codexComponents: assetsResult?.data?.codexComponents,
             },
             totalDurationMs: Date.now() - startTime,
             timestamp: new Date(),

package/dist/init/phases/05-learning.js

@@ -3,6 +3,7 @@
  * Initializes the learning system with HNSW index and pattern storage
  */
 import { existsSync, mkdirSync, writeFileSync } from 'fs';
+import { writeJsonIfChanged } from '../idempotent-write.js';
 import { join } from 'path';
 import { BasePhase, } from './phase-interface.js';
 import { getAQEVersion } from '../types.js';
@@ -54,7 +55,8 @@ export class LearningPhase extends BasePhase {
             hnswIndexPath: join(hnswDir, 'index.bin'),
             initialized: new Date().toISOString(),
         };
-        writeFileSync(learningConfigPath, JSON.stringify(learningConfig, null, 2), 'utf-8');
+        // #778: leave an equivalent file (and its `initialized` stamp) untouched.
+        writeJsonIfChanged(learningConfigPath, learningConfig, [['initialized']]);
         // Load pre-trained patterns if available and not skipped
         let patternsLoaded = 0;
         if (config.learning.pretrainedPatterns && !options.skipPatterns) {

package/dist/init/phases/07-hooks.js

@@ -14,7 +14,10 @@ import { safeJsonParse } from '../../shared/safe-json.js';
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = dirname(__filename);
 import { isAqeHookEntry, mergeHooksSmart, generateAqeEnvVars, generateV3SettingsSections, applyV3Sections, mergeAqeEnv, backupSettingsFile, } from '../settings-merge.js';
+import { copyFileIfChanged, stabilizeVolatileFields } from '../idempotent-write.js';
 import { BasePhase, } from './phase-interface.js';
+/** settings.json fields that change on every run without a real change (#778). */
+const SETTINGS_VOLATILE_FIELDS = [['aqe', 'initialized']];
 /**
  * Hooks phase - configures Claude Code hooks
  */
@@ -53,13 +56,16 @@ export class HooksPhase extends BasePhase {
         if (!existsSync(hooksDir)) {
             mkdirSync(hooksDir, { recursive: true });
         }
-        // Load existing settings
+        // Load existing settings. `previousSettings` is an untouched parse used to
+        // decide whether this run changes anything (#778); `settings` is mutated.
         const settingsPath = join(claudeDir, 'settings.json');
         let settings = {};
+        let previousSettings;
         if (existsSync(settingsPath)) {
             try {
                 const content = readFileSync(settingsPath, 'utf-8');
                 settings = safeJsonParse(content);
+                previousSettings = safeJsonParse(content);
             }
             catch {
                 settings = {};
@@ -98,13 +104,23 @@ export class HooksPhase extends BasePhase {
             existingMcp.push('agentic-qe');
         }
         settings.enabledMcpjsonServers = existingMcp;
-        // Back up the pristine original settings.json before writing (like CLAUDE.md)
-        const backupPath = backupSettingsFile(settingsPath);
-        if (backupPath) {
-            context.services.log(`  Backup created: ${backupPath}`);
+        // Converge instead of rewriting (#778): keep the original `aqe.initialized`
+        // stamp and skip the write (and the backup) entirely when the merged
+        // settings are equivalent to what is already on disk. Any real change —
+        // a version upgrade, a restored AQE hook, a new flag — still writes, and
+        // then records a fresh initialization timestamp.
+        const settingsChanged = stabilizeVolatileFields(previousSettings, settings, SETTINGS_VOLATILE_FIELDS);
+        if (settingsChanged) {
+            // Back up the pristine original settings.json before writing (like CLAUDE.md)
+            const backupPath = backupSettingsFile(settingsPath);
+            if (backupPath) {
+                context.services.log(`  Backup created: ${backupPath}`);
+            }
+            writeFileSync(settingsPath, JSON.stringify(settings, null, 2), 'utf-8');
+        }
+        else {
+            context.services.log('  Settings unchanged — .claude/settings.json left as-is');
         }
-        // Write settings
-        writeFileSync(settingsPath, JSON.stringify(settings, null, 2), 'utf-8');
         // Write README and install hook assets (bridge script, cross-phase memory)
         this.writeHooksReadme(hooksDir, hookTypes);
         this.installHookAssets(hooksDir, context);
@@ -250,9 +266,9 @@ export class HooksPhase extends BasePhase {
         ];
         for (const src of sourcePaths) {
             if (existsSync(src) && src !== destPath) {
-                const { copyFileSync } = require('fs');
-                copyFileSync(src, destPath);
-                context.services.log('  Installed brain-checkpoint.cjs (copied)');
+                if (copyFileIfChanged(src, destPath)) {
+                    context.services.log('  Installed brain-checkpoint.cjs (copied)');
+                }
                 return;
             }
         }
@@ -280,9 +296,9 @@ export class HooksPhase extends BasePhase {
         ];
         for (const src of sourcePaths) {
             if (existsSync(src) && src !== destPath) {
-                const { copyFileSync } = require('fs');
-                copyFileSync(src, destPath);
-                context.services.log('  Installed statusline-v3.cjs (copied)');
+                if (copyFileIfChanged(src, destPath)) {
+                    context.services.log('  Installed statusline-v3.cjs (copied)');
+                }
                 return;
             }
         }
@@ -312,9 +328,9 @@ export class HooksPhase extends BasePhase {
         ];
         for (const src of sourcePaths) {
             if (existsSync(src) && src !== destPath) {
-                const { copyFileSync } = require('fs');
-                copyFileSync(src, destPath);
-                context.services.log('  Installed aqe-hook.cjs (copied)');
+                if (copyFileIfChanged(src, destPath)) {
+                    context.services.log('  Installed aqe-hook.cjs (copied)');
+                }
                 return;
             }
         }

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

@@ -11,7 +11,8 @@
  * walks up looking for .agentic-qe/, .git/, or package.json. This
  * makes the config portable across machines, devcontainers, and CI.
  */
-import { existsSync, readFileSync, writeFileSync } from 'fs';
+import { existsSync, readFileSync } from 'fs';
+import { writeFileIfChanged } from '../idempotent-write.js';
 import { join } from 'path';
 import { safeJsonParse } from '../../shared/safe-json.js';
 import { BasePhase, } from './phase-interface.js';
@@ -85,7 +86,8 @@ export class MCPPhase extends BasePhase {
         }
         const rootServers = rootMcpConfig.mcpServers;
         rootServers['agentic-qe'] = aqeServerConfig;
-        writeFileSync(rootMcpPath, JSON.stringify(rootMcpConfig, null, 2), 'utf-8');
+        // #778: no rewrite (mtime churn) when the merged config is unchanged.
+        writeFileIfChanged(rootMcpPath, JSON.stringify(rootMcpConfig, null, 2));
         context.services.log(`  MCP config: ${rootMcpPath}`);
         context.services.log(`  Server: agentic-qe`);
         if (dbFree) {

package/dist/init/phases/09-assets.d.ts

@@ -20,6 +20,16 @@ export interface AssetsResult {
         policy: 'full' | 'compact' | 'none';
         ownedBytes: number;
     };
+    codexComponents?: {
+        hooks: {
+            status: string;
+            error?: string;
+        };
+        skills: {
+            status: string;
+            error?: string;
+        };
+    };
 }
 /**
  * Assets phase - installs skills and agents

package/dist/init/phases/09-assets.js

@@ -37,6 +37,7 @@ export class AssetsPhase extends BasePhase {
         let kiroSkills = 0;
         let kiroHooks = 0;
         let codexGuidance;
+        let codexComponents;
         if (options.upgrade) {
             context.services.log(`  Upgrade mode: overwriting existing files`);
         }
@@ -303,6 +304,7 @@ export class AssetsPhase extends BasePhase {
             });
             const res = await installer.install();
             codexGuidance = { policy: res.guidancePolicy, ownedBytes: res.ownedGuidanceBytes };
+            codexComponents = { hooks: res.components.hooks, skills: res.components.skills };
             if (res.mcpConfigured)
                 platformsConfigured.push('codex');
             if (res.errors.length > 0)
@@ -361,6 +363,7 @@ export class AssetsPhase extends BasePhase {
             platformsConfigured,
             browserEngine,
             codexGuidance,
+            codexComponents,
         };
     }
     /**

package/dist/init/phases/10-workers.js

@@ -2,7 +2,8 @@
  * Phase 10: Workers
  * Configures background workers for continuous monitoring
  */
-import { existsSync, mkdirSync, writeFileSync } from 'fs';
+import { existsSync, mkdirSync } from 'fs';
+import { writeFileIfChanged, writeJsonIfChanged } from '../idempotent-write.js';
 import { join, dirname } from 'path';
 import { fileURLToPath } from 'url';
 import { BasePhase, } from './phase-interface.js';
@@ -86,7 +87,8 @@ export class WorkersPhase extends BasePhase {
             createdAt: new Date().toISOString(),
             daemonPid: null,
         };
-        writeFileSync(registryPath, JSON.stringify(registryData, null, 2), 'utf-8');
+        // #778: an unchanged registry keeps its bytes and original createdAt.
+        writeJsonIfChanged(registryPath, registryData, [['createdAt']]);
         // Write individual worker configs
         for (const workerName of config.workers.enabled) {
             const workerConfigPath = join(workersDir, `${workerName}.json`);
@@ -98,7 +100,7 @@ export class WorkersPhase extends BasePhase {
                 dataDir: join(projectRoot, '.agentic-qe', 'data'),
                 createdAt: new Date().toISOString(),
             };
-            writeFileSync(workerConfigPath, JSON.stringify(workerConfig, null, 2), 'utf-8');
+            writeJsonIfChanged(workerConfigPath, workerConfig, [['createdAt']]);
         }
         // Write cross-platform daemon startup script
         const daemonScriptPath = join(workersDir, 'start-daemon.cjs');
@@ -178,7 +180,7 @@ console.log('AQE v3 Worker Daemon started (PID: ' + child.pid + ')');
 console.log('Log file: ' + logFile);
 console.log('To stop: node ' + join(workersDir, 'stop-daemon.cjs'));
 `;
-        writeFileSync(daemonScriptPath, daemonScript);
+        writeFileIfChanged(daemonScriptPath, daemonScript);
         // Also write a cross-platform stop script
         const stopScriptPath = join(workersDir, 'stop-daemon.cjs');
         const stopScript = `#!/usr/bin/env node
@@ -205,7 +207,7 @@ try {
   try { unlinkSync(pidFile); } catch {}
 }
 `;
-        writeFileSync(stopScriptPath, stopScript);
+        writeFileIfChanged(stopScriptPath, stopScript);
         context.services.log(`  Workers dir: ${workersDir}`);
         context.services.log(`  Workers: ${config.workers.enabled.join(', ')}`);
         context.services.log(`  Registry: ${registryPath}`);

package/dist/init/phases/12-verification.js

@@ -7,9 +7,12 @@
  */
 import { existsSync, readFileSync } from 'fs';
 import { join, dirname } from 'path';
-import { mkdirSync, writeFileSync } from 'fs';
+import { mkdirSync } from 'fs';
+import { writeTextIfChangedIgnoring } from '../idempotent-write.js';
 import { BasePhase, } from './phase-interface.js';
 import { openDatabase } from '../../shared/safe-db.js';
+/** The `# <ISO timestamp>` header line written by configToYAML(). */
+const CONFIG_TIMESTAMP_LINE = /^# \d{4}-\d{2}-\d{2}T[\d:.]+Z$/;
 /**
  * Verification phase - verifies installation and writes markers
  */
@@ -135,7 +138,9 @@ export class VerificationPhase extends BasePhase {
             }
         }
         const yaml = this.configToYAML(config);
-        writeFileSync(configPath, yaml, 'utf-8');
+        // #778: the header carries a generation timestamp; ignore that line when
+        // deciding whether the file actually changed, so a repeat init is a no-op.
+        writeTextIfChangedIgnoring(configPath, yaml, CONFIG_TIMESTAMP_LINE);
     }
     /**
      * Load existing config.yaml and parse it

package/dist/init/project-analyzer.d.ts

@@ -5,6 +5,15 @@
  * Analyzes a project to detect frameworks, languages, tests, and configuration.
  */
 import type { ProjectAnalysis, DetectedFramework, DetectedLanguage, ExistingTests, CodeComplexity, CoverageMetrics } from './types.js';
+/**
+ * Directories never scanned by the analyzer: build/vendor output plus the
+ * tool-generated trees that `aqe init` itself (and the agent platforms it
+ * configures) writes into the project. Scanning AQE's own installed skills,
+ * helpers and hook scripts made a repeat `aqe init` "see" a different project
+ * than the first run (new languages, tests, complexity) and silently change
+ * the generated configuration (#778).
+ */
+export declare const ANALYZER_EXCLUDED_DIRS: readonly string[];
 export declare class ProjectAnalyzer {
     private projectRoot;
     constructor(projectRoot: string);

package/dist/init/project-analyzer.js

@@ -165,8 +165,27 @@ function getPackageVersion(root, packageName) {
         return undefined;
     return pkg.devDependencies?.[packageName] || pkg.dependencies?.[packageName];
 }
+/**
+ * Directories never scanned by the analyzer: build/vendor output plus the
+ * tool-generated trees that `aqe init` itself (and the agent platforms it
+ * configures) writes into the project. Scanning AQE's own installed skills,
+ * helpers and hook scripts made a repeat `aqe init` "see" a different project
+ * than the first run (new languages, tests, complexity) and silently change
+ * the generated configuration (#778).
+ */
+export const ANALYZER_EXCLUDED_DIRS = [
+    // build / vendor output
+    'node_modules', '.git', 'dist', 'build', 'coverage', '.next', '__pycache__',
+    // AQE-generated state and assets
+    '.agentic-qe', '.claude',
+    // agent-platform trees written by `aqe init --with-<platform>`
+    '.agents', '.codex', '.opencode', '.kiro', '.cursor', '.roo', '.kilocode',
+    '.windsurf', '.continue', '.clinerules',
+    // companion tooling state (claude-flow / ruflo)
+    '.swarm', '.claude-flow', '.hive-mind',
+];
 function walkDir(dir, callback, options = {}) {
-    const { maxDepth = 10, exclude = ['node_modules', '.git', 'dist', 'build', 'coverage', '.next', '__pycache__'] } = options;
+    const { maxDepth = 10, exclude = ANALYZER_EXCLUDED_DIRS } = options;
     function walk(currentDir, depth) {
         if (depth > maxDepth)
             return;

package/dist/init/self-configurator.d.ts

@@ -56,9 +56,11 @@ export declare class SelfConfigurator {
     /**
      * Recommend enabled domains
      *
-     * IMPORTANT: Always enable ALL 12 domains by default.
-     * Limiting domains causes "No factory registered" errors in fleet_init
-     * when MCP tools try to use domains that aren't enabled.
+     * IMPORTANT: Always enable ALL default domains (init's ALL_DOMAINS, derived
+     * from the canonical shared domain list). Limiting domains causes "No factory
+     * registered" errors in fleet_init when MCP tools try to use domains that
+     * aren't enabled. A hand-maintained copy here previously omitted
+     * enterprise-integration, so fresh and repeat inits disagreed (#778).
      *
      * Project analysis is used for prioritization and worker selection,
      * but all domains remain available for users who need them.

package/dist/init/self-configurator.js

@@ -51,7 +51,7 @@ const configurationRules = [
             // Complex code needs more careful testing
             config.autoTuning.parameters.push('complexity.analysisDepth');
             // Enable all quality domains
-            config.domains.enabled = ALL_DOMAINS;
+            config.domains.enabled = [...ALL_DOMAINS];
         },
     },
     // Low coverage rules
@@ -136,10 +136,11 @@ const configurationRules = [
             // Focus on test generation - but keep ALL domains enabled
             // Limiting domains causes "No factory registered" errors in fleet_init
             config.workers.enabled = ['pattern-consolidator'];
-            // Don't override domains.enabled - keep all 12 domains from createDefaultConfig
-            // Lower thresholds for new projects
-            config.learning.qualityThreshold = 0.5;
-            config.learning.promotionThreshold = 2;
+            // Don't override domains.enabled - keep every default domain.
+            // Pattern-promotion thresholds are NOT lowered here: the learning
+            // runtime always enforces PROMOTION_THRESHOLD / PROMOTION_MIN_SUCCESS_RATE,
+            // so a per-project override only made the generated settings misreport
+            // the runtime and flip between fresh and repeat inits (#778).
         },
     },
     // Many existing tests
@@ -222,7 +223,7 @@ export class SelfConfigurator {
      * Recommend learning configuration
      */
     recommendLearning(analysis) {
-        const config = { ...DEFAULT_LEARNING_CONFIG };
+        const config = structuredClone(DEFAULT_LEARNING_CONFIG);
         // Adjust HNSW based on project size
         if (analysis.codeComplexity.totalFiles > 1000) {
             config.hnswConfig = {
@@ -248,7 +249,7 @@ export class SelfConfigurator {
      * Recommend routing configuration
      */
     recommendRouting(analysis) {
-        const config = { ...DEFAULT_ROUTING_CONFIG };
+        const config = structuredClone(DEFAULT_ROUTING_CONFIG);
         // ML routing for complex projects, rules for simple
         if (analysis.codeComplexity.recommendation === 'simple') {
             config.mode = 'rules';
@@ -265,7 +266,7 @@ export class SelfConfigurator {
      * Recommend workers configuration
      */
     recommendWorkers(analysis) {
-        const config = { ...DEFAULT_WORKERS_CONFIG };
+        const config = structuredClone(DEFAULT_WORKERS_CONFIG);
         // Always enable core workers
         const workers = new Set(['pattern-consolidator', 'routing-accuracy-monitor']);
         // Add coverage scanner if coverage is low or missing
@@ -290,7 +291,7 @@ export class SelfConfigurator {
      * Recommend hooks configuration
      */
     recommendHooks(analysis) {
-        const config = { ...DEFAULT_HOOKS_CONFIG };
+        const config = structuredClone(DEFAULT_HOOKS_CONFIG);
         // Enable CI integration if CI is configured
         config.ciIntegration = analysis.hasCIConfig;
         // Enable pre-commit for projects with many tests
@@ -301,7 +302,7 @@ export class SelfConfigurator {
      * Recommend skills configuration
      */
     recommendSkills(analysis) {
-        const config = { ...DEFAULT_SKILLS_CONFIG };
+        const config = structuredClone(DEFAULT_SKILLS_CONFIG);
         // Always install by default
         config.install = true;
         // Install v2 methodology skills - version-agnostic best practices
@@ -316,7 +317,7 @@ export class SelfConfigurator {
      * Recommend auto-tuning configuration
      */
     recommendAutoTuning(analysis) {
-        const config = { ...DEFAULT_AUTO_TUNING_CONFIG };
+        const config = structuredClone(DEFAULT_AUTO_TUNING_CONFIG);
         // Disable auto-tuning for small projects
         if (analysis.codeComplexity.totalFiles < 20) {
             config.enabled = false;
@@ -326,30 +327,18 @@ export class SelfConfigurator {
     /**
      * Recommend enabled domains
      *
-     * IMPORTANT: Always enable ALL 12 domains by default.
-     * Limiting domains causes "No factory registered" errors in fleet_init
-     * when MCP tools try to use domains that aren't enabled.
+     * IMPORTANT: Always enable ALL default domains (init's ALL_DOMAINS, derived
+     * from the canonical shared domain list). Limiting domains causes "No factory
+     * registered" errors in fleet_init when MCP tools try to use domains that
+     * aren't enabled. A hand-maintained copy here previously omitted
+     * enterprise-integration, so fresh and repeat inits disagreed (#778).
      *
      * Project analysis is used for prioritization and worker selection,
      * but all domains remain available for users who need them.
      */
     recommendDomains(_analysis) {
-        // All 12 DDD domains - always enabled to prevent fleet_init failures
         // Users can disable domains manually in config.yaml if needed
-        return [
-            'test-generation',
-            'test-execution',
-            'coverage-analysis',
-            'quality-assessment',
-            'defect-intelligence',
-            'requirements-validation',
-            'code-intelligence',
-            'security-compliance',
-            'contract-testing',
-            'visual-accessibility',
-            'chaos-resilience',
-            'learning-optimization',
-        ];
+        return [...ALL_DOMAINS];
     }
     /**
      * Recommend max concurrent agents

package/dist/init/skills-installer.js

@@ -5,10 +5,11 @@
  * Installs AQE skills (both v2 methodology and v3 domain skills) to user projects.
  * Skills are copied from the bundled skills directory to the project's .claude/skills/.
  */
-import { existsSync, mkdirSync, readdirSync, statSync, readFileSync, writeFileSync, copyFileSync, unlinkSync, rmdirSync } from 'fs';
+import { existsSync, mkdirSync, readdirSync, statSync, readFileSync, copyFileSync, unlinkSync, rmdirSync } from 'fs';
 import { join } from 'path';
 import { toErrorMessage } from '../shared/error-utils.js';
 import { findPackageRoot } from './find-package-root.js';
+import { GENERATED_ON_LINE, writeTextIfChangedIgnoring } from './idempotent-write.js';
 // ============================================================================
 // Skill Categories (QE Skills Only - Claude Flow skills are managed separately)
 // ============================================================================
@@ -472,7 +473,8 @@ See \`.validation/README.md\` for usage instructions.
 
 *Generated by AQE v3 init on ${new Date().toISOString()}*
 `;
-        writeFileSync(join(skillsDir, 'README.md'), indexContent, 'utf-8');
+        // #778: ignore the generation-timestamp footer when deciding to rewrite.
+        writeTextIfChangedIgnoring(join(skillsDir, 'README.md'), indexContent, GENERATED_ON_LINE);
     }
     /**
      * Scan the skills directory to get all present skills

package/dist/init/token-bootstrap.d.ts

@@ -13,7 +13,7 @@ export interface TokenBootstrapConfig {
     enableOptimization: boolean;
     /** Enable persistence (default: true) */
     enablePersistence: boolean;
-    /** Storage directory for metrics (default: .aqe) */
+    /** Storage directory for metrics (default: <project>/.agentic-qe) */
     storagePath: string;
     /** Auto-save interval in ms (default: 60000 = 1 minute) */
     autoSaveIntervalMs: number;