@renseiai/agentfactory-cli 0.8.9 → 0.8.11

package/dist/src/agent.js

@@ -19,7 +19,7 @@
 import path from 'path';
 import { config } from 'dotenv';
 // Load environment variables from .env.local in CWD
-config({ path: path.resolve(process.cwd(), '.env.local') });
+config({ path: path.resolve(process.cwd(), '.env.local'), quiet: true });
 import { runAgent, C } from './lib/agent-runner.js';
 // ---------------------------------------------------------------------------
 // Usage

package/dist/src/analyze-logs.js

@@ -25,7 +25,7 @@
 import path from 'path';
 import { config } from 'dotenv';
 // Load environment variables from .env.local in CWD
-config({ path: path.resolve(process.cwd(), '.env.local') });
+config({ path: path.resolve(process.cwd(), '.env.local'), quiet: true });
 import { runLogAnalyzer, printSummary } from './lib/analyze-logs-runner.js';
 import { getVersion, checkForUpdate, printUpdateNotification } from './lib/version.js';
 const DEFAULT_POLL_INTERVAL = 5000;

package/dist/src/cleanup.d.ts

@@ -10,7 +10,7 @@
  * Options:
  *   --dry-run              Show what would be cleaned up without removing anything
  *   --force                Force removal / include branches with gone remotes
- *   --path <dir>           Custom worktrees directory (default: .worktrees)
+ *   --path <dir>           Custom worktrees directory (default: ../{repoName}.wt)
  *   --skip-worktrees       Skip worktree cleanup
  *   --skip-branches        Skip branch cleanup
  *   --help, -h             Show this help message

package/dist/src/cleanup.js

@@ -10,7 +10,7 @@
  * Options:
  *   --dry-run              Show what would be cleaned up without removing anything
  *   --force                Force removal / include branches with gone remotes
- *   --path <dir>           Custom worktrees directory (default: .worktrees)
+ *   --path <dir>           Custom worktrees directory (default: ../{repoName}.wt)
  *   --skip-worktrees       Skip worktree cleanup
  *   --skip-branches        Skip branch cleanup
  *   --help, -h             Show this help message
@@ -62,7 +62,7 @@ Usage:
 Options:
   --dry-run              Show what would be cleaned up without removing
   --force                Force worktree removal + delete branches with gone remotes
-  --path <dir>           Custom worktrees directory (default: .worktrees)
+  --path <dir>           Custom worktrees directory (default: ../{repoName}.wt)
   --skip-worktrees       Skip worktree cleanup
   --skip-branches        Skip branch cleanup
   --help, -h             Show this help message

package/dist/src/governor.js

@@ -25,7 +25,7 @@
 import path from 'path';
 import { config } from 'dotenv';
 // Load environment variables from .env.local
-config({ path: path.resolve(process.cwd(), '.env.local') });
+config({ path: path.resolve(process.cwd(), '.env.local'), quiet: true });
 import { parseGovernorArgs, runGovernor, } from './lib/governor-runner.js';
 import { createRealDependencies } from './lib/governor-dependencies.js';
 import { printStartupBanner, printScanSummary, printCircuitBreakerWarning, } from './lib/governor-logger.js';

package/dist/src/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/index.ts"],"names":[],"mappings":";AACA;;;;;GAKG;AAEH,QAAA,MAAM,OAAO,QAAkB,CAAA;AAE/B,iBAAS,SAAS,IAAI,IAAI,CAyBzB"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/index.ts"],"names":[],"mappings":";AACA;;;;;GAKG;AAEH,QAAA,MAAM,OAAO,QAAkB,CAAA;AAE/B,iBAAS,SAAS,IAAI,IAAI,CA0BzB"}

package/dist/src/index.js

@@ -25,6 +25,7 @@ Commands:
   analyze-logs    Analyze agent session logs for errors
   linear          Linear issue tracker operations
   sync-routes     Generate missing route and page files from manifest
+  setup           Configure development tools (mergiraf, etc.)
   status          Show fleet status (inline one-line summary)
   help            Show this help message
 
@@ -64,6 +65,9 @@ switch (command) {
     case 'sync-routes':
         import('./sync-routes');
         break;
+    case 'setup':
+        import('./setup');
+        break;
     case 'status':
         import('./status');
         break;

package/dist/src/lib/cleanup-runner.d.ts

@@ -9,7 +9,7 @@ export interface CleanupRunnerConfig {
     dryRun?: boolean;
     /** Force removal even if worktree appears active (default: false) */
     force?: boolean;
-    /** Custom worktrees directory (default: {gitRoot}/.worktrees) */
+    /** Custom worktrees directory (default: ../{repoName}.wt) */
     worktreePath?: string;
     /** Git root for default worktree path (default: auto-detect) */
     gitRoot?: string;

package/dist/src/lib/cleanup-runner.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cleanup-runner.d.ts","sourceRoot":"","sources":["../../../src/lib/cleanup-runner.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAaH,MAAM,WAAW,mBAAmB;IAClC,sEAAsE;IACtE,MAAM,CAAC,EAAE,OAAO,CAAA;IAChB,qEAAqE;IACrE,KAAK,CAAC,EAAE,OAAO,CAAA;IACf,iEAAiE;IACjE,YAAY,CAAC,EAAE,MAAM,CAAA;IACrB,gEAAgE;IAChE,OAAO,CAAC,EAAE,MAAM,CAAA;IAChB,6CAA6C;IAC7C,aAAa,CAAC,EAAE,OAAO,CAAA;IACvB,2CAA2C;IAC3C,YAAY,CAAC,EAAE,OAAO,CAAA;CACvB;AAED,MAAM,WAAW,qBAAqB;IACpC,OAAO,EAAE,MAAM,CAAA;IACf,QAAQ,EAAE,MAAM,CAAA;IAChB,OAAO,EAAE,MAAM,CAAA;IACf,OAAO,EAAE,MAAM,CAAA;IACf,MAAM,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,CAAA;CAC/C;AAED,MAAM,WAAW,aAAc,SAAQ,qBAAqB;IAC1D,QAAQ,EAAE,mBAAmB,CAAA;CAC9B;AAED,MAAM,WAAW,mBAAmB;IAClC,OAAO,EAAE,MAAM,CAAA;IACf,OAAO,EAAE,MAAM,CAAA;IACf,MAAM,EAAE,KAAK,CAAC;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,CAAA;CACjD;AAuBD,wBAAgB,UAAU,IAAI,MAAM,CASnC;AA8bD,wBAAgB,UAAU,CAAC,MAAM,CAAC,EAAE,mBAAmB,GAAG,aAAa,CAkBtE"}
+{"version":3,"file":"cleanup-runner.d.ts","sourceRoot":"","sources":["../../../src/lib/cleanup-runner.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAaH,MAAM,WAAW,mBAAmB;IAClC,sEAAsE;IACtE,MAAM,CAAC,EAAE,OAAO,CAAA;IAChB,qEAAqE;IACrE,KAAK,CAAC,EAAE,OAAO,CAAA;IACf,6DAA6D;IAC7D,YAAY,CAAC,EAAE,MAAM,CAAA;IACrB,gEAAgE;IAChE,OAAO,CAAC,EAAE,MAAM,CAAA;IAChB,6CAA6C;IAC7C,aAAa,CAAC,EAAE,OAAO,CAAA;IACvB,2CAA2C;IAC3C,YAAY,CAAC,EAAE,OAAO,CAAA;CACvB;AAED,MAAM,WAAW,qBAAqB;IACpC,OAAO,EAAE,MAAM,CAAA;IACf,QAAQ,EAAE,MAAM,CAAA;IAChB,OAAO,EAAE,MAAM,CAAA;IACf,OAAO,EAAE,MAAM,CAAA;IACf,MAAM,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,CAAA;CAC/C;AAED,MAAM,WAAW,aAAc,SAAQ,qBAAqB;IAC1D,QAAQ,EAAE,mBAAmB,CAAA;CAC9B;AAED,MAAM,WAAW,mBAAmB;IAClC,OAAO,EAAE,MAAM,CAAA;IACf,OAAO,EAAE,MAAM,CAAA;IACf,MAAM,EAAE,KAAK,CAAC;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,CAAA;CACjD;AAuBD,wBAAgB,UAAU,IAAI,MAAM,CASnC;AA8bD,wBAAgB,UAAU,CAAC,MAAM,CAAC,EAAE,mBAAmB,GAAG,aAAa,CAyCtE"}

package/dist/src/lib/cleanup-runner.js

@@ -430,14 +430,36 @@ function cleanupBranches(options) {
 // ---------------------------------------------------------------------------
 export function runCleanup(config) {
     const gitRoot = config?.gitRoot ?? getGitRoot();
+    const defaultWorktreePath = resolve(gitRoot, '..', basename(gitRoot) + '.wt');
     const options = {
         dryRun: config?.dryRun ?? false,
         force: config?.force ?? false,
-        worktreePath: config?.worktreePath ?? resolve(gitRoot, '.worktrees'),
+        worktreePath: config?.worktreePath ?? defaultWorktreePath,
     };
-    const worktreeResult = config?.skipWorktrees
-        ? { scanned: 0, orphaned: 0, cleaned: 0, skipped: 0, errors: [] }
-        : cleanup(options);
+    // Also scan legacy .worktrees/ location during migration period
+    const legacyPath = resolve(gitRoot, '.worktrees');
+    const hasLegacyWorktrees = !config?.worktreePath && existsSync(legacyPath);
+    if (hasLegacyWorktrees) {
+        console.log(`\nNote: Found worktrees at legacy location ${legacyPath}`);
+        console.log('  Run "af-migrate-worktrees" to move them to the new default location.\n');
+    }
+    let worktreeResult;
+    if (config?.skipWorktrees) {
+        worktreeResult = { scanned: 0, orphaned: 0, cleaned: 0, skipped: 0, errors: [] };
+    }
+    else {
+        worktreeResult = cleanup(options);
+        // Merge results from legacy .worktrees/ location if it exists
+        if (hasLegacyWorktrees) {
+            const legacyOptions = { ...options, worktreePath: legacyPath };
+            const legacyResult = cleanup(legacyOptions);
+            worktreeResult.scanned += legacyResult.scanned;
+            worktreeResult.orphaned += legacyResult.orphaned;
+            worktreeResult.cleaned += legacyResult.cleaned;
+            worktreeResult.skipped += legacyResult.skipped;
+            worktreeResult.errors.push(...legacyResult.errors);
+        }
+    }
     const branchResult = config?.skipBranches
         ? { scanned: 0, deleted: 0, errors: [] }
         : cleanupBranches(options);

package/dist/src/lib/orchestrator-runner.js

@@ -84,7 +84,7 @@ export async function runOrchestrator(config) {
     const orchestratorConfig = {
         project: config.project,
         maxConcurrent,
-        worktreePath: path.resolve(gitRoot, '.worktrees'),
+        worktreePath: path.resolve(gitRoot, '..', path.basename(gitRoot) + '.wt'),
         linearApiKey: config.linearApiKey,
         issueTrackerClient,
         statusMappings,

package/dist/src/lib/setup-mergiraf-runner.d.ts

@@ -0,0 +1,58 @@
+/**
+ * Setup Mergiraf Runner — Programmatic API for configuring mergiraf as git merge driver.
+ *
+ * Exports `setupMergiraf()` so mergiraf configuration can be invoked from code
+ * without going through process.argv / process.env / process.exit.
+ */
+export interface SetupMergirafConfig {
+    /** Show what would be done without making changes (default: false) */
+    dryRun?: boolean;
+    /** Only configure for agent worktrees, not the whole repo (default: false) */
+    worktreeOnly?: boolean;
+    /** Skip mergiraf binary check (default: false) */
+    skipCheck?: boolean;
+    /** Git root directory (default: auto-detect) */
+    gitRoot?: string;
+    /** Worktree path for per-worktree configuration (used with worktreeOnly) */
+    worktreePath?: string;
+}
+export interface SetupMergirafResult {
+    mergirafFound: boolean;
+    mergirafVersion: string;
+    configuredFileTypes: string[];
+    gitattributesWritten: boolean;
+    mergeDriverConfigured: boolean;
+    worktreeMode: boolean;
+    repoConfigUpdated: boolean;
+    errors: string[];
+    /** Process exit code: 0 = success, 1 = error, 2 = mergiraf not found */
+    exitCode: number;
+}
+export declare function getGitRoot(): string;
+/**
+ * Detect mergiraf binary and return version info.
+ * Uses `which` to find the binary and `mergiraf --version` for the version string.
+ */
+export declare function detectMergiraf(): {
+    found: boolean;
+    version: string;
+};
+/**
+ * Configure .gitattributes with mergiraf merge driver entries.
+ * Idempotent — skips entries that already exist.
+ */
+export declare function configureGitattributes(gitRoot: string, config: SetupMergirafConfig): {
+    written: boolean;
+    fileTypes: string[];
+};
+/**
+ * Configure git merge driver for mergiraf via `git config`.
+ * In worktree-only mode, uses `--worktree` flag for worktree-local config.
+ */
+export declare function configureMergeDriver(targetPath: string, config: SetupMergirafConfig): boolean;
+/**
+ * Update .agentfactory/config.yaml with mergeDriver: mergiraf.
+ */
+export declare function updateRepoConfig(gitRoot: string, config: SetupMergirafConfig): boolean;
+export declare function setupMergiraf(config?: SetupMergirafConfig): SetupMergirafResult;
+//# sourceMappingURL=setup-mergiraf-runner.d.ts.map

package/dist/src/lib/setup-mergiraf-runner.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"setup-mergiraf-runner.d.ts","sourceRoot":"","sources":["../../../src/lib/setup-mergiraf-runner.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAUH,MAAM,WAAW,mBAAmB;IAClC,sEAAsE;IACtE,MAAM,CAAC,EAAE,OAAO,CAAA;IAChB,8EAA8E;IAC9E,YAAY,CAAC,EAAE,OAAO,CAAA;IACtB,kDAAkD;IAClD,SAAS,CAAC,EAAE,OAAO,CAAA;IACnB,gDAAgD;IAChD,OAAO,CAAC,EAAE,MAAM,CAAA;IAChB,4EAA4E;IAC5E,YAAY,CAAC,EAAE,MAAM,CAAA;CACtB;AAED,MAAM,WAAW,mBAAmB;IAClC,aAAa,EAAE,OAAO,CAAA;IACtB,eAAe,EAAE,MAAM,CAAA;IACvB,mBAAmB,EAAE,MAAM,EAAE,CAAA;IAC7B,oBAAoB,EAAE,OAAO,CAAA;IAC7B,qBAAqB,EAAE,OAAO,CAAA;IAC9B,YAAY,EAAE,OAAO,CAAA;IACrB,iBAAiB,EAAE,OAAO,CAAA;IAC1B,MAAM,EAAE,MAAM,EAAE,CAAA;IAChB,wEAAwE;IACxE,QAAQ,EAAE,MAAM,CAAA;CACjB;AAMD,wBAAgB,UAAU,IAAI,MAAM,CASnC;AAMD;;;GAGG;AACH,wBAAgB,cAAc,IAAI;IAAE,KAAK,EAAE,OAAO,CAAC;IAAC,OAAO,EAAE,MAAM,CAAA;CAAE,CAuBpE;AAgBD;;;GAGG;AACH,wBAAgB,sBAAsB,CACpC,OAAO,EAAE,MAAM,EACf,MAAM,EAAE,mBAAmB,GAC1B;IAAE,OAAO,EAAE,OAAO,CAAC;IAAC,SAAS,EAAE,MAAM,EAAE,CAAA;CAAE,CAkD3C;AAED;;;GAGG;AACH,wBAAgB,oBAAoB,CAClC,UAAU,EAAE,MAAM,EAClB,MAAM,EAAE,mBAAmB,GAC1B,OAAO,CAoCT;AAED;;GAEG;AACH,wBAAgB,gBAAgB,CAC9B,OAAO,EAAE,MAAM,EACf,MAAM,EAAE,mBAAmB,GAC1B,OAAO,CAsCT;AAMD,wBAAgB,aAAa,CAAC,MAAM,CAAC,EAAE,mBAAmB,GAAG,mBAAmB,CA0D/E"}

package/dist/src/lib/setup-mergiraf-runner.js

@@ -0,0 +1,239 @@
+/**
+ * Setup Mergiraf Runner — Programmatic API for configuring mergiraf as git merge driver.
+ *
+ * Exports `setupMergiraf()` so mergiraf configuration can be invoked from code
+ * without going through process.argv / process.env / process.exit.
+ */
+import { execSync } from 'child_process';
+import { existsSync, readFileSync, writeFileSync } from 'fs';
+import { resolve } from 'path';
+// ---------------------------------------------------------------------------
+// Helpers
+// ---------------------------------------------------------------------------
+export function getGitRoot() {
+    try {
+        return execSync('git rev-parse --show-toplevel', {
+            encoding: 'utf-8',
+            stdio: ['pipe', 'pipe', 'pipe'],
+        }).trim();
+    }
+    catch {
+        return process.cwd();
+    }
+}
+// ---------------------------------------------------------------------------
+// Step functions
+// ---------------------------------------------------------------------------
+/**
+ * Detect mergiraf binary and return version info.
+ * Uses `which` to find the binary and `mergiraf --version` for the version string.
+ */
+export function detectMergiraf() {
+    try {
+        execSync('which mergiraf', { stdio: 'pipe', encoding: 'utf-8' });
+    }
+    catch {
+        console.log('mergiraf binary not found on PATH.\n');
+        console.log('Install mergiraf:');
+        console.log('  macOS:  brew install mergiraf');
+        console.log('  Linux:  cargo install mergiraf  (or download from Codeberg releases)');
+        console.log('  Any:    cargo install mergiraf  (requires Rust toolchain)\n');
+        return { found: false, version: '' };
+    }
+    let version = '';
+    try {
+        version = execSync('mergiraf --version', {
+            encoding: 'utf-8',
+            stdio: ['pipe', 'pipe', 'pipe'],
+        }).trim();
+    }
+    catch {
+        version = '(unknown)';
+    }
+    return { found: true, version };
+}
+/** File types that mergiraf supports for AST-aware merging. */
+const MERGIRAF_FILE_TYPES = [
+    '*.ts', '*.tsx', '*.js', '*.jsx', '*.mjs', '*.json',
+    '*.yaml', '*.yml', '*.py', '*.go', '*.rs',
+    '*.java', '*.css', '*.html',
+];
+/** Lock files that should use merge=ours strategy. */
+const LOCK_FILE_ENTRIES = [
+    'pnpm-lock.yaml merge=ours',
+    'package-lock.json merge=ours',
+    'yarn.lock merge=ours',
+];
+/**
+ * Configure .gitattributes with mergiraf merge driver entries.
+ * Idempotent — skips entries that already exist.
+ */
+export function configureGitattributes(gitRoot, config) {
+    const gitattributesPath = resolve(gitRoot, '.gitattributes');
+    let existing = '';
+    if (existsSync(gitattributesPath)) {
+        existing = readFileSync(gitattributesPath, 'utf-8');
+    }
+    const lines = [];
+    const addedTypes = [];
+    // Add mergiraf merge driver entries
+    for (const ft of MERGIRAF_FILE_TYPES) {
+        const entry = `${ft} merge=mergiraf`;
+        if (!existing.includes(entry)) {
+            lines.push(entry);
+            addedTypes.push(ft);
+        }
+    }
+    // Add lock file entries
+    for (const entry of LOCK_FILE_ENTRIES) {
+        if (!existing.includes(entry)) {
+            lines.push(entry);
+        }
+    }
+    if (lines.length === 0) {
+        console.log('  .gitattributes already configured — no changes needed');
+        return { written: true, fileTypes: MERGIRAF_FILE_TYPES };
+    }
+    if (config.dryRun) {
+        console.log('[DRY RUN] Would add to .gitattributes:');
+        for (const line of lines) {
+            console.log(`  ${line}`);
+        }
+        return { written: false, fileTypes: MERGIRAF_FILE_TYPES };
+    }
+    // Append new entries with a header comment
+    const newContent = existing.trimEnd() +
+        (existing.length > 0 ? '\n\n' : '') +
+        '# AST-aware merge driver (mergiraf)\n' +
+        lines.join('\n') + '\n';
+    writeFileSync(gitattributesPath, newContent, 'utf-8');
+    console.log(`  .gitattributes updated: ${addedTypes.length} file type(s) added`);
+    return { written: true, fileTypes: MERGIRAF_FILE_TYPES };
+}
+/**
+ * Configure git merge driver for mergiraf via `git config`.
+ * In worktree-only mode, uses `--worktree` flag for worktree-local config.
+ */
+export function configureMergeDriver(targetPath, config) {
+    const scope = config.worktreeOnly ? ' --worktree' : '';
+    const label = config.worktreeOnly ? 'worktree-local config' : '.git/config';
+    if (config.dryRun) {
+        console.log('[DRY RUN] Would configure git merge driver:');
+        console.log(`  git config${scope} merge.mergiraf.name "mergiraf"`);
+        console.log(`  git config${scope} merge.mergiraf.driver "mergiraf merge --git %O %A %B -s %S -x %X -y %Y -p %P"`);
+        return false;
+    }
+    try {
+        // Enable worktree config extension if using worktree-only mode
+        if (config.worktreeOnly) {
+            execSync('git config extensions.worktreeConfig true', {
+                stdio: 'pipe',
+                encoding: 'utf-8',
+                cwd: targetPath,
+            });
+        }
+        execSync(`git config${scope} merge.mergiraf.name "mergiraf"`, {
+            stdio: 'pipe',
+            encoding: 'utf-8',
+            cwd: targetPath,
+        });
+        execSync(`git config${scope} merge.mergiraf.driver "mergiraf merge --git %O %A %B -s %S -x %X -y %Y -p %P"`, { stdio: 'pipe', encoding: 'utf-8', cwd: targetPath });
+        console.log(`  Merge driver configured in ${label}`);
+        return true;
+    }
+    catch (error) {
+        console.error(`  Failed to configure merge driver: ${error instanceof Error ? error.message : String(error)}`);
+        return false;
+    }
+}
+/**
+ * Update .agentfactory/config.yaml with mergeDriver: mergiraf.
+ */
+export function updateRepoConfig(gitRoot, config) {
+    const configDir = resolve(gitRoot, '.agentfactory');
+    const configPath = resolve(configDir, 'config.yaml');
+    if (config.dryRun) {
+        console.log('[DRY RUN] Would set mergeDriver: mergiraf in .agentfactory/config.yaml');
+        return false;
+    }
+    if (!existsSync(configPath)) {
+        // Config file doesn't exist — skip (don't create one from scratch)
+        console.log('  .agentfactory/config.yaml not found — skipping repo config update');
+        return false;
+    }
+    try {
+        let content = readFileSync(configPath, 'utf-8');
+        if (content.includes('mergeDriver: mergiraf')) {
+            console.log('  .agentfactory/config.yaml already has mergeDriver: mergiraf');
+            return true;
+        }
+        if (content.includes('mergeDriver:')) {
+            // Replace existing mergeDriver value
+            content = content.replace(/mergeDriver:\s*\S+/, 'mergeDriver: mergiraf');
+        }
+        else {
+            // Append mergeDriver setting
+            content = content.trimEnd() + '\nmergeDriver: mergiraf\n';
+        }
+        writeFileSync(configPath, content, 'utf-8');
+        console.log('  .agentfactory/config.yaml updated: mergeDriver: mergiraf');
+        return true;
+    }
+    catch (error) {
+        console.error(`  Failed to update repo config: ${error instanceof Error ? error.message : String(error)}`);
+        return false;
+    }
+}
+// ---------------------------------------------------------------------------
+// Runner
+// ---------------------------------------------------------------------------
+export function setupMergiraf(config) {
+    const gitRoot = config?.gitRoot ?? getGitRoot();
+    const isWorktreeMode = config?.worktreeOnly ?? false;
+    // In worktree-only mode, use the worktree path for .gitattributes and git config
+    const targetPath = isWorktreeMode && config?.worktreePath
+        ? config.worktreePath
+        : gitRoot;
+    const result = {
+        mergirafFound: false,
+        mergirafVersion: '',
+        configuredFileTypes: [],
+        gitattributesWritten: false,
+        mergeDriverConfigured: false,
+        worktreeMode: isWorktreeMode,
+        repoConfigUpdated: false,
+        errors: [],
+        exitCode: 0,
+    };
+    // Step 1: Detect mergiraf binary
+    if (!config?.skipCheck) {
+        const detection = detectMergiraf();
+        result.mergirafFound = detection.found;
+        result.mergirafVersion = detection.version;
+        if (!detection.found) {
+            result.errors.push('mergiraf binary not found on PATH. Install with: brew install mergiraf (macOS) or cargo install mergiraf');
+            result.exitCode = 2;
+            return result;
+        }
+    }
+    else {
+        result.mergirafFound = true;
+        result.mergirafVersion = '(check skipped)';
+    }
+    if (config?.dryRun) {
+        console.log('[DRY RUN] Would configure mergiraf in:', targetPath);
+        console.log('[DRY RUN] Worktree-only mode:', isWorktreeMode);
+        return result;
+    }
+    // Step 2: Configure .gitattributes (in worktree root or repo root)
+    const gitattributes = configureGitattributes(targetPath, config ?? {});
+    result.gitattributesWritten = gitattributes.written;
+    result.configuredFileTypes = gitattributes.fileTypes;
+    // Step 3: Configure git merge driver (worktree-local or repo-wide)
+    result.mergeDriverConfigured = configureMergeDriver(targetPath, config ?? {});
+    // Step 4: Update repo config (always in git root, not worktree)
+    if (!isWorktreeMode) {
+        result.repoConfigUpdated = updateRepoConfig(gitRoot, config ?? {});
+    }
+    return result;
+}

package/dist/src/lib/worker-runner.js

@@ -421,7 +421,7 @@ export async function runWorker(config, signal) {
             const statusMappings = createLinearStatusMappings();
             const orchestrator = createOrchestrator({
                 maxConcurrent: 1,
-                worktreePath: path.resolve(gitRoot, '.worktrees'),
+                worktreePath: path.resolve(gitRoot, '..', path.basename(gitRoot) + '.wt'),
                 issueTrackerClient,
                 statusMappings,
                 toolPlugins: [linearPlugin, codeIntelligencePlugin],

package/dist/src/linear.js

@@ -37,7 +37,7 @@
 import path from 'path';
 import { config } from 'dotenv';
 // Load environment variables from .env.local
-config({ path: path.resolve(process.cwd(), '.env.local') });
+config({ path: path.resolve(process.cwd(), '.env.local'), quiet: true });
 import { runLinear, parseLinearArgs } from './lib/linear-runner.js';
 function printHelp() {
     console.log(`

package/dist/src/migrate-worktrees.d.ts

@@ -0,0 +1,17 @@
+#!/usr/bin/env node
+/**
+ * AgentFactory Worktree Migration CLI
+ *
+ * Migrates worktrees from the legacy .worktrees/ directory (inside repo)
+ * to the new sibling directory pattern (../{repoName}.wt/).
+ *
+ * Usage:
+ *   af-migrate-worktrees [options]
+ *
+ * Options:
+ *   --dry-run    Preview changes without executing
+ *   --force      Move even if processes are using worktrees
+ *   --help, -h   Show this help message
+ */
+export {};
+//# sourceMappingURL=migrate-worktrees.d.ts.map

package/dist/src/migrate-worktrees.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"migrate-worktrees.d.ts","sourceRoot":"","sources":["../../src/migrate-worktrees.ts"],"names":[],"mappings":";AACA;;;;;;;;;;;;;GAaG"}

package/dist/src/migrate-worktrees.js

@@ -0,0 +1,231 @@
+#!/usr/bin/env node
+/**
+ * AgentFactory Worktree Migration CLI
+ *
+ * Migrates worktrees from the legacy .worktrees/ directory (inside repo)
+ * to the new sibling directory pattern (../{repoName}.wt/).
+ *
+ * Usage:
+ *   af-migrate-worktrees [options]
+ *
+ * Options:
+ *   --dry-run    Preview changes without executing
+ *   --force      Move even if processes are using worktrees
+ *   --help, -h   Show this help message
+ */
+import { execSync } from 'child_process';
+import { existsSync, mkdirSync, readdirSync, renameSync, rmSync, statSync } from 'fs';
+import { basename, resolve } from 'path';
+function getGitRoot() {
+    try {
+        return execSync('git rev-parse --show-toplevel', {
+            encoding: 'utf-8',
+            stdio: ['pipe', 'pipe', 'pipe'],
+        }).trim();
+    }
+    catch {
+        return process.cwd();
+    }
+}
+function parseArgs() {
+    const args = process.argv.slice(2);
+    const result = { dryRun: false, force: false };
+    for (const arg of args) {
+        switch (arg) {
+            case '--dry-run':
+                result.dryRun = true;
+                break;
+            case '--force':
+                result.force = true;
+                break;
+            case '--help':
+            case '-h':
+                printHelp();
+                process.exit(0);
+        }
+    }
+    return result;
+}
+function printHelp() {
+    console.log(`
+AgentFactory Worktree Migration
+
+Migrates worktrees from .worktrees/ (inside repo) to ../{repoName}.wt/ (sibling directory).
+This prevents VSCode file watcher crashes when running multiple concurrent agents.
+
+Usage:
+  af-migrate-worktrees [options]
+
+Options:
+  --dry-run    Preview changes without executing
+  --force      Move even if processes are using worktrees
+  --help, -h   Show this help message
+`);
+}
+function main() {
+    const { dryRun, force } = parseArgs();
+    const gitRoot = getGitRoot();
+    const repoName = basename(gitRoot);
+    const legacyDir = resolve(gitRoot, '.worktrees');
+    const newDir = resolve(gitRoot, '..', `${repoName}.wt`);
+    console.log('\n=== AgentFactory Worktree Migration ===\n');
+    if (dryRun) {
+        console.log('[DRY RUN MODE - No changes will be made]\n');
+    }
+    if (!existsSync(legacyDir)) {
+        console.log(`No legacy worktrees directory found at ${legacyDir}`);
+        console.log('Nothing to migrate.\n');
+        return;
+    }
+    // List worktree entries (skip hidden directories like .patches)
+    const entries = readdirSync(legacyDir).filter(entry => {
+        if (entry.startsWith('.'))
+            return false;
+        try {
+            return statSync(resolve(legacyDir, entry)).isDirectory();
+        }
+        catch {
+            return false;
+        }
+    });
+    if (entries.length === 0) {
+        console.log(`Legacy worktrees directory exists but is empty: ${legacyDir}`);
+        if (!dryRun) {
+            rmSync(legacyDir, { recursive: true, force: true });
+            console.log('Removed empty legacy directory.\n');
+        }
+        return;
+    }
+    console.log(`Found ${entries.length} worktree(s) to migrate:`);
+    console.log(`  From: ${legacyDir}`);
+    console.log(`  To:   ${newDir}\n`);
+    // Check for running processes unless --force
+    if (!force && !dryRun) {
+        for (const entry of entries) {
+            const entryPath = resolve(legacyDir, entry);
+            try {
+                const lsofOutput = execSync(`lsof +D "${entryPath}" 2>/dev/null || true`, {
+                    encoding: 'utf-8',
+                    stdio: ['pipe', 'pipe', 'pipe'],
+                }).trim();
+                if (lsofOutput) {
+                    console.log(`WARNING: Processes are using worktree ${entry}:`);
+                    console.log(`  ${lsofOutput.split('\n')[0]}`);
+                    console.log('  Use --force to move anyway, or stop the processes first.\n');
+                    process.exit(1);
+                }
+            }
+            catch {
+                // lsof not available or failed, skip check
+            }
+        }
+    }
+    // Ensure target directory exists
+    if (!dryRun && !existsSync(newDir)) {
+        mkdirSync(newDir, { recursive: true });
+    }
+    let migrated = 0;
+    let failed = 0;
+    for (const entry of entries) {
+        const oldPath = resolve(legacyDir, entry);
+        const newPath = resolve(newDir, entry);
+        console.log(`  ${entry}:`);
+        console.log(`    ${oldPath} -> ${newPath}`);
+        if (dryRun) {
+            console.log('    [DRY RUN] Would move\n');
+            migrated++;
+            continue;
+        }
+        if (existsSync(newPath)) {
+            console.log(`    SKIPPED: Target already exists\n`);
+            failed++;
+            continue;
+        }
+        try {
+            // Try git worktree move first (preferred — updates git tracking)
+            execSync(`git worktree move "${oldPath}" "${newPath}"`, {
+                stdio: 'pipe',
+                encoding: 'utf-8',
+                cwd: gitRoot,
+            });
+            console.log('    OK (git worktree move)\n');
+            migrated++;
+        }
+        catch {
+            // Fallback: manual move + repair
+            try {
+                renameSync(oldPath, newPath);
+                execSync(`git worktree repair`, {
+                    stdio: 'pipe',
+                    encoding: 'utf-8',
+                    cwd: gitRoot,
+                });
+                console.log('    OK (manual move + repair)\n');
+                migrated++;
+            }
+            catch (fallbackError) {
+                console.log(`    FAILED: ${fallbackError instanceof Error ? fallbackError.message : String(fallbackError)}\n`);
+                failed++;
+            }
+        }
+    }
+    // Move .patches directory if it exists
+    const legacyPatchDir = resolve(legacyDir, '.patches');
+    if (existsSync(legacyPatchDir)) {
+        const newPatchDir = resolve(newDir, '.patches');
+        if (!dryRun) {
+            try {
+                renameSync(legacyPatchDir, newPatchDir);
+                console.log('  Moved .patches directory\n');
+            }
+            catch (error) {
+                console.log(`  Failed to move .patches: ${error instanceof Error ? error.message : String(error)}\n`);
+            }
+        }
+        else {
+            console.log('  [DRY RUN] Would move .patches directory\n');
+        }
+    }
+    // Clean up empty legacy directory
+    if (!dryRun && migrated > 0) {
+        try {
+            const remaining = readdirSync(legacyDir);
+            if (remaining.length === 0) {
+                rmSync(legacyDir, { recursive: true, force: true });
+                console.log(`Removed empty legacy directory: ${legacyDir}\n`);
+            }
+            else {
+                console.log(`Legacy directory not empty (${remaining.length} remaining entries), keeping it.\n`);
+            }
+        }
+        catch {
+            // Ignore cleanup errors
+        }
+    }
+    // Summary
+    console.log('=== Summary ===\n');
+    console.log(`  Migrated: ${migrated}`);
+    if (failed > 0) {
+        console.log(`  Failed:   ${failed}`);
+    }
+    console.log('');
+    // Verify git tracking
+    if (!dryRun && migrated > 0) {
+        try {
+            const worktreeList = execSync('git worktree list', {
+                encoding: 'utf-8',
+                cwd: gitRoot,
+            }).trim();
+            console.log('Git worktree list after migration:');
+            console.log(worktreeList);
+            console.log('');
+        }
+        catch {
+            // Ignore
+        }
+    }
+    if (failed > 0) {
+        process.exit(1);
+    }
+}
+main();

package/dist/src/orchestrator.js

@@ -20,7 +20,7 @@
 import path from 'path';
 import { config } from 'dotenv';
 // Load environment variables from .env.local
-config({ path: path.resolve(process.cwd(), '.env.local') });
+config({ path: path.resolve(process.cwd(), '.env.local'), quiet: true });
 import { runOrchestrator } from './lib/orchestrator-runner.js';
 import { getVersion, checkForUpdate, printUpdateNotification } from './lib/version.js';
 function parseArgs() {

package/dist/src/queue-admin.js

@@ -24,7 +24,7 @@
 import path from 'path';
 import { config } from 'dotenv';
 // Load environment variables from .env.local in CWD
-config({ path: path.resolve(process.cwd(), '.env.local') });
+config({ path: path.resolve(process.cwd(), '.env.local'), quiet: true });
 import { runQueueAdmin, C } from './lib/queue-admin-runner.js';
 // ---------------------------------------------------------------------------
 // Usage

package/dist/src/setup.d.ts

@@ -0,0 +1,21 @@
+#!/usr/bin/env node
+/**
+ * AgentFactory Setup CLI
+ *
+ * Configure development tools for agent workflows.
+ *
+ * Usage:
+ *   af-setup <tool> [options]
+ *   agentfactory setup <tool> [options]
+ *
+ * Tools:
+ *   mergiraf    Configure mergiraf AST-aware merge driver
+ *
+ * Options:
+ *   --dry-run          Show what would be done without making changes
+ *   --worktree-only    Only configure for agent worktrees
+ *   --skip-check       Skip mergiraf binary availability check
+ *   --help, -h         Show this help message
+ */
+export {};
+//# sourceMappingURL=setup.d.ts.map

package/dist/src/setup.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"setup.d.ts","sourceRoot":"","sources":["../../src/setup.ts"],"names":[],"mappings":";AACA;;;;;;;;;;;;;;;;;GAiBG"}

package/dist/src/setup.js

@@ -0,0 +1,142 @@
+#!/usr/bin/env node
+/**
+ * AgentFactory Setup CLI
+ *
+ * Configure development tools for agent workflows.
+ *
+ * Usage:
+ *   af-setup <tool> [options]
+ *   agentfactory setup <tool> [options]
+ *
+ * Tools:
+ *   mergiraf    Configure mergiraf AST-aware merge driver
+ *
+ * Options:
+ *   --dry-run          Show what would be done without making changes
+ *   --worktree-only    Only configure for agent worktrees
+ *   --skip-check       Skip mergiraf binary availability check
+ *   --help, -h         Show this help message
+ */
+import { setupMergiraf, getGitRoot } from './lib/setup-mergiraf-runner.js';
+function parseArgs() {
+    const args = process.argv.slice(2);
+    const result = {
+        subcommand: undefined,
+        dryRun: false,
+        worktreeOnly: false,
+        skipCheck: false,
+    };
+    for (let i = 0; i < args.length; i++) {
+        const arg = args[i];
+        switch (arg) {
+            case '--dry-run':
+                result.dryRun = true;
+                break;
+            case '--worktree-only':
+                result.worktreeOnly = true;
+                break;
+            case '--skip-check':
+                result.skipCheck = true;
+                break;
+            case '--help':
+            case '-h':
+                printHelp();
+                process.exit(0);
+                break;
+            default:
+                // First non-flag argument is the subcommand (skip 'setup' if present)
+                if (!arg.startsWith('-') && arg !== 'setup') {
+                    result.subcommand = arg;
+                }
+                break;
+        }
+    }
+    return result;
+}
+function printHelp() {
+    console.log(`
+AgentFactory Setup - Configure development tools for agent workflows
+
+Usage:
+  af-setup <tool> [options]
+  agentfactory setup <tool> [options]
+
+Tools:
+  mergiraf    Configure mergiraf AST-aware merge driver
+
+Options:
+  --dry-run          Show what would be done without making changes
+  --worktree-only    Only configure for agent worktrees (not whole repo)
+  --skip-check       Skip mergiraf binary availability check
+  --help, -h         Show this help message
+
+Examples:
+  # Configure mergiraf for the entire repository
+  af-setup mergiraf
+
+  # Configure only for agent worktrees (recommended)
+  af-setup mergiraf --worktree-only
+
+  # Preview changes without modifying anything
+  af-setup mergiraf --dry-run
+`);
+}
+function printSummary(result) {
+    console.log('=== Summary ===\n');
+    if (result.mergirafFound) {
+        console.log(`  Mergiraf:       found (${result.mergirafVersion})`);
+    }
+    else {
+        console.log('  Mergiraf:       NOT FOUND');
+    }
+    if (result.configuredFileTypes.length > 0) {
+        console.log(`  File types:     ${result.configuredFileTypes.join(', ')}`);
+    }
+    console.log(`  .gitattributes: ${result.gitattributesWritten ? 'configured' : 'not configured'}`);
+    console.log(`  Merge driver:   ${result.mergeDriverConfigured ? 'configured' : 'not configured'}`);
+    console.log(`  Worktree mode:  ${result.worktreeMode ? 'yes' : 'no (repo-wide)'}`);
+    console.log(`  Repo config:    ${result.repoConfigUpdated ? 'updated' : 'not updated'}`);
+    if (result.errors.length > 0) {
+        console.log('\n  Errors:');
+        for (const err of result.errors) {
+            console.log(`    - ${err}`);
+        }
+    }
+    if (result.gitattributesWritten && result.mergeDriverConfigured) {
+        console.log('\n  See: https://github.com/RenseiAI/agentfactory/blob/main/docs/guides/mergiraf-setup.md');
+    }
+    console.log('');
+}
+// Main execution
+function main() {
+    const args = parseArgs();
+    if (!args.subcommand) {
+        console.error('Error: No tool specified.\n');
+        printHelp();
+        process.exit(1);
+    }
+    switch (args.subcommand) {
+        case 'mergiraf': {
+            console.log('\n=== AgentFactory Setup: Mergiraf ===\n');
+            if (args.dryRun) {
+                console.log('[DRY RUN MODE - No changes will be made]\n');
+            }
+            const result = setupMergiraf({
+                dryRun: args.dryRun,
+                worktreeOnly: args.worktreeOnly,
+                skipCheck: args.skipCheck,
+                gitRoot: getGitRoot(),
+            });
+            printSummary(result);
+            if (result.errors.length > 0) {
+                process.exit(result.exitCode || 1);
+            }
+            break;
+        }
+        default:
+            console.error(`Unknown tool: ${args.subcommand}\n`);
+            printHelp();
+            process.exit(1);
+    }
+}
+main();

package/dist/src/status.js

@@ -17,7 +17,7 @@
 import path from 'path';
 import { config } from 'dotenv';
 // Load environment variables from .env.local in CWD
-config({ path: path.resolve(process.cwd(), '.env.local') });
+config({ path: path.resolve(process.cwd(), '.env.local'), quiet: true });
 import { runStatus, C } from './lib/status-runner.js';
 // ---------------------------------------------------------------------------
 // Usage

package/dist/src/worker-fleet.js

@@ -25,7 +25,7 @@ import path from 'path';
 import os from 'os';
 import { config as loadEnv } from 'dotenv';
 // Load environment variables from .env.local in CWD
-loadEnv({ path: path.resolve(process.cwd(), '.env.local') });
+loadEnv({ path: path.resolve(process.cwd(), '.env.local'), quiet: true });
 import { runWorkerFleet } from './lib/worker-fleet-runner.js';
 // ANSI colors (kept for help output)
 const colors = {

package/dist/src/worker.js

@@ -25,7 +25,7 @@
 import path from 'path';
 import { config } from 'dotenv';
 // Load environment variables from .env.local in CWD
-config({ path: path.resolve(process.cwd(), '.env.local') });
+config({ path: path.resolve(process.cwd(), '.env.local'), quiet: true });
 import os from 'os';
 import { runWorker } from './lib/worker-runner.js';
 function parseArgs() {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@renseiai/agentfactory-cli",
-  "version": "0.8.9",
+  "version": "0.8.11",
   "type": "module",
   "description": "CLI tools for AgentFactory — local orchestrator, remote worker, queue admin",
   "author": "Rensei AI (https://rensei.ai)",
@@ -38,7 +38,9 @@
     "af-linear": "dist/src/linear.js",
     "af-governor": "dist/src/governor.js",
     "af-sync-routes": "dist/src/sync-routes.js",
-    "af-status": "dist/src/status.js"
+    "af-setup": "dist/src/setup.js",
+    "af-status": "dist/src/status.js",
+    "af-migrate-worktrees": "dist/src/migrate-worktrees.js"
   },
   "main": "./dist/src/index.js",
   "module": "./dist/src/index.js",
@@ -94,6 +96,11 @@
       "import": "./dist/src/lib/sync-routes-runner.js",
       "default": "./dist/src/lib/sync-routes-runner.js"
     },
+    "./setup": {
+      "types": "./dist/src/lib/setup-mergiraf-runner.d.ts",
+      "import": "./dist/src/lib/setup-mergiraf-runner.js",
+      "default": "./dist/src/lib/setup-mergiraf-runner.js"
+    },
     "./status": {
       "types": "./dist/src/lib/status-runner.d.ts",
       "import": "./dist/src/lib/status-runner.js",
@@ -107,10 +114,10 @@
   ],
   "dependencies": {
     "dotenv": "^17.2.3",
-    "@renseiai/agentfactory": "0.8.9",
-    "@renseiai/plugin-linear": "0.8.9",
-    "@renseiai/agentfactory-server": "0.8.9",
-    "@renseiai/agentfactory-code-intelligence": "0.8.9"
+    "@renseiai/agentfactory-server": "0.8.11",
+    "@renseiai/agentfactory-code-intelligence": "0.8.11",
+    "@renseiai/plugin-linear": "0.8.11",
+    "@renseiai/agentfactory": "0.8.11"
   },
   "devDependencies": {
     "@types/node": "^22.5.4",