Merge pull request #409 from AutoMaker-Org/feat/worktrees-init-script

feat: worktrees init script

apps/server/src/index.ts

@@ -217,7 +217,7 @@ app.use('/api/sessions', createSessionsRoutes(agentService));
 app.use('/api/features', createFeaturesRoutes(featureLoader));
 app.use('/api/auto-mode', createAutoModeRoutes(autoModeService));
 app.use('/api/enhance-prompt', createEnhancePromptRoutes(settingsService));
-app.use('/api/worktree', createWorktreeRoutes());
+app.use('/api/worktree', createWorktreeRoutes(events));
 app.use('/api/git', createGitRoutes());
 app.use('/api/suggestions', createSuggestionsRoutes(events, settingsService));
 app.use('/api/models', createModelsRoutes());

apps/server/src/lib/worktree-metadata.ts

@@ -21,6 +21,12 @@ export interface WorktreeMetadata {
   branch: string;
   createdAt: string;
   pr?: WorktreePRInfo;
+  /** Whether the init script has been executed for this worktree */
+  initScriptRan?: boolean;
+  /** Status of the init script execution */
+  initScriptStatus?: 'running' | 'success' | 'failed';
+  /** Error message if init script failed */
+  initScriptError?: string;
 }
 
 /**

apps/server/src/routes/backlog-plan/routes/apply.ts

@@ -12,11 +12,22 @@ const featureLoader = new FeatureLoader();
 export function createApplyHandler() {
   return async (req: Request, res: Response): Promise<void> => {
     try {
-      const { projectPath, plan } = req.body as {
+      const {
+        projectPath,
+        plan,
+        branchName: rawBranchName,
+      } = req.body as {
         projectPath: string;
         plan: BacklogPlanResult;
+        branchName?: string;
       };
 
+      // Validate branchName: must be undefined or a non-empty trimmed string
+      const branchName =
+        typeof rawBranchName === 'string' && rawBranchName.trim().length > 0
+          ? rawBranchName.trim()
+          : undefined;
+
       if (!projectPath) {
         res.status(400).json({ success: false, error: 'projectPath required' });
         return;
@@ -82,6 +93,7 @@ export function createApplyHandler() {
             dependencies: change.feature.dependencies,
             priority: change.feature.priority,
             status: 'backlog',
+            branchName,
           });
 
           appliedChanges.push(`added:${newFeature.id}`);

apps/server/src/routes/worktree/common.ts

@@ -3,15 +3,51 @@
  */
 
 import { createLogger } from '@automaker/utils';
+import { spawnProcess } from '@automaker/platform';
 import { exec } from 'child_process';
 import { promisify } from 'util';
-import path from 'path';
 import { getErrorMessage as getErrorMessageShared, createLogError } from '../common.js';
-import { FeatureLoader } from '../../services/feature-loader.js';
 
 const logger = createLogger('Worktree');
 export const execAsync = promisify(exec);
-const featureLoader = new FeatureLoader();
+
+// ============================================================================
+// Secure Command Execution
+// ============================================================================
+
+/**
+ * Execute git command with array arguments to prevent command injection.
+ * Uses spawnProcess from @automaker/platform for secure, cross-platform execution.
+ *
+ * @param args - Array of git command arguments (e.g., ['worktree', 'add', path])
+ * @param cwd - Working directory to execute the command in
+ * @returns Promise resolving to stdout output
+ * @throws Error with stderr message if command fails
+ *
+ * @example
+ * ```typescript
+ * // Safe: no injection possible
+ * await execGitCommand(['branch', '-D', branchName], projectPath);
+ *
+ * // Instead of unsafe:
+ * // await execAsync(`git branch -D ${branchName}`, { cwd });
+ * ```
+ */
+export async function execGitCommand(args: string[], cwd: string): Promise<string> {
+  const result = await spawnProcess({
+    command: 'git',
+    args,
+    cwd,
+  });
+
+  // spawnProcess returns { stdout, stderr, exitCode }
+  if (result.exitCode === 0) {
+    return result.stdout;
+  } else {
+    const errorMessage = result.stderr || `Git command failed with code ${result.exitCode}`;
+    throw new Error(errorMessage);
+  }
+}
 
 // ============================================================================
 // Constants
@@ -99,18 +135,6 @@ export function normalizePath(p: string): string {
   return p.replace(/\\/g, '/');
 }
 
-/**
- * Check if a path is a git repo
- */
-export async function isGitRepo(repoPath: string): Promise<boolean> {
-  try {
-    await execAsync('git rev-parse --is-inside-work-tree', { cwd: repoPath });
-    return true;
-  } catch {
-    return false;
-  }
-}
-
 /**
  * Check if a git repository has at least one commit (i.e., HEAD exists)
  * Returns false for freshly initialized repos with no commits

apps/server/src/routes/worktree/index.ts

@@ -3,6 +3,7 @@
  */
 
 import { Router } from 'express';
+import type { EventEmitter } from '../../lib/events.js';
 import { validatePathParams } from '../../middleware/validate-paths.js';
 import { requireValidWorktree, requireValidProject, requireGitRepoOnly } from './middleware.js';
 import { createInfoHandler } from './routes/info.js';
@@ -32,8 +33,14 @@ import { createMigrateHandler } from './routes/migrate.js';
 import { createStartDevHandler } from './routes/start-dev.js';
 import { createStopDevHandler } from './routes/stop-dev.js';
 import { createListDevServersHandler } from './routes/list-dev-servers.js';
+import {
+  createGetInitScriptHandler,
+  createPutInitScriptHandler,
+  createDeleteInitScriptHandler,
+  createRunInitScriptHandler,
+} from './routes/init-script.js';
 
-export function createWorktreeRoutes(): Router {
+export function createWorktreeRoutes(events: EventEmitter): Router {
   const router = Router();
 
   router.post('/info', validatePathParams('projectPath'), createInfoHandler());
@@ -47,7 +54,7 @@ export function createWorktreeRoutes(): Router {
     requireValidProject,
     createMergeHandler()
   );
-  router.post('/create', validatePathParams('projectPath'), createCreateHandler());
+  router.post('/create', validatePathParams('projectPath'), createCreateHandler(events));
   router.post('/delete', validatePathParams('projectPath', 'worktreePath'), createDeleteHandler());
   router.post('/create-pr', createCreatePRHandler());
   router.post('/pr-info', createPRInfoHandler());
@@ -91,5 +98,15 @@ export function createWorktreeRoutes(): Router {
   router.post('/stop-dev', createStopDevHandler());
   router.post('/list-dev-servers', createListDevServersHandler());
 
+  // Init script routes
+  router.get('/init-script', createGetInitScriptHandler());
+  router.put('/init-script', validatePathParams('projectPath'), createPutInitScriptHandler());
+  router.delete('/init-script', validatePathParams('projectPath'), createDeleteInitScriptHandler());
+  router.post(
+    '/run-init-script',
+    validatePathParams('projectPath', 'worktreePath'),
+    createRunInitScriptHandler(events)
+  );
+
   return router;
 }

apps/server/src/routes/worktree/middleware.ts

@@ -3,7 +3,8 @@
  */
 
 import type { Request, Response, NextFunction } from 'express';
-import { isGitRepo, hasCommits } from './common.js';
+import { isGitRepo } from '@automaker/git-utils';
+import { hasCommits } from './common.js';
 
 interface ValidationOptions {
   /** Check if the path is a git repository (default: true) */

apps/server/src/routes/worktree/routes/create.ts

@@ -12,15 +12,19 @@ import { exec } from 'child_process';
 import { promisify } from 'util';
 import path from 'path';
 import * as secureFs from '../../../lib/secure-fs.js';
+import type { EventEmitter } from '../../../lib/events.js';
+import { isGitRepo } from '@automaker/git-utils';
 import {
-  isGitRepo,
   getErrorMessage,
   logError,
   normalizePath,
   ensureInitialCommit,
+  isValidBranchName,
+  execGitCommand,
 } from '../common.js';
 import { trackBranch } from './branch-tracking.js';
 import { createLogger } from '@automaker/utils';
+import { runInitScript } from '../../../services/init-script-service.js';
 
 const logger = createLogger('Worktree');
 
@@ -77,7 +81,7 @@ async function findExistingWorktreeForBranch(
   }
 }
 
-export function createCreateHandler() {
+export function createCreateHandler(events: EventEmitter) {
   return async (req: Request, res: Response): Promise<void> => {
     try {
       const { projectPath, branchName, baseBranch } = req.body as {
@@ -94,6 +98,26 @@ export function createCreateHandler() {
         return;
       }
 
+      // Validate branch name to prevent command injection
+      if (!isValidBranchName(branchName)) {
+        res.status(400).json({
+          success: false,
+          error:
+            'Invalid branch name. Branch names must contain only letters, numbers, dots, hyphens, underscores, and forward slashes.',
+        });
+        return;
+      }
+
+      // Validate base branch if provided
+      if (baseBranch && !isValidBranchName(baseBranch) && baseBranch !== 'HEAD') {
+        res.status(400).json({
+          success: false,
+          error:
+            'Invalid base branch name. Branch names must contain only letters, numbers, dots, hyphens, underscores, and forward slashes.',
+        });
+        return;
+      }
+
       if (!(await isGitRepo(projectPath))) {
         res.status(400).json({
           success: false,
@@ -143,30 +167,28 @@ export function createCreateHandler() {
       // Create worktrees directory if it doesn't exist
       await secureFs.mkdir(worktreesDir, { recursive: true });
 
-      // Check if branch exists
+      // Check if branch exists (using array arguments to prevent injection)
       let branchExists = false;
       try {
-        await execAsync(`git rev-parse --verify ${branchName}`, {
+        await execGitCommand(['rev-parse', '--verify', branchName], projectPath);
-          cwd: projectPath,
-        });
         branchExists = true;
       } catch {
         // Branch doesn't exist
       }
 
-      // Create worktree
+      // Create worktree (using array arguments to prevent injection)
-      let createCmd: string;
       if (branchExists) {
         // Use existing branch
-        createCmd = `git worktree add "${worktreePath}" ${branchName}`;
+        await execGitCommand(['worktree', 'add', worktreePath, branchName], projectPath);
       } else {
         // Create new branch from base or HEAD
         const base = baseBranch || 'HEAD';
-        createCmd = `git worktree add -b ${branchName} "${worktreePath}" ${base}`;
+        await execGitCommand(
+          ['worktree', 'add', '-b', branchName, worktreePath, base],
+          projectPath
+        );
       }
 
-      await execAsync(createCmd, { cwd: projectPath });
-
       // Note: We intentionally do NOT symlink .automaker to worktrees
       // Features and config are always accessed from the main project path
       // This avoids symlink loop issues when activating worktrees
@@ -177,6 +199,8 @@ export function createCreateHandler() {
       // Resolve to absolute path for cross-platform compatibility
       // normalizePath converts to forward slashes for API consistency
       const absoluteWorktreePath = path.resolve(worktreePath);
+
+      // Respond immediately (non-blocking)
       res.json({
         success: true,
         worktree: {
@@ -185,6 +209,17 @@ export function createCreateHandler() {
           isNew: !branchExists,
         },
       });
+
+      // Trigger init script asynchronously after response
+      // runInitScript internally checks if script exists and hasn't already run
+      runInitScript({
+        projectPath,
+        worktreePath: absoluteWorktreePath,
+        branch: branchName,
+        emitter: events,
+      }).catch((err) => {
+        logger.error(`Init script failed for ${branchName}:`, err);
+      });
     } catch (error) {
       logError(error, 'Create worktree failed');
       res.status(500).json({ success: false, error: getErrorMessage(error) });

apps/server/src/routes/worktree/routes/delete.ts

@@ -6,9 +6,11 @@ import type { Request, Response } from 'express';
 import { exec } from 'child_process';
 import { promisify } from 'util';
 import { isGitRepo } from '@automaker/git-utils';
-import { getErrorMessage, logError } from '../common.js';
+import { getErrorMessage, logError, isValidBranchName, execGitCommand } from '../common.js';
+import { createLogger } from '@automaker/utils';
 
 const execAsync = promisify(exec);
+const logger = createLogger('Worktree');
 
 export function createDeleteHandler() {
   return async (req: Request, res: Response): Promise<void> => {
@@ -46,22 +48,25 @@ export function createDeleteHandler() {
         // Could not get branch name
       }
 
-      // Remove the worktree
+      // Remove the worktree (using array arguments to prevent injection)
       try {
-        await execAsync(`git worktree remove "${worktreePath}" --force`, {
+        await execGitCommand(['worktree', 'remove', worktreePath, '--force'], projectPath);
-          cwd: projectPath,
-        });
       } catch (error) {
         // Try with prune if remove fails
-        await execAsync('git worktree prune', { cwd: projectPath });
+        await execGitCommand(['worktree', 'prune'], projectPath);
       }
 
       // Optionally delete the branch
       if (deleteBranch && branchName && branchName !== 'main' && branchName !== 'master') {
-        try {
+        // Validate branch name to prevent command injection
-          await execAsync(`git branch -D ${branchName}`, { cwd: projectPath });
+        if (!isValidBranchName(branchName)) {
-        } catch {
+          logger.warn(`Invalid branch name detected, skipping deletion: ${branchName}`);
-          // Branch deletion failed, not critical
+        } else {
+          try {
+            await execGitCommand(['branch', '-D', branchName], projectPath);
+          } catch {
+            // Branch deletion failed, not critical
+          }
         }
       }
 

apps/server/src/routes/worktree/routes/init-script.ts

@@ -0,0 +1,270 @@
+/**
+ * Init Script routes - Read/write/run the worktree-init.sh file
+ *
+ * POST /init-script - Read the init script content
+ * PUT /init-script - Write content to the init script file
+ * DELETE /init-script - Delete the init script file
+ * POST /run-init-script - Run the init script for a worktree
+ */
+
+import type { Request, Response } from 'express';
+import path from 'path';
+import * as secureFs from '../../../lib/secure-fs.js';
+import { getErrorMessage, logError, isValidBranchName } from '../common.js';
+import { createLogger } from '@automaker/utils';
+import type { EventEmitter } from '../../../lib/events.js';
+import { forceRunInitScript } from '../../../services/init-script-service.js';
+
+const logger = createLogger('InitScript');
+
+/** Fixed path for init script within .automaker directory */
+const INIT_SCRIPT_FILENAME = 'worktree-init.sh';
+
+/** Maximum allowed size for init scripts (1MB) */
+const MAX_SCRIPT_SIZE_BYTES = 1024 * 1024;
+
+/**
+ * Get the full path to the init script for a project
+ */
+function getInitScriptPath(projectPath: string): string {
+  return path.join(projectPath, '.automaker', INIT_SCRIPT_FILENAME);
+}
+
+/**
+ * GET /init-script - Read the init script content
+ */
+export function createGetInitScriptHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const projectPath = req.query.projectPath as string;
+
+      if (!projectPath) {
+        res.status(400).json({
+          success: false,
+          error: 'projectPath query parameter is required',
+        });
+        return;
+      }
+
+      const scriptPath = getInitScriptPath(projectPath);
+
+      try {
+        const content = await secureFs.readFile(scriptPath, 'utf-8');
+        res.json({
+          success: true,
+          exists: true,
+          content: content as string,
+          path: scriptPath,
+        });
+      } catch {
+        // File doesn't exist
+        res.json({
+          success: true,
+          exists: false,
+          content: '',
+          path: scriptPath,
+        });
+      }
+    } catch (error) {
+      logError(error, 'Read init script failed');
+      res.status(500).json({
+        success: false,
+        error: getErrorMessage(error),
+      });
+    }
+  };
+}
+
+/**
+ * PUT /init-script - Write content to the init script file
+ */
+export function createPutInitScriptHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, content } = req.body as {
+        projectPath: string;
+        content: string;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({
+          success: false,
+          error: 'projectPath is required',
+        });
+        return;
+      }
+
+      if (typeof content !== 'string') {
+        res.status(400).json({
+          success: false,
+          error: 'content must be a string',
+        });
+        return;
+      }
+
+      // Validate script size to prevent disk exhaustion
+      const sizeBytes = Buffer.byteLength(content, 'utf-8');
+      if (sizeBytes > MAX_SCRIPT_SIZE_BYTES) {
+        res.status(400).json({
+          success: false,
+          error: `Script size (${Math.round(sizeBytes / 1024)}KB) exceeds maximum allowed size (${Math.round(MAX_SCRIPT_SIZE_BYTES / 1024)}KB)`,
+        });
+        return;
+      }
+
+      // Log warning if potentially dangerous patterns are detected (non-blocking)
+      const dangerousPatterns = [
+        /rm\s+-rf\s+\/(?!\s*\$)/i, // rm -rf / (not followed by variable)
+        /curl\s+.*\|\s*(?:bash|sh)/i, // curl | bash
+        /wget\s+.*\|\s*(?:bash|sh)/i, // wget | sh
+      ];
+
+      for (const pattern of dangerousPatterns) {
+        if (pattern.test(content)) {
+          logger.warn(
+            `Init script contains potentially dangerous pattern: ${pattern.source}. User responsibility to verify script safety.`
+          );
+        }
+      }
+
+      const scriptPath = getInitScriptPath(projectPath);
+      const automakerDir = path.dirname(scriptPath);
+
+      // Ensure .automaker directory exists
+      await secureFs.mkdir(automakerDir, { recursive: true });
+
+      // Write the script content
+      await secureFs.writeFile(scriptPath, content, 'utf-8');
+
+      logger.info(`Wrote init script to ${scriptPath}`);
+
+      res.json({
+        success: true,
+        path: scriptPath,
+      });
+    } catch (error) {
+      logError(error, 'Write init script failed');
+      res.status(500).json({
+        success: false,
+        error: getErrorMessage(error),
+      });
+    }
+  };
+}
+
+/**
+ * DELETE /init-script - Delete the init script file
+ */
+export function createDeleteInitScriptHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath } = req.body as { projectPath: string };
+
+      if (!projectPath) {
+        res.status(400).json({
+          success: false,
+          error: 'projectPath is required',
+        });
+        return;
+      }
+
+      const scriptPath = getInitScriptPath(projectPath);
+
+      await secureFs.rm(scriptPath, { force: true });
+      logger.info(`Deleted init script at ${scriptPath}`);
+      res.json({
+        success: true,
+      });
+    } catch (error) {
+      logError(error, 'Delete init script failed');
+      res.status(500).json({
+        success: false,
+        error: getErrorMessage(error),
+      });
+    }
+  };
+}
+
+/**
+ * POST /run-init-script - Run (or re-run) the init script for a worktree
+ */
+export function createRunInitScriptHandler(events: EventEmitter) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, worktreePath, branch } = req.body as {
+        projectPath: string;
+        worktreePath: string;
+        branch: string;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({
+          success: false,
+          error: 'projectPath is required',
+        });
+        return;
+      }
+
+      if (!worktreePath) {
+        res.status(400).json({
+          success: false,
+          error: 'worktreePath is required',
+        });
+        return;
+      }
+
+      if (!branch) {
+        res.status(400).json({
+          success: false,
+          error: 'branch is required',
+        });
+        return;
+      }
+
+      // Validate branch name to prevent injection via environment variables
+      if (!isValidBranchName(branch)) {
+        res.status(400).json({
+          success: false,
+          error:
+            'Invalid branch name. Branch names must contain only letters, numbers, dots, hyphens, underscores, and forward slashes.',
+        });
+        return;
+      }
+
+      const scriptPath = getInitScriptPath(projectPath);
+
+      // Check if script exists
+      try {
+        await secureFs.access(scriptPath);
+      } catch {
+        res.status(404).json({
+          success: false,
+          error: 'No init script found. Create one in Settings > Worktrees.',
+        });
+        return;
+      }
+
+      logger.info(`Running init script for branch "${branch}" (forced)`);
+
+      // Run the script asynchronously (non-blocking)
+      forceRunInitScript({
+        projectPath,
+        worktreePath,
+        branch,
+        emitter: events,
+      });
+
+      // Return immediately - progress will be streamed via WebSocket events
+      res.json({
+        success: true,
+        message: 'Init script started',
+      });
+    } catch (error) {
+      logError(error, 'Run init script failed');
+      res.status(500).json({
+        success: false,
+        error: getErrorMessage(error),
+      });
+    }
+  };
+}

apps/server/src/services/init-script-service.ts

@@ -0,0 +1,360 @@
+/**
+ * Init Script Service - Executes worktree initialization scripts
+ *
+ * Runs the .automaker/worktree-init.sh script after worktree creation.
+ * Uses Git Bash on Windows for cross-platform shell script compatibility.
+ */
+
+import { spawn } from 'child_process';
+import path from 'path';
+import { createLogger } from '@automaker/utils';
+import { systemPathExists, getShellPaths, findGitBashPath } from '@automaker/platform';
+import { findCommand } from '../lib/cli-detection.js';
+import type { EventEmitter } from '../lib/events.js';
+import { readWorktreeMetadata, writeWorktreeMetadata } from '../lib/worktree-metadata.js';
+import * as secureFs from '../lib/secure-fs.js';
+
+const logger = createLogger('InitScript');
+
+export interface InitScriptOptions {
+  /** Absolute path to the project root */
+  projectPath: string;
+  /** Absolute path to the worktree directory */
+  worktreePath: string;
+  /** Branch name for this worktree */
+  branch: string;
+  /** Event emitter for streaming output */
+  emitter: EventEmitter;
+}
+
+interface ShellCommand {
+  shell: string;
+  args: string[];
+}
+
+/**
+ * Init Script Service
+ *
+ * Handles execution of worktree initialization scripts with cross-platform
+ * shell detection and proper streaming of output via WebSocket events.
+ */
+export class InitScriptService {
+  private cachedShellCommand: ShellCommand | null | undefined = undefined;
+
+  /**
+   * Get the path to the init script for a project
+   */
+  getInitScriptPath(projectPath: string): string {
+    return path.join(projectPath, '.automaker', 'worktree-init.sh');
+  }
+
+  /**
+   * Check if the init script has already been run for a worktree
+   */
+  async hasInitScriptRun(projectPath: string, branch: string): Promise<boolean> {
+    const metadata = await readWorktreeMetadata(projectPath, branch);
+    return metadata?.initScriptRan === true;
+  }
+
+  /**
+   * Find the appropriate shell for running scripts
+   * Uses findGitBashPath() on Windows to avoid WSL bash, then falls back to PATH
+   */
+  async findShellCommand(): Promise<ShellCommand | null> {
+    // Return cached result if available
+    if (this.cachedShellCommand !== undefined) {
+      return this.cachedShellCommand;
+    }
+
+    if (process.platform === 'win32') {
+      // On Windows, prioritize Git Bash over WSL bash (C:\Windows\System32\bash.exe)
+      // WSL bash may not be properly configured and causes ENOENT errors
+
+      // First try known Git Bash installation paths
+      const gitBashPath = await findGitBashPath();
+      if (gitBashPath) {
+        logger.debug(`Found Git Bash at: ${gitBashPath}`);
+        this.cachedShellCommand = { shell: gitBashPath, args: [] };
+        return this.cachedShellCommand;
+      }
+
+      // Fall back to finding bash in PATH, but skip WSL bash
+      const bashInPath = await findCommand(['bash']);
+      if (bashInPath && !bashInPath.toLowerCase().includes('system32')) {
+        logger.debug(`Found bash in PATH at: ${bashInPath}`);
+        this.cachedShellCommand = { shell: bashInPath, args: [] };
+        return this.cachedShellCommand;
+      }
+
+      logger.warn('Git Bash not found. WSL bash was skipped to avoid compatibility issues.');
+      this.cachedShellCommand = null;
+      return null;
+    }
+
+    // Unix-like systems: use getShellPaths() and check existence
+    const shellPaths = getShellPaths();
+    const posixShells = shellPaths.filter(
+      (p) => p.includes('bash') || p === '/bin/sh' || p === '/usr/bin/sh'
+    );
+
+    for (const shellPath of posixShells) {
+      try {
+        if (systemPathExists(shellPath)) {
+          this.cachedShellCommand = { shell: shellPath, args: [] };
+          return this.cachedShellCommand;
+        }
+      } catch {
+        // Path not allowed or doesn't exist, continue
+      }
+    }
+
+    // Ultimate fallback
+    if (systemPathExists('/bin/sh')) {
+      this.cachedShellCommand = { shell: '/bin/sh', args: [] };
+      return this.cachedShellCommand;
+    }
+
+    this.cachedShellCommand = null;
+    return null;
+  }
+
+  /**
+   * Run the worktree initialization script
+   * Non-blocking - returns immediately after spawning
+   */
+  async runInitScript(options: InitScriptOptions): Promise<void> {
+    const { projectPath, worktreePath, branch, emitter } = options;
+
+    const scriptPath = this.getInitScriptPath(projectPath);
+
+    // Check if script exists using secureFs (respects ALLOWED_ROOT_DIRECTORY)
+    try {
+      await secureFs.access(scriptPath);
+    } catch {
+      logger.debug(`No init script found at ${scriptPath}`);
+      return;
+    }
+
+    // Check if already run
+    if (await this.hasInitScriptRun(projectPath, branch)) {
+      logger.info(`Init script already ran for branch "${branch}", skipping`);
+      return;
+    }
+
+    // Get shell command
+    const shellCmd = await this.findShellCommand();
+    if (!shellCmd) {
+      const error =
+        process.platform === 'win32'
+          ? 'Git Bash not found. Please install Git for Windows to run init scripts.'
+          : 'No shell found (/bin/bash or /bin/sh)';
+      logger.error(error);
+
+      // Update metadata with error, preserving existing metadata
+      const existingMetadata = await readWorktreeMetadata(projectPath, branch);
+      await writeWorktreeMetadata(projectPath, branch, {
+        branch,
+        createdAt: existingMetadata?.createdAt || new Date().toISOString(),
+        pr: existingMetadata?.pr,
+        initScriptRan: true,
+        initScriptStatus: 'failed',
+        initScriptError: error,
+      });
+
+      emitter.emit('worktree:init-completed', {
+        projectPath,
+        worktreePath,
+        branch,
+        success: false,
+        error,
+      });
+      return;
+    }
+
+    logger.info(`Running init script for branch "${branch}" in ${worktreePath}`);
+    logger.debug(`Using shell: ${shellCmd.shell}`);
+
+    // Update metadata to mark as running
+    const existingMetadata = await readWorktreeMetadata(projectPath, branch);
+    await writeWorktreeMetadata(projectPath, branch, {
+      branch,
+      createdAt: existingMetadata?.createdAt || new Date().toISOString(),
+      pr: existingMetadata?.pr,
+      initScriptRan: false,
+      initScriptStatus: 'running',
+    });
+
+    // Emit started event
+    emitter.emit('worktree:init-started', {
+      projectPath,
+      worktreePath,
+      branch,
+    });
+
+    // Build safe environment - only pass necessary variables, not all of process.env
+    // This prevents exposure of sensitive credentials like ANTHROPIC_API_KEY
+    const safeEnv: Record<string, string> = {
+      // Automaker-specific variables
+      AUTOMAKER_PROJECT_PATH: projectPath,
+      AUTOMAKER_WORKTREE_PATH: worktreePath,
+      AUTOMAKER_BRANCH: branch,
+
+      // Essential system variables
+      PATH: process.env.PATH || '',
+      HOME: process.env.HOME || '',
+      USER: process.env.USER || '',
+      TMPDIR: process.env.TMPDIR || process.env.TEMP || process.env.TMP || '/tmp',
+
+      // Shell and locale
+      SHELL: process.env.SHELL || '',
+      LANG: process.env.LANG || 'en_US.UTF-8',
+      LC_ALL: process.env.LC_ALL || '',
+
+      // Force color output even though we're not a TTY
+      FORCE_COLOR: '1',
+      npm_config_color: 'always',
+      CLICOLOR_FORCE: '1',
+
+      // Git configuration
+      GIT_TERMINAL_PROMPT: '0',
+    };
+
+    // Platform-specific additions
+    if (process.platform === 'win32') {
+      safeEnv.USERPROFILE = process.env.USERPROFILE || '';
+      safeEnv.APPDATA = process.env.APPDATA || '';
+      safeEnv.LOCALAPPDATA = process.env.LOCALAPPDATA || '';
+      safeEnv.SystemRoot = process.env.SystemRoot || 'C:\\Windows';
+      safeEnv.TEMP = process.env.TEMP || '';
+    }
+
+    // Spawn the script with safe environment
+    const child = spawn(shellCmd.shell, [...shellCmd.args, scriptPath], {
+      cwd: worktreePath,
+      env: safeEnv,
+      stdio: ['ignore', 'pipe', 'pipe'],
+    });
+
+    // Stream stdout
+    child.stdout?.on('data', (data: Buffer) => {
+      const content = data.toString();
+      emitter.emit('worktree:init-output', {
+        projectPath,
+        branch,
+        type: 'stdout',
+        content,
+      });
+    });
+
+    // Stream stderr
+    child.stderr?.on('data', (data: Buffer) => {
+      const content = data.toString();
+      emitter.emit('worktree:init-output', {
+        projectPath,
+        branch,
+        type: 'stderr',
+        content,
+      });
+    });
+
+    // Handle completion
+    child.on('exit', async (code) => {
+      const success = code === 0;
+      const status = success ? 'success' : 'failed';
+
+      logger.info(`Init script for branch "${branch}" ${status} with exit code ${code}`);
+
+      // Update metadata
+      const metadata = await readWorktreeMetadata(projectPath, branch);
+      await writeWorktreeMetadata(projectPath, branch, {
+        branch,
+        createdAt: metadata?.createdAt || new Date().toISOString(),
+        pr: metadata?.pr,
+        initScriptRan: true,
+        initScriptStatus: status,
+        initScriptError: success ? undefined : `Exit code: ${code}`,
+      });
+
+      // Emit completion event
+      emitter.emit('worktree:init-completed', {
+        projectPath,
+        worktreePath,
+        branch,
+        success,
+        exitCode: code,
+      });
+    });
+
+    child.on('error', async (error) => {
+      logger.error(`Init script error for branch "${branch}":`, error);
+
+      // Update metadata
+      const metadata = await readWorktreeMetadata(projectPath, branch);
+      await writeWorktreeMetadata(projectPath, branch, {
+        branch,
+        createdAt: metadata?.createdAt || new Date().toISOString(),
+        pr: metadata?.pr,
+        initScriptRan: true,
+        initScriptStatus: 'failed',
+        initScriptError: error.message,
+      });
+
+      // Emit completion with error
+      emitter.emit('worktree:init-completed', {
+        projectPath,
+        worktreePath,
+        branch,
+        success: false,
+        error: error.message,
+      });
+    });
+  }
+
+  /**
+   * Force re-run the worktree initialization script
+   * Ignores the initScriptRan flag - useful for testing or re-setup
+   */
+  async forceRunInitScript(options: InitScriptOptions): Promise<void> {
+    const { projectPath, branch } = options;
+
+    // Reset the initScriptRan flag so the script will run
+    const metadata = await readWorktreeMetadata(projectPath, branch);
+    if (metadata) {
+      await writeWorktreeMetadata(projectPath, branch, {
+        ...metadata,
+        initScriptRan: false,
+        initScriptStatus: undefined,
+        initScriptError: undefined,
+      });
+    }
+
+    // Now run the script
+    await this.runInitScript(options);
+  }
+}
+
+// Singleton instance for convenience
+let initScriptService: InitScriptService | null = null;
+
+/**
+ * Get the singleton InitScriptService instance
+ */
+export function getInitScriptService(): InitScriptService {
+  if (!initScriptService) {
+    initScriptService = new InitScriptService();
+  }
+  return initScriptService;
+}
+
+// Export convenience functions that use the singleton
+export const getInitScriptPath = (projectPath: string) =>
+  getInitScriptService().getInitScriptPath(projectPath);
+
+export const hasInitScriptRun = (projectPath: string, branch: string) =>
+  getInitScriptService().hasInitScriptRun(projectPath, branch);
+
+export const runInitScript = (options: InitScriptOptions) =>
+  getInitScriptService().runInitScript(options);
+
+export const forceRunInitScript = (options: InitScriptOptions) =>
+  getInitScriptService().forceRunInitScript(options);

apps/ui/package.json

@@ -42,6 +42,8 @@
     "@automaker/dependency-resolver": "1.0.0",
     "@automaker/types": "1.0.0",
     "@codemirror/lang-xml": "6.1.0",
+    "@codemirror/language": "^6.12.1",
+    "@codemirror/legacy-modes": "^6.5.2",
     "@codemirror/theme-one-dark": "6.1.3",
     "@dnd-kit/core": "6.3.1",
     "@dnd-kit/sortable": "10.0.0",

apps/ui/src/components/ui/ansi-output.tsx

@@ -0,0 +1,276 @@
+import { useMemo } from 'react';
+import { cn } from '@/lib/utils';
+
+interface AnsiOutputProps {
+  text: string;
+  className?: string;
+}
+
+// ANSI color codes to CSS color mappings
+const ANSI_COLORS: Record<number, string> = {
+  // Standard colors
+  30: '#6b7280', // Black (use gray for visibility on dark bg)
+  31: '#ef4444', // Red
+  32: '#22c55e', // Green
+  33: '#eab308', // Yellow
+  34: '#3b82f6', // Blue
+  35: '#a855f7', // Magenta
+  36: '#06b6d4', // Cyan
+  37: '#d1d5db', // White
+  // Bright colors
+  90: '#9ca3af', // Bright Black (Gray)
+  91: '#f87171', // Bright Red
+  92: '#4ade80', // Bright Green
+  93: '#facc15', // Bright Yellow
+  94: '#60a5fa', // Bright Blue
+  95: '#c084fc', // Bright Magenta
+  96: '#22d3ee', // Bright Cyan
+  97: '#ffffff', // Bright White
+};
+
+const ANSI_BG_COLORS: Record<number, string> = {
+  40: 'transparent',
+  41: '#ef4444',
+  42: '#22c55e',
+  43: '#eab308',
+  44: '#3b82f6',
+  45: '#a855f7',
+  46: '#06b6d4',
+  47: '#f3f4f6',
+  // Bright backgrounds
+  100: '#374151',
+  101: '#f87171',
+  102: '#4ade80',
+  103: '#facc15',
+  104: '#60a5fa',
+  105: '#c084fc',
+  106: '#22d3ee',
+  107: '#ffffff',
+};
+
+interface TextSegment {
+  text: string;
+  style: {
+    color?: string;
+    backgroundColor?: string;
+    fontWeight?: string;
+    fontStyle?: string;
+    textDecoration?: string;
+  };
+}
+
+/**
+ * Strip hyperlink escape sequences (OSC 8)
+ * Format: ESC]8;;url ESC\ text ESC]8;; ESC\
+ */
+function stripHyperlinks(text: string): string {
+  // Remove OSC 8 hyperlink sequences
+  // eslint-disable-next-line no-control-regex
+  return text.replace(/\x1b\]8;;[^\x07\x1b]*(?:\x07|\x1b\\)/g, '');
+}
+
+/**
+ * Strip other OSC sequences (title, etc.)
+ */
+function stripOtherOSC(text: string): string {
+  // Remove OSC sequences (ESC ] ... BEL or ESC ] ... ST)
+  // eslint-disable-next-line no-control-regex
+  return text.replace(/\x1b\][^\x07\x1b]*(?:\x07|\x1b\\)/g, '');
+}
+
+function parseAnsi(text: string): TextSegment[] {
+  // Pre-process: strip hyperlinks and other OSC sequences
+  let processedText = stripHyperlinks(text);
+  processedText = stripOtherOSC(processedText);
+
+  const segments: TextSegment[] = [];
+
+  // Match ANSI escape sequences: ESC[...m (SGR - Select Graphic Rendition)
+  // Also handle ESC[K (erase line) and other CSI sequences by stripping them
+  // The ESC character can be \x1b, \033, \u001b
+  // eslint-disable-next-line no-control-regex
+  const ansiRegex = /\x1b\[([0-9;]*)([a-zA-Z])/g;
+
+  let currentStyle: TextSegment['style'] = {};
+  let lastIndex = 0;
+  let match;
+
+  while ((match = ansiRegex.exec(processedText)) !== null) {
+    // Add text before this escape sequence
+    if (match.index > lastIndex) {
+      const content = processedText.slice(lastIndex, match.index);
+      if (content) {
+        segments.push({ text: content, style: { ...currentStyle } });
+      }
+    }
+
+    const params = match[1];
+    const command = match[2];
+
+    // Only process 'm' command (SGR - graphics/color)
+    // Ignore other commands like K (erase), H (cursor), J (clear), etc.
+    if (command === 'm') {
+      // Parse the escape sequence codes
+      const codes = params ? params.split(';').map((c) => parseInt(c, 10) || 0) : [0];
+
+      for (let i = 0; i < codes.length; i++) {
+        const code = codes[i];
+
+        if (code === 0) {
+          // Reset all attributes
+          currentStyle = {};
+        } else if (code === 1) {
+          // Bold
+          currentStyle.fontWeight = 'bold';
+        } else if (code === 2) {
+          // Dim/faint
+          currentStyle.color = 'var(--muted-foreground)';
+        } else if (code === 3) {
+          // Italic
+          currentStyle.fontStyle = 'italic';
+        } else if (code === 4) {
+          // Underline
+          currentStyle.textDecoration = 'underline';
+        } else if (code === 22) {
+          // Normal intensity (not bold, not dim)
+          currentStyle.fontWeight = undefined;
+        } else if (code === 23) {
+          // Not italic
+          currentStyle.fontStyle = undefined;
+        } else if (code === 24) {
+          // Not underlined
+          currentStyle.textDecoration = undefined;
+        } else if (code === 38) {
+          // Extended foreground color
+          if (codes[i + 1] === 5 && codes[i + 2] !== undefined) {
+            // 256 color mode: 38;5;n
+            const colorIndex = codes[i + 2];
+            currentStyle.color = get256Color(colorIndex);
+            i += 2;
+          } else if (codes[i + 1] === 2 && codes[i + 4] !== undefined) {
+            // RGB mode: 38;2;r;g;b
+            const r = codes[i + 2];
+            const g = codes[i + 3];
+            const b = codes[i + 4];
+            currentStyle.color = `rgb(${r}, ${g}, ${b})`;
+            i += 4;
+          }
+        } else if (code === 48) {
+          // Extended background color
+          if (codes[i + 1] === 5 && codes[i + 2] !== undefined) {
+            // 256 color mode: 48;5;n
+            const colorIndex = codes[i + 2];
+            currentStyle.backgroundColor = get256Color(colorIndex);
+            i += 2;
+          } else if (codes[i + 1] === 2 && codes[i + 4] !== undefined) {
+            // RGB mode: 48;2;r;g;b
+            const r = codes[i + 2];
+            const g = codes[i + 3];
+            const b = codes[i + 4];
+            currentStyle.backgroundColor = `rgb(${r}, ${g}, ${b})`;
+            i += 4;
+          }
+        } else if (ANSI_COLORS[code]) {
+          // Standard foreground color (30-37, 90-97)
+          currentStyle.color = ANSI_COLORS[code];
+        } else if (ANSI_BG_COLORS[code]) {
+          // Standard background color (40-47, 100-107)
+          currentStyle.backgroundColor = ANSI_BG_COLORS[code];
+        } else if (code === 39) {
+          // Default foreground
+          currentStyle.color = undefined;
+        } else if (code === 49) {
+          // Default background
+          currentStyle.backgroundColor = undefined;
+        }
+      }
+    }
+
+    lastIndex = match.index + match[0].length;
+  }
+
+  // Add remaining text after last escape sequence
+  if (lastIndex < processedText.length) {
+    const content = processedText.slice(lastIndex);
+    if (content) {
+      segments.push({ text: content, style: { ...currentStyle } });
+    }
+  }
+
+  // If no segments were created (no ANSI codes), return the whole text
+  if (segments.length === 0 && processedText) {
+    segments.push({ text: processedText, style: {} });
+  }
+
+  return segments;
+}
+
+/**
+ * Convert 256-color palette index to CSS color
+ */
+function get256Color(index: number): string {
+  // 0-15: Standard colors
+  if (index < 16) {
+    const standardColors = [
+      '#000000',
+      '#cd0000',
+      '#00cd00',
+      '#cdcd00',
+      '#0000ee',
+      '#cd00cd',
+      '#00cdcd',
+      '#e5e5e5',
+      '#7f7f7f',
+      '#ff0000',
+      '#00ff00',
+      '#ffff00',
+      '#5c5cff',
+      '#ff00ff',
+      '#00ffff',
+      '#ffffff',
+    ];
+    return standardColors[index];
+  }
+
+  // 16-231: 6x6x6 color cube
+  if (index < 232) {
+    const n = index - 16;
+    const b = n % 6;
+    const g = Math.floor(n / 6) % 6;
+    const r = Math.floor(n / 36);
+    const toHex = (v: number) => (v === 0 ? 0 : 55 + v * 40);
+    return `rgb(${toHex(r)}, ${toHex(g)}, ${toHex(b)})`;
+  }
+
+  // 232-255: Grayscale
+  const gray = 8 + (index - 232) * 10;
+  return `rgb(${gray}, ${gray}, ${gray})`;
+}
+
+export function AnsiOutput({ text, className }: AnsiOutputProps) {
+  const segments = useMemo(() => parseAnsi(text), [text]);
+
+  return (
+    <pre
+      className={cn(
+        'font-mono text-xs whitespace-pre-wrap break-words text-muted-foreground',
+        className
+      )}
+    >
+      {segments.map((segment, index) => (
+        <span
+          key={index}
+          style={{
+            color: segment.style.color,
+            backgroundColor: segment.style.backgroundColor,
+            fontWeight: segment.style.fontWeight,
+            fontStyle: segment.style.fontStyle,
+            textDecoration: segment.style.textDecoration,
+          }}
+        >
+          {segment.text}
+        </span>
+      ))}
+    </pre>
+  );
+}

apps/ui/src/components/ui/shell-syntax-editor.tsx

@@ -0,0 +1,142 @@
+import CodeMirror from '@uiw/react-codemirror';
+import { StreamLanguage } from '@codemirror/language';
+import { shell } from '@codemirror/legacy-modes/mode/shell';
+import { EditorView } from '@codemirror/view';
+import { Extension } from '@codemirror/state';
+import { HighlightStyle, syntaxHighlighting } from '@codemirror/language';
+import { tags as t } from '@lezer/highlight';
+import { cn } from '@/lib/utils';
+
+interface ShellSyntaxEditorProps {
+  value: string;
+  onChange: (value: string) => void;
+  placeholder?: string;
+  className?: string;
+  minHeight?: string;
+  maxHeight?: string;
+  'data-testid'?: string;
+}
+
+// Syntax highlighting using CSS variables for theme compatibility
+const syntaxColors = HighlightStyle.define([
+  // Keywords (if, then, else, fi, for, while, do, done, case, esac, etc.)
+  { tag: t.keyword, color: 'var(--chart-4, oklch(0.7 0.15 280))' },
+
+  // Strings (single and double quoted)
+  { tag: t.string, color: 'var(--chart-1, oklch(0.646 0.222 41.116))' },
+
+  // Comments
+  { tag: t.comment, color: 'var(--muted-foreground)', fontStyle: 'italic' },
+
+  // Variables ($VAR, ${VAR})
+  { tag: t.variableName, color: 'var(--chart-2, oklch(0.6 0.118 184.704))' },
+
+  // Operators
+  { tag: t.operator, color: 'var(--muted-foreground)' },
+
+  // Numbers
+  { tag: t.number, color: 'var(--chart-3, oklch(0.7 0.15 150))' },
+
+  // Function names / commands
+  { tag: t.function(t.variableName), color: 'var(--primary)' },
+  { tag: t.attributeName, color: 'var(--chart-5, oklch(0.65 0.2 30))' },
+
+  // Default text
+  { tag: t.content, color: 'var(--foreground)' },
+]);
+
+// Editor theme using CSS variables
+const editorTheme = EditorView.theme({
+  '&': {
+    height: '100%',
+    fontSize: '0.875rem',
+    fontFamily: 'ui-monospace, SFMono-Regular, "SF Mono", Menlo, Consolas, monospace',
+    backgroundColor: 'transparent',
+    color: 'var(--foreground)',
+  },
+  '.cm-scroller': {
+    overflow: 'auto',
+    fontFamily: 'ui-monospace, SFMono-Regular, "SF Mono", Menlo, Consolas, monospace',
+  },
+  '.cm-content': {
+    padding: '0.75rem',
+    minHeight: '100%',
+    caretColor: 'var(--primary)',
+  },
+  '.cm-cursor, .cm-dropCursor': {
+    borderLeftColor: 'var(--primary)',
+  },
+  '&.cm-focused .cm-selectionBackground, .cm-selectionBackground, .cm-content ::selection': {
+    backgroundColor: 'oklch(0.55 0.25 265 / 0.3)',
+  },
+  '.cm-activeLine': {
+    backgroundColor: 'var(--accent)',
+    opacity: '0.3',
+  },
+  '.cm-line': {
+    padding: '0 0.25rem',
+  },
+  '&.cm-focused': {
+    outline: 'none',
+  },
+  '.cm-gutters': {
+    backgroundColor: 'transparent',
+    color: 'var(--muted-foreground)',
+    border: 'none',
+    paddingRight: '0.5rem',
+  },
+  '.cm-lineNumbers .cm-gutterElement': {
+    minWidth: '2rem',
+    textAlign: 'right',
+    paddingRight: '0.5rem',
+  },
+  '.cm-placeholder': {
+    color: 'var(--muted-foreground)',
+    fontStyle: 'italic',
+  },
+});
+
+// Combine all extensions
+const extensions: Extension[] = [
+  StreamLanguage.define(shell),
+  syntaxHighlighting(syntaxColors),
+  editorTheme,
+];
+
+export function ShellSyntaxEditor({
+  value,
+  onChange,
+  placeholder,
+  className,
+  minHeight = '200px',
+  maxHeight,
+  'data-testid': testId,
+}: ShellSyntaxEditorProps) {
+  return (
+    <div
+      className={cn('w-full rounded-lg border border-border bg-muted/30', className)}
+      style={{ minHeight }}
+      data-testid={testId}
+    >
+      <CodeMirror
+        value={value}
+        onChange={onChange}
+        extensions={extensions}
+        theme="none"
+        placeholder={placeholder}
+        height={maxHeight}
+        minHeight={minHeight}
+        className="[&_.cm-editor]:min-h-[inherit]"
+        basicSetup={{
+          lineNumbers: true,
+          foldGutter: false,
+          highlightActiveLine: true,
+          highlightSelectionMatches: true,
+          autocompletion: false,
+          bracketMatching: true,
+          indentOnInput: true,
+        }}
+      />
+    </div>
+  );
+}

apps/ui/src/components/views/board-view.tsx

@@ -75,6 +75,8 @@ import {
 } from './board-view/hooks';
 import { SelectionActionBar } from './board-view/components';
 import { MassEditDialog } from './board-view/dialogs';
+import { InitScriptIndicator } from './board-view/init-script-indicator';
+import { useInitScriptEvents } from '@/hooks/use-init-script-events';
 
 // Stable empty array to avoid infinite loop in selector
 const EMPTY_WORKTREES: ReturnType<ReturnType<typeof useAppStore.getState>['getWorktrees']> = [];
@@ -99,6 +101,8 @@ export function BoardView() {
     useWorktrees,
     enableDependencyBlocking,
     skipVerificationInAutoMode,
+    planUseSelectedWorktreeBranch,
+    addFeatureUseSelectedWorktreeBranch,
     isPrimaryWorktreeBranch,
     getPrimaryWorktreeBranch,
     setPipelineConfig,
@@ -107,6 +111,12 @@ export function BoardView() {
   const pipelineConfigByProject = useAppStore((state) => state.pipelineConfigByProject);
   // Subscribe to worktreePanelVisibleByProject to trigger re-renders when it changes
   const worktreePanelVisibleByProject = useAppStore((state) => state.worktreePanelVisibleByProject);
+  // Subscribe to showInitScriptIndicatorByProject to trigger re-renders when it changes
+  const showInitScriptIndicatorByProject = useAppStore(
+    (state) => state.showInitScriptIndicatorByProject
+  );
+  const getShowInitScriptIndicator = useAppStore((state) => state.getShowInitScriptIndicator);
+  const getDefaultDeleteBranch = useAppStore((state) => state.getDefaultDeleteBranch);
   const shortcuts = useKeyboardShortcutsConfig();
   const {
     features: hookFeatures,
@@ -252,6 +262,9 @@ export function BoardView() {
   // Window state hook for compact dialog mode
   const { isMaximized } = useWindowState();
 
+  // Init script events hook - subscribe to worktree init script events
+  useInitScriptEvents(currentProject?.path ?? null);
+
   // Keyboard shortcuts hook will be initialized after actions hook
 
   // Prevent hydration issues
@@ -1361,6 +1374,14 @@ export function BoardView() {
         isMaximized={isMaximized}
         parentFeature={spawnParentFeature}
         allFeatures={hookFeatures}
+        // When setting is enabled and a non-main worktree is selected, pass its branch to default to 'custom' work mode
+        selectedNonMainWorktreeBranch={
+          addFeatureUseSelectedWorktreeBranch && currentWorktreePath !== null
+            ? currentWorktreeBranch || undefined
+            : undefined
+        }
+        // When the worktree setting is disabled, force 'current' branch mode
+        forceCurrentBranchMode={!addFeatureUseSelectedWorktreeBranch}
       />
 
       {/* Edit Feature Dialog */}
@@ -1440,6 +1461,7 @@ export function BoardView() {
         setPendingPlanResult={setPendingBacklogPlan}
         isGeneratingPlan={isGeneratingPlan}
         setIsGeneratingPlan={setIsGeneratingPlan}
+        currentBranch={planUseSelectedWorktreeBranch ? selectedWorktreeBranch : undefined}
       />
 
       {/* Plan Approval Dialog */}
@@ -1507,6 +1529,7 @@ export function BoardView() {
             ? hookFeatures.filter((f) => f.branchName === selectedWorktreeForAction.branch).length
             : 0
         }
+        defaultDeleteBranch={getDefaultDeleteBranch(currentProject.path)}
         onDeleted={(deletedWorktree, _deletedBranch) => {
           // Reset features that were assigned to the deleted worktree (by branch)
           hookFeatures.forEach((feature) => {
@@ -1574,6 +1597,11 @@ export function BoardView() {
           setSelectedWorktreeForAction(null);
         }}
       />
+
+      {/* Init Script Indicator - floating overlay for worktree init script status */}
+      {getShowInitScriptIndicator(currentProject.path) && (
+        <InitScriptIndicator projectPath={currentProject.path} />
+      )}
     </div>
   );
 }

apps/ui/src/components/views/board-view/board-header.tsx

@@ -9,6 +9,8 @@ import { UsagePopover } from '@/components/usage-popover';
 import { useAppStore } from '@/store/app-store';
 import { useSetupStore } from '@/store/setup-store';
 import { AutoModeSettingsDialog } from './dialogs/auto-mode-settings-dialog';
+import { WorktreeSettingsDialog } from './dialogs/worktree-settings-dialog';
+import { PlanSettingsDialog } from './dialogs/plan-settings-dialog';
 import { getHttpApiClient } from '@/lib/http-api-client';
 import { BoardSearchBar } from './board-search-bar';
 import { BoardControls } from './board-controls';
@@ -55,10 +57,22 @@ export function BoardHeader({
   completedCount,
 }: BoardHeaderProps) {
   const [showAutoModeSettings, setShowAutoModeSettings] = useState(false);
+  const [showWorktreeSettings, setShowWorktreeSettings] = useState(false);
+  const [showPlanSettings, setShowPlanSettings] = useState(false);
   const apiKeys = useAppStore((state) => state.apiKeys);
   const claudeAuthStatus = useSetupStore((state) => state.claudeAuthStatus);
   const skipVerificationInAutoMode = useAppStore((state) => state.skipVerificationInAutoMode);
   const setSkipVerificationInAutoMode = useAppStore((state) => state.setSkipVerificationInAutoMode);
+  const planUseSelectedWorktreeBranch = useAppStore((state) => state.planUseSelectedWorktreeBranch);
+  const setPlanUseSelectedWorktreeBranch = useAppStore(
+    (state) => state.setPlanUseSelectedWorktreeBranch
+  );
+  const addFeatureUseSelectedWorktreeBranch = useAppStore(
+    (state) => state.addFeatureUseSelectedWorktreeBranch
+  );
+  const setAddFeatureUseSelectedWorktreeBranch = useAppStore(
+    (state) => state.setAddFeatureUseSelectedWorktreeBranch
+  );
   const codexAuthStatus = useSetupStore((state) => state.codexAuthStatus);
 
   // Worktree panel visibility (per-project)
@@ -132,9 +146,25 @@ export function BoardHeader({
               onCheckedChange={handleWorktreePanelToggle}
               data-testid="worktrees-toggle"
             />
+            <button
+              onClick={() => setShowWorktreeSettings(true)}
+              className="p-1 rounded hover:bg-accent/50 transition-colors"
+              title="Worktree Settings"
+              data-testid="worktree-settings-button"
+            >
+              <Settings2 className="w-4 h-4 text-muted-foreground" />
+            </button>
           </div>
         )}
 
+        {/* Worktree Settings Dialog */}
+        <WorktreeSettingsDialog
+          open={showWorktreeSettings}
+          onOpenChange={setShowWorktreeSettings}
+          addFeatureUseSelectedWorktreeBranch={addFeatureUseSelectedWorktreeBranch}
+          onAddFeatureUseSelectedWorktreeBranchChange={setAddFeatureUseSelectedWorktreeBranch}
+        />
+
         {/* Concurrency Control - only show after mount to prevent hydration issues */}
         {isMounted && (
           <Popover>
@@ -209,15 +239,33 @@ export function BoardHeader({
           onSkipVerificationChange={setSkipVerificationInAutoMode}
         />
 
-        <Button
+        {/* Plan Button with Settings */}
-          size="sm"
+        <div className={controlContainerClass} data-testid="plan-button-container">
-          variant="outline"
+          <button
-          onClick={onOpenPlanDialog}
+            onClick={onOpenPlanDialog}
-          data-testid="plan-backlog-button"
+            className="flex items-center gap-1.5 hover:text-foreground transition-colors"
-        >
+            data-testid="plan-backlog-button"
-          <Wand2 className="w-4 h-4 mr-2" />
+          >
-          Plan
+            <Wand2 className="w-4 h-4 text-muted-foreground" />
-        </Button>
+            <span className="text-sm font-medium">Plan</span>
+          </button>
+          <button
+            onClick={() => setShowPlanSettings(true)}
+            className="p-1 rounded hover:bg-accent/50 transition-colors"
+            title="Plan Settings"
+            data-testid="plan-settings-button"
+          >
+            <Settings2 className="w-4 h-4 text-muted-foreground" />
+          </button>
+        </div>
+
+        {/* Plan Settings Dialog */}
+        <PlanSettingsDialog
+          open={showPlanSettings}
+          onOpenChange={setShowPlanSettings}
+          planUseSelectedWorktreeBranch={planUseSelectedWorktreeBranch}
+          onPlanUseSelectedWorktreeBranchChange={setPlanUseSelectedWorktreeBranch}
+        />
       </div>
     </div>
   );

apps/ui/src/components/views/board-view/dialogs/add-feature-dialog.tsx

@@ -56,6 +56,32 @@ import {
 
 const logger = createLogger('AddFeatureDialog');
 
+/**
+ * Determines the default work mode based on global settings and current worktree selection.
+ *
+ * Priority:
+ * 1. If forceCurrentBranchMode is true, always defaults to 'current' (work on current branch)
+ * 2. If a non-main worktree is selected in the board header, defaults to 'custom' (use that branch)
+ * 3. If useWorktrees global setting is enabled, defaults to 'auto' (automatic worktree creation)
+ * 4. Otherwise, defaults to 'current' (work on current branch without isolation)
+ */
+const getDefaultWorkMode = (
+  useWorktrees: boolean,
+  selectedNonMainWorktreeBranch?: string,
+  forceCurrentBranchMode?: boolean
+): WorkMode => {
+  // If force current branch mode is enabled (worktree setting is off), always use 'current'
+  if (forceCurrentBranchMode) {
+    return 'current';
+  }
+  // If a non-main worktree is selected, default to 'custom' mode with that branch
+  if (selectedNonMainWorktreeBranch) {
+    return 'custom';
+  }
+  // Otherwise, respect the global worktree setting
+  return useWorktrees ? 'auto' : 'current';
+};
+
 type FeatureData = {
   title: string;
   category: string;
@@ -89,6 +115,16 @@ interface AddFeatureDialogProps {
   isMaximized: boolean;
   parentFeature?: Feature | null;
   allFeatures?: Feature[];
+  /**
+   * When a non-main worktree is selected in the board header, this will be set to that worktree's branch.
+   * When set, the dialog will default to 'custom' work mode with this branch pre-filled.
+   */
+  selectedNonMainWorktreeBranch?: string;
+  /**
+   * When true, forces the dialog to default to 'current' work mode (work on current branch).
+   * This is used when the "Use selected worktree branch" setting is disabled.
+   */
+  forceCurrentBranchMode?: boolean;
 }
 
 /**
@@ -112,6 +148,8 @@ export function AddFeatureDialog({
   isMaximized,
   parentFeature = null,
   allFeatures = [],
+  selectedNonMainWorktreeBranch,
+  forceCurrentBranchMode,
 }: AddFeatureDialogProps) {
   const isSpawnMode = !!parentFeature;
   const [workMode, setWorkMode] = useState<WorkMode>('current');
@@ -149,7 +187,7 @@ export function AddFeatureDialog({
   const [selectedAncestorIds, setSelectedAncestorIds] = useState<Set<string>>(new Set());
 
   // Get defaults from store
-  const { defaultPlanningMode, defaultRequirePlanApproval } = useAppStore();
+  const { defaultPlanningMode, defaultRequirePlanApproval, useWorktrees } = useAppStore();
 
   // Track previous open state to detect when dialog opens
   const wasOpenRef = useRef(false);
@@ -161,8 +199,12 @@ export function AddFeatureDialog({
 
     if (justOpened) {
       setSkipTests(defaultSkipTests);
-      setBranchName(defaultBranch || '');
+      // When a non-main worktree is selected, use its branch name for custom mode
-      setWorkMode('current');
+      // Otherwise, use the default branch
+      setBranchName(selectedNonMainWorktreeBranch || defaultBranch || '');
+      setWorkMode(
+        getDefaultWorkMode(useWorktrees, selectedNonMainWorktreeBranch, forceCurrentBranchMode)
+      );
       setPlanningMode(defaultPlanningMode);
       setRequirePlanApproval(defaultRequirePlanApproval);
       setModelEntry({ model: 'opus' });
@@ -186,6 +228,9 @@ export function AddFeatureDialog({
     defaultBranch,
     defaultPlanningMode,
     defaultRequirePlanApproval,
+    useWorktrees,
+    selectedNonMainWorktreeBranch,
+    forceCurrentBranchMode,
     parentFeature,
     allFeatures,
   ]);
@@ -270,10 +315,13 @@ export function AddFeatureDialog({
     setImagePaths([]);
     setTextFilePaths([]);
     setSkipTests(defaultSkipTests);
-    setBranchName('');
+    // When a non-main worktree is selected, use its branch name for custom mode
+    setBranchName(selectedNonMainWorktreeBranch || '');
     setPriority(2);
     setModelEntry({ model: 'opus' });
-    setWorkMode('current');
+    setWorkMode(
+      getDefaultWorkMode(useWorktrees, selectedNonMainWorktreeBranch, forceCurrentBranchMode)
+    );
     setPlanningMode(defaultPlanningMode);
     setRequirePlanApproval(defaultRequirePlanApproval);
     setPreviewMap(new Map());

apps/ui/src/components/views/board-view/dialogs/backlog-plan-dialog.tsx

@@ -63,6 +63,8 @@ interface BacklogPlanDialogProps {
   setPendingPlanResult: (result: BacklogPlanResult | null) => void;
   isGeneratingPlan: boolean;
   setIsGeneratingPlan: (generating: boolean) => void;
+  // Branch to use for created features (defaults to main if not provided)
+  currentBranch?: string;
 }
 
 type DialogMode = 'input' | 'review' | 'applying';
@@ -76,6 +78,7 @@ export function BacklogPlanDialog({
   setPendingPlanResult,
   isGeneratingPlan,
   setIsGeneratingPlan,
+  currentBranch,
 }: BacklogPlanDialogProps) {
   const [mode, setMode] = useState<DialogMode>('input');
   const [prompt, setPrompt] = useState('');
@@ -167,7 +170,7 @@ export function BacklogPlanDialog({
         }) || [],
     };
 
-    const result = await api.backlogPlan.apply(projectPath, filteredPlanResult);
+    const result = await api.backlogPlan.apply(projectPath, filteredPlanResult, currentBranch);
     if (result.success) {
       toast.success(`Applied ${result.appliedChanges?.length || 0} changes`);
       setPendingPlanResult(null);
@@ -184,6 +187,7 @@ export function BacklogPlanDialog({
     setPendingPlanResult,
     onPlanApplied,
     onClose,
+    currentBranch,
   ]);
 
   const handleDiscard = useCallback(() => {

apps/ui/src/components/views/board-view/dialogs/create-worktree-dialog.tsx

@@ -10,10 +10,73 @@ import {
 import { Button } from '@/components/ui/button';
 import { Input } from '@/components/ui/input';
 import { Label } from '@/components/ui/label';
-import { GitBranch, Loader2 } from 'lucide-react';
+import { GitBranch, Loader2, AlertCircle } from 'lucide-react';
 import { getElectronAPI } from '@/lib/electron';
 import { toast } from 'sonner';
 
+/**
+ * Parse git/worktree error messages and return user-friendly versions
+ */
+function parseWorktreeError(error: string): { title: string; description?: string } {
+  const errorLower = error.toLowerCase();
+
+  // Worktree already exists
+  if (errorLower.includes('already exists') && errorLower.includes('worktree')) {
+    return {
+      title: 'A worktree with this name already exists',
+      description: 'Try a different branch name or delete the existing worktree first.',
+    };
+  }
+
+  // Branch already checked out in another worktree
+  if (
+    errorLower.includes('already checked out') ||
+    errorLower.includes('is already used by worktree')
+  ) {
+    return {
+      title: 'This branch is already in use',
+      description: 'The branch is checked out in another worktree. Use a different branch name.',
+    };
+  }
+
+  // Branch name conflicts with existing branch
+  if (errorLower.includes('already exists') && errorLower.includes('branch')) {
+    return {
+      title: 'A branch with this name already exists',
+      description: 'The worktree will use the existing branch, or try a different name.',
+    };
+  }
+
+  // Not a git repository
+  if (errorLower.includes('not a git repository')) {
+    return {
+      title: 'Not a git repository',
+      description: 'Initialize git in this project first with "git init".',
+    };
+  }
+
+  // Lock file exists (another git operation in progress)
+  if (errorLower.includes('.lock') || errorLower.includes('lock file')) {
+    return {
+      title: 'Another git operation is in progress',
+      description: 'Wait for it to complete or remove stale lock files.',
+    };
+  }
+
+  // Permission denied
+  if (errorLower.includes('permission denied') || errorLower.includes('access denied')) {
+    return {
+      title: 'Permission denied',
+      description: 'Check file permissions for the project directory.',
+    };
+  }
+
+  // Default: return original error but cleaned up
+  return {
+    title: error.replace(/^(fatal|error):\s*/i, '').split('\n')[0],
+  };
+}
+
 interface CreatedWorktreeInfo {
   path: string;
   branch: string;
@@ -34,20 +97,21 @@ export function CreateWorktreeDialog({
 }: CreateWorktreeDialogProps) {
   const [branchName, setBranchName] = useState('');
   const [isLoading, setIsLoading] = useState(false);
-  const [error, setError] = useState<string | null>(null);
+  const [error, setError] = useState<{ title: string; description?: string } | null>(null);
 
   const handleCreate = async () => {
     if (!branchName.trim()) {
-      setError('Branch name is required');
+      setError({ title: 'Branch name is required' });
       return;
     }
 
     // Validate branch name (git-compatible)
     const validBranchRegex = /^[a-zA-Z0-9._/-]+$/;
     if (!validBranchRegex.test(branchName)) {
-      setError(
+      setError({
-        'Invalid branch name. Use only letters, numbers, dots, underscores, hyphens, and slashes.'
+        title: 'Invalid branch name',
-      );
+        description: 'Use only letters, numbers, dots, underscores, hyphens, and slashes.',
+      });
       return;
     }
 
@@ -57,7 +121,7 @@ export function CreateWorktreeDialog({
     try {
       const api = getElectronAPI();
       if (!api?.worktree?.create) {
-        setError('Worktree API not available');
+        setError({ title: 'Worktree API not available' });
         return;
       }
       const result = await api.worktree.create(projectPath, branchName);
@@ -70,10 +134,12 @@ export function CreateWorktreeDialog({
         onOpenChange(false);
         setBranchName('');
       } else {
-        setError(result.error || 'Failed to create worktree');
+        setError(parseWorktreeError(result.error || 'Failed to create worktree'));
       }
     } catch (err) {
-      setError(err instanceof Error ? err.message : 'Failed to create worktree');
+      setError(
+        parseWorktreeError(err instanceof Error ? err.message : 'Failed to create worktree')
+      );
     } finally {
       setIsLoading(false);
     }
@@ -114,7 +180,17 @@ export function CreateWorktreeDialog({
               className="font-mono text-sm"
               autoFocus
             />
-            {error && <p className="text-sm text-destructive">{error}</p>}
+            {error && (
+              <div className="flex items-start gap-2 p-3 rounded-md bg-destructive/10 border border-destructive/20">
+                <AlertCircle className="w-4 h-4 text-destructive mt-0.5 flex-shrink-0" />
+                <div className="space-y-1">
+                  <p className="text-sm font-medium text-destructive">{error.title}</p>
+                  {error.description && (
+                    <p className="text-xs text-destructive/80">{error.description}</p>
+                  )}
+                </div>
+              </div>
+            )}
           </div>
 
           <div className="text-xs text-muted-foreground space-y-1">

apps/ui/src/components/views/board-view/dialogs/delete-worktree-dialog.tsx

@@ -1,4 +1,4 @@
-import { useState } from 'react';
+import { useState, useEffect } from 'react';
 import {
   Dialog,
   DialogContent,
@@ -30,6 +30,8 @@ interface DeleteWorktreeDialogProps {
   onDeleted: (deletedWorktree: WorktreeInfo, deletedBranch: boolean) => void;
   /** Number of features assigned to this worktree's branch */
   affectedFeatureCount?: number;
+  /** Default value for the "delete branch" checkbox */
+  defaultDeleteBranch?: boolean;
 }
 
 export function DeleteWorktreeDialog({
@@ -39,10 +41,18 @@ export function DeleteWorktreeDialog({
   worktree,
   onDeleted,
   affectedFeatureCount = 0,
+  defaultDeleteBranch = false,
 }: DeleteWorktreeDialogProps) {
-  const [deleteBranch, setDeleteBranch] = useState(false);
+  const [deleteBranch, setDeleteBranch] = useState(defaultDeleteBranch);
   const [isLoading, setIsLoading] = useState(false);
 
+  // Reset deleteBranch to default when dialog opens
+  useEffect(() => {
+    if (open) {
+      setDeleteBranch(defaultDeleteBranch);
+    }
+  }, [open, defaultDeleteBranch]);
+
   const handleDelete = async () => {
     if (!worktree) return;
 

apps/ui/src/components/views/board-view/dialogs/plan-settings-dialog.tsx

@@ -0,0 +1,67 @@
+import {
+  Dialog,
+  DialogContent,
+  DialogDescription,
+  DialogHeader,
+  DialogTitle,
+} from '@/components/ui/dialog';
+import { Label } from '@/components/ui/label';
+import { Switch } from '@/components/ui/switch';
+import { GitBranch, Settings2 } from 'lucide-react';
+
+interface PlanSettingsDialogProps {
+  open: boolean;
+  onOpenChange: (open: boolean) => void;
+  planUseSelectedWorktreeBranch: boolean;
+  onPlanUseSelectedWorktreeBranchChange: (value: boolean) => void;
+}
+
+export function PlanSettingsDialog({
+  open,
+  onOpenChange,
+  planUseSelectedWorktreeBranch,
+  onPlanUseSelectedWorktreeBranchChange,
+}: PlanSettingsDialogProps) {
+  return (
+    <Dialog open={open} onOpenChange={onOpenChange}>
+      <DialogContent className="sm:max-w-md" data-testid="plan-settings-dialog">
+        <DialogHeader>
+          <DialogTitle className="flex items-center gap-2">
+            <Settings2 className="w-5 h-5" />
+            Plan Settings
+          </DialogTitle>
+          <DialogDescription>
+            Configure how the Plan feature creates and organizes new features.
+          </DialogDescription>
+        </DialogHeader>
+
+        <div className="space-y-4 py-4">
+          {/* Use Selected Worktree Branch Setting */}
+          <div className="flex items-start space-x-3 p-3 rounded-lg bg-secondary/50">
+            <div className="flex-1 space-y-1">
+              <div className="flex items-center justify-between">
+                <Label
+                  htmlFor="plan-worktree-branch-toggle"
+                  className="text-sm font-medium cursor-pointer flex items-center gap-2"
+                >
+                  <GitBranch className="w-4 h-4 text-brand-500" />
+                  Use selected worktree branch
+                </Label>
+                <Switch
+                  id="plan-worktree-branch-toggle"
+                  checked={planUseSelectedWorktreeBranch}
+                  onCheckedChange={onPlanUseSelectedWorktreeBranchChange}
+                  data-testid="plan-worktree-branch-toggle"
+                />
+              </div>
+              <p className="text-xs text-muted-foreground leading-relaxed">
+                When enabled, features created via the Plan dialog will be assigned to the currently
+                selected worktree branch. When disabled, features will be added to the main branch.
+              </p>
+            </div>
+          </div>
+        </div>
+      </DialogContent>
+    </Dialog>
+  );
+}

apps/ui/src/components/views/board-view/dialogs/worktree-settings-dialog.tsx

@@ -0,0 +1,67 @@
+import {
+  Dialog,
+  DialogContent,
+  DialogDescription,
+  DialogHeader,
+  DialogTitle,
+} from '@/components/ui/dialog';
+import { Label } from '@/components/ui/label';
+import { Switch } from '@/components/ui/switch';
+import { GitBranch, Settings2 } from 'lucide-react';
+
+interface WorktreeSettingsDialogProps {
+  open: boolean;
+  onOpenChange: (open: boolean) => void;
+  addFeatureUseSelectedWorktreeBranch: boolean;
+  onAddFeatureUseSelectedWorktreeBranchChange: (value: boolean) => void;
+}
+
+export function WorktreeSettingsDialog({
+  open,
+  onOpenChange,
+  addFeatureUseSelectedWorktreeBranch,
+  onAddFeatureUseSelectedWorktreeBranchChange,
+}: WorktreeSettingsDialogProps) {
+  return (
+    <Dialog open={open} onOpenChange={onOpenChange}>
+      <DialogContent className="sm:max-w-md" data-testid="worktree-settings-dialog">
+        <DialogHeader>
+          <DialogTitle className="flex items-center gap-2">
+            <Settings2 className="w-5 h-5" />
+            Worktree Settings
+          </DialogTitle>
+          <DialogDescription>
+            Configure how worktrees affect feature creation and organization.
+          </DialogDescription>
+        </DialogHeader>
+
+        <div className="space-y-4 py-4">
+          {/* Use Selected Worktree Branch Setting */}
+          <div className="flex items-start space-x-3 p-3 rounded-lg bg-secondary/50">
+            <div className="flex-1 space-y-1">
+              <div className="flex items-center justify-between">
+                <Label
+                  htmlFor="worktree-branch-toggle"
+                  className="text-sm font-medium cursor-pointer flex items-center gap-2"
+                >
+                  <GitBranch className="w-4 h-4 text-brand-500" />
+                  Use selected worktree branch
+                </Label>
+                <Switch
+                  id="worktree-branch-toggle"
+                  checked={addFeatureUseSelectedWorktreeBranch}
+                  onCheckedChange={onAddFeatureUseSelectedWorktreeBranchChange}
+                  data-testid="worktree-branch-toggle"
+                />
+              </div>
+              <p className="text-xs text-muted-foreground leading-relaxed">
+                When enabled, the Add Feature dialog will default to custom branch mode with the
+                currently selected worktree branch pre-filled.
+              </p>
+            </div>
+          </div>
+        </div>
+      </DialogContent>
+    </Dialog>
+  );
+}

apps/ui/src/components/views/board-view/init-script-indicator.tsx

@@ -0,0 +1,209 @@
+import { useState, useRef, useEffect, useCallback } from 'react';
+import { Terminal, Check, X, Loader2, ChevronDown, ChevronUp } from 'lucide-react';
+import { cn } from '@/lib/utils';
+import { useAppStore, type InitScriptState } from '@/store/app-store';
+import { AnsiOutput } from '@/components/ui/ansi-output';
+
+interface InitScriptIndicatorProps {
+  projectPath: string;
+}
+
+interface SingleIndicatorProps {
+  stateKey: string;
+  state: InitScriptState;
+  onDismiss: (key: string) => void;
+  isOnlyOne: boolean; // Whether this is the only indicator shown
+  autoDismiss: boolean; // Whether to auto-dismiss after completion
+}
+
+function SingleIndicator({
+  stateKey,
+  state,
+  onDismiss,
+  isOnlyOne,
+  autoDismiss,
+}: SingleIndicatorProps) {
+  const [showLogs, setShowLogs] = useState(false);
+  const logsEndRef = useRef<HTMLDivElement>(null);
+
+  const { status, output, branch, error } = state;
+
+  // Auto-scroll to bottom when new output arrives
+  useEffect(() => {
+    if (showLogs && logsEndRef.current) {
+      logsEndRef.current.scrollIntoView({ behavior: 'smooth' });
+    }
+  }, [output, showLogs]);
+
+  // Auto-expand logs when script starts (only if it's the only one or running)
+  useEffect(() => {
+    if (status === 'running' && isOnlyOne) {
+      setShowLogs(true);
+    }
+  }, [status, isOnlyOne]);
+
+  // Auto-dismiss after completion (5 seconds)
+  useEffect(() => {
+    if (autoDismiss && (status === 'success' || status === 'failed')) {
+      const timer = setTimeout(() => {
+        onDismiss(stateKey);
+      }, 5000);
+      return () => clearTimeout(timer);
+    }
+  }, [status, autoDismiss, stateKey, onDismiss]);
+
+  if (status === 'idle') return null;
+
+  return (
+    <div
+      className={cn(
+        'bg-card border border-border rounded-lg shadow-lg',
+        'min-w-[350px] max-w-[500px]',
+        'animate-in slide-in-from-right-5 duration-200'
+      )}
+    >
+      {/* Header */}
+      <div className="flex items-center justify-between p-3 border-b border-border/50">
+        <div className="flex items-center gap-2">
+          {status === 'running' && <Loader2 className="w-4 h-4 animate-spin text-blue-500" />}
+          {status === 'success' && <Check className="w-4 h-4 text-green-500" />}
+          {status === 'failed' && <X className="w-4 h-4 text-red-500" />}
+          <span className="font-medium text-sm">
+            Init Script{' '}
+            {status === 'running' ? 'Running' : status === 'success' ? 'Completed' : 'Failed'}
+          </span>
+        </div>
+        <div className="flex items-center gap-1">
+          <button
+            onClick={() => setShowLogs(!showLogs)}
+            className="p-1 hover:bg-accent rounded transition-colors"
+            title={showLogs ? 'Hide logs' : 'Show logs'}
+          >
+            {showLogs ? (
+              <ChevronDown className="w-4 h-4 text-muted-foreground" />
+            ) : (
+              <ChevronUp className="w-4 h-4 text-muted-foreground" />
+            )}
+          </button>
+          {status !== 'running' && (
+            <button
+              onClick={() => onDismiss(stateKey)}
+              className="p-1 hover:bg-accent rounded transition-colors"
+              title="Dismiss"
+            >
+              <X className="w-4 h-4 text-muted-foreground" />
+            </button>
+          )}
+        </div>
+      </div>
+
+      {/* Branch info */}
+      <div className="px-3 py-2 text-xs text-muted-foreground flex items-center gap-2">
+        <Terminal className="w-3.5 h-3.5" />
+        <span>Branch: {branch}</span>
+      </div>
+
+      {/* Logs (collapsible) */}
+      {showLogs && (
+        <div className="border-t border-border/50">
+          <div className="p-3 max-h-[300px] overflow-y-auto">
+            {output.length > 0 ? (
+              <AnsiOutput text={output.join('')} />
+            ) : (
+              <div className="text-xs text-muted-foreground/60 text-center py-2">
+                {status === 'running' ? 'Waiting for output...' : 'No output'}
+              </div>
+            )}
+            {error && <div className="mt-2 text-red-500 text-xs font-medium">Error: {error}</div>}
+            <div ref={logsEndRef} />
+          </div>
+        </div>
+      )}
+
+      {/* Status bar for completed states */}
+      {status !== 'running' && (
+        <div
+          className={cn(
+            'px-3 py-2 text-xs',
+            status === 'success' ? 'bg-green-500/10 text-green-600' : 'bg-red-500/10 text-red-600'
+          )}
+        >
+          {status === 'success'
+            ? 'Initialization completed successfully'
+            : 'Initialization failed - worktree is still usable'}
+        </div>
+      )}
+    </div>
+  );
+}
+
+export function InitScriptIndicator({ projectPath }: InitScriptIndicatorProps) {
+  const getInitScriptStatesForProject = useAppStore((s) => s.getInitScriptStatesForProject);
+  const clearInitScriptState = useAppStore((s) => s.clearInitScriptState);
+  const getAutoDismissInitScriptIndicator = useAppStore((s) => s.getAutoDismissInitScriptIndicator);
+  const [dismissedKeys, setDismissedKeys] = useState<Set<string>>(new Set());
+
+  // Get auto-dismiss setting
+  const autoDismiss = getAutoDismissInitScriptIndicator(projectPath);
+
+  // Get all init script states for this project
+  const allStates = getInitScriptStatesForProject(projectPath);
+
+  // Filter out dismissed and idle states
+  const activeStates = allStates.filter(
+    ({ key, state }) => !dismissedKeys.has(key) && state.status !== 'idle'
+  );
+
+  // Reset dismissed keys when a new script starts for a branch
+  useEffect(() => {
+    const runningKeys = allStates
+      .filter(({ state }) => state.status === 'running')
+      .map(({ key }) => key);
+
+    if (runningKeys.length > 0) {
+      setDismissedKeys((prev) => {
+        const newSet = new Set(prev);
+        runningKeys.forEach((key) => newSet.delete(key));
+        return newSet;
+      });
+    }
+  }, [allStates]);
+
+  const handleDismiss = useCallback(
+    (key: string) => {
+      setDismissedKeys((prev) => new Set(prev).add(key));
+      // Extract branch from key (format: "projectPath::branch")
+      const branch = key.split('::')[1];
+      if (branch) {
+        // Clear state after a delay to allow for future scripts
+        setTimeout(() => {
+          clearInitScriptState(projectPath, branch);
+        }, 100);
+      }
+    },
+    [projectPath, clearInitScriptState]
+  );
+
+  if (activeStates.length === 0) return null;
+
+  return (
+    <div
+      className={cn(
+        'fixed bottom-4 right-4 z-50 flex flex-col gap-2',
+        'max-h-[calc(100vh-120px)] overflow-y-auto',
+        'scrollbar-thin scrollbar-thumb-border scrollbar-track-transparent'
+      )}
+    >
+      {activeStates.map(({ key, state }) => (
+        <SingleIndicator
+          key={key}
+          stateKey={key}
+          state={state}
+          onDismiss={handleDismiss}
+          isOnlyOne={activeStates.length === 1}
+          autoDismiss={autoDismiss}
+        />
+      ))}
+    </div>
+  );
+}

apps/ui/src/components/views/board-view/worktree-panel/components/worktree-actions-dropdown.tsx

@@ -23,6 +23,7 @@ import {
   MessageSquare,
   GitMerge,
   AlertCircle,
+  RefreshCw,
   Copy,
 } from 'lucide-react';
 import { toast } from 'sonner';
@@ -55,6 +56,8 @@ interface WorktreeActionsDropdownProps {
   onStartDevServer: (worktree: WorktreeInfo) => void;
   onStopDevServer: (worktree: WorktreeInfo) => void;
   onOpenDevServerUrl: (worktree: WorktreeInfo) => void;
+  onRunInitScript: (worktree: WorktreeInfo) => void;
+  hasInitScript: boolean;
 }
 
 export function WorktreeActionsDropdown({
@@ -80,6 +83,8 @@ export function WorktreeActionsDropdown({
   onStartDevServer,
   onStopDevServer,
   onOpenDevServerUrl,
+  onRunInitScript,
+  hasInitScript,
 }: WorktreeActionsDropdownProps) {
   // Get available editors for the "Open In" submenu
   const { editors } = useAvailableEditors();
@@ -266,6 +271,12 @@ export function WorktreeActionsDropdown({
             </DropdownMenuSubContent>
           </DropdownMenuSub>
         )}
+        {!worktree.isMain && hasInitScript && (
+          <DropdownMenuItem onClick={() => onRunInitScript(worktree)} className="text-xs">
+            <RefreshCw className="w-3.5 h-3.5 mr-2" />
+            Re-run Init Script
+          </DropdownMenuItem>
+        )}
         <DropdownMenuSeparator />
         {worktree.hasChanges && (
           <TooltipWrapper

apps/ui/src/components/views/board-view/worktree-panel/components/worktree-tab.tsx

@@ -45,6 +45,8 @@ interface WorktreeTabProps {
   onStartDevServer: (worktree: WorktreeInfo) => void;
   onStopDevServer: (worktree: WorktreeInfo) => void;
   onOpenDevServerUrl: (worktree: WorktreeInfo) => void;
+  onRunInitScript: (worktree: WorktreeInfo) => void;
+  hasInitScript: boolean;
 }
 
 export function WorktreeTab({
@@ -85,6 +87,8 @@ export function WorktreeTab({
   onStartDevServer,
   onStopDevServer,
   onOpenDevServerUrl,
+  onRunInitScript,
+  hasInitScript,
 }: WorktreeTabProps) {
   let prBadge: JSX.Element | null = null;
   if (worktree.pr) {
@@ -333,6 +337,8 @@ export function WorktreeTab({
         onStartDevServer={onStartDevServer}
         onStopDevServer={onStopDevServer}
         onOpenDevServerUrl={onOpenDevServerUrl}
+        onRunInitScript={onRunInitScript}
+        hasInitScript={hasInitScript}
       />
     </div>
   );

apps/ui/src/components/views/board-view/worktree-panel/worktree-panel.tsx

@@ -1,7 +1,9 @@
-import { useEffect, useRef } from 'react';
+import { useEffect, useRef, useCallback, useState } from 'react';
 import { Button } from '@/components/ui/button';
 import { GitBranch, Plus, RefreshCw } from 'lucide-react';
 import { cn, pathsEqual } from '@/lib/utils';
+import { toast } from 'sonner';
+import { getHttpApiClient } from '@/lib/http-api-client';
 import type { WorktreePanelProps, WorktreeInfo } from './types';
 import {
   useWorktrees,
@@ -79,6 +81,28 @@ export function WorktreePanel({
     features,
   });
 
+  // Track whether init script exists for the project
+  const [hasInitScript, setHasInitScript] = useState(false);
+
+  useEffect(() => {
+    if (!projectPath) {
+      setHasInitScript(false);
+      return;
+    }
+
+    const checkInitScript = async () => {
+      try {
+        const api = getHttpApiClient();
+        const result = await api.worktree.getInitScript(projectPath);
+        setHasInitScript(result.success && result.exists);
+      } catch {
+        setHasInitScript(false);
+      }
+    };
+
+    checkInitScript();
+  }, [projectPath]);
+
   // Periodic interval check (5 seconds) to detect branch changes on disk
   // Reduced from 1s to 5s to minimize GPU/CPU usage from frequent re-renders
   const intervalRef = useRef<NodeJS.Timeout | null>(null);
@@ -113,6 +137,33 @@ export function WorktreePanel({
     }
   };
 
+  const handleRunInitScript = useCallback(
+    async (worktree: WorktreeInfo) => {
+      if (!projectPath) return;
+
+      try {
+        const api = getHttpApiClient();
+        const result = await api.worktree.runInitScript(
+          projectPath,
+          worktree.path,
+          worktree.branch
+        );
+
+        if (!result.success) {
+          toast.error('Failed to run init script', {
+            description: result.error,
+          });
+        }
+        // Success feedback will come via WebSocket events (init-started, init-output, init-completed)
+      } catch (error) {
+        toast.error('Failed to run init script', {
+          description: error instanceof Error ? error.message : 'Unknown error',
+        });
+      }
+    },
+    [projectPath]
+  );
+
   const mainWorktree = worktrees.find((w) => w.isMain);
   const nonMainWorktrees = worktrees.filter((w) => !w.isMain);
 
@@ -162,6 +213,8 @@ export function WorktreePanel({
             onStartDevServer={handleStartDevServer}
             onStopDevServer={handleStopDevServer}
             onOpenDevServerUrl={handleOpenDevServerUrl}
+            onRunInitScript={handleRunInitScript}
+            hasInitScript={hasInitScript}
           />
         )}
       </div>
@@ -216,6 +269,8 @@ export function WorktreePanel({
                   onStartDevServer={handleStartDevServer}
                   onStopDevServer={handleStopDevServer}
                   onOpenDevServerUrl={handleOpenDevServerUrl}
+                  onRunInitScript={handleRunInitScript}
+                  hasInitScript={hasInitScript}
                 />
               );
             })}

apps/ui/src/components/views/settings-view.tsx

@@ -15,6 +15,7 @@ import { TerminalSection } from './settings-view/terminal/terminal-section';
 import { AudioSection } from './settings-view/audio/audio-section';
 import { KeyboardShortcutsSection } from './settings-view/keyboard-shortcuts/keyboard-shortcuts-section';
 import { FeatureDefaultsSection } from './settings-view/feature-defaults/feature-defaults-section';
+import { WorktreesSection } from './settings-view/worktrees';
 import { DangerZoneSection } from './settings-view/danger-zone/danger-zone-section';
 import { AccountSection } from './settings-view/account';
 import { SecuritySection } from './settings-view/security';
@@ -149,17 +150,19 @@ export function SettingsView() {
             defaultSkipTests={defaultSkipTests}
             enableDependencyBlocking={enableDependencyBlocking}
             skipVerificationInAutoMode={skipVerificationInAutoMode}
-            useWorktrees={useWorktrees}
             defaultPlanningMode={defaultPlanningMode}
             defaultRequirePlanApproval={defaultRequirePlanApproval}
             onDefaultSkipTestsChange={setDefaultSkipTests}
             onEnableDependencyBlockingChange={setEnableDependencyBlocking}
             onSkipVerificationInAutoModeChange={setSkipVerificationInAutoMode}
-            onUseWorktreesChange={setUseWorktrees}
             onDefaultPlanningModeChange={setDefaultPlanningMode}
             onDefaultRequirePlanApprovalChange={setDefaultRequirePlanApproval}
           />
         );
+      case 'worktrees':
+        return (
+          <WorktreesSection useWorktrees={useWorktrees} onUseWorktreesChange={setUseWorktrees} />
+        );
       case 'account':
         return <AccountSection />;
       case 'security':

apps/ui/src/components/views/settings-view/config/navigation.ts

@@ -14,6 +14,8 @@ import {
   MessageSquareText,
   User,
   Shield,
+  Cpu,
+  GitBranch,
 } from 'lucide-react';
 import { AnthropicIcon, CursorIcon, OpenAIIcon, OpenCodeIcon } from '@/components/ui/provider-icon';
 import type { SettingsViewId } from '../hooks/use-settings-view';
@@ -37,6 +39,7 @@ export const GLOBAL_NAV_GROUPS: NavigationGroup[] = [
     items: [
       { id: 'model-defaults', label: 'Model Defaults', icon: Workflow },
       { id: 'defaults', label: 'Feature Defaults', icon: FlaskConical },
+      { id: 'worktrees', label: 'Worktrees', icon: GitBranch },
       { id: 'prompts', label: 'Prompt Customization', icon: MessageSquareText },
       { id: 'api-keys', label: 'API Keys', icon: Key },
       {

apps/ui/src/components/views/settings-view/feature-defaults/feature-defaults-section.tsx

@@ -3,7 +3,6 @@ import { Checkbox } from '@/components/ui/checkbox';
 import {
   FlaskConical,
   TestTube,
-  GitBranch,
   AlertCircle,
   Zap,
   ClipboardList,
@@ -27,13 +26,11 @@ interface FeatureDefaultsSectionProps {
   defaultSkipTests: boolean;
   enableDependencyBlocking: boolean;
   skipVerificationInAutoMode: boolean;
-  useWorktrees: boolean;
   defaultPlanningMode: PlanningMode;
   defaultRequirePlanApproval: boolean;
   onDefaultSkipTestsChange: (value: boolean) => void;
   onEnableDependencyBlockingChange: (value: boolean) => void;
   onSkipVerificationInAutoModeChange: (value: boolean) => void;
-  onUseWorktreesChange: (value: boolean) => void;
   onDefaultPlanningModeChange: (value: PlanningMode) => void;
   onDefaultRequirePlanApprovalChange: (value: boolean) => void;
 }
@@ -42,13 +39,11 @@ export function FeatureDefaultsSection({
   defaultSkipTests,
   enableDependencyBlocking,
   skipVerificationInAutoMode,
-  useWorktrees,
   defaultPlanningMode,
   defaultRequirePlanApproval,
   onDefaultSkipTestsChange,
   onEnableDependencyBlockingChange,
   onSkipVerificationInAutoModeChange,
-  onUseWorktreesChange,
   onDefaultPlanningModeChange,
   onDefaultRequirePlanApprovalChange,
 }: FeatureDefaultsSectionProps) {
@@ -256,33 +251,6 @@ export function FeatureDefaultsSection({
             </p>
           </div>
         </div>
-
-        {/* Separator */}
-        <div className="border-t border-border/30" />
-
-        {/* Worktree Isolation Setting */}
-        <div className="group flex items-start space-x-3 p-3 rounded-xl hover:bg-accent/30 transition-colors duration-200 -mx-3">
-          <Checkbox
-            id="use-worktrees"
-            checked={useWorktrees}
-            onCheckedChange={(checked) => onUseWorktreesChange(checked === true)}
-            className="mt-1"
-            data-testid="use-worktrees-checkbox"
-          />
-          <div className="space-y-1.5">
-            <Label
-              htmlFor="use-worktrees"
-              className="text-foreground cursor-pointer font-medium flex items-center gap-2"
-            >
-              <GitBranch className="w-4 h-4 text-brand-500" />
-              Enable Git Worktree Isolation
-            </Label>
-            <p className="text-xs text-muted-foreground/80 leading-relaxed">
-              Creates isolated git branches for each feature. When disabled, agents work directly in
-              the main project directory.
-            </p>
-          </div>
-        </div>
       </div>
     </div>
   );

apps/ui/src/components/views/settings-view/hooks/use-settings-view.ts

@@ -16,6 +16,7 @@ export type SettingsViewId =
   | 'keyboard'
   | 'audio'
   | 'defaults'
+  | 'worktrees'
   | 'account'
   | 'security'
   | 'danger';

apps/ui/src/components/views/settings-view/worktrees/index.ts

@@ -0,0 +1 @@
+export { WorktreesSection } from './worktrees-section';

apps/ui/src/components/views/settings-view/worktrees/worktrees-section.tsx

@@ -0,0 +1,430 @@
+import { useState, useEffect, useCallback } from 'react';
+import { Label } from '@/components/ui/label';
+import { Checkbox } from '@/components/ui/checkbox';
+import { Button } from '@/components/ui/button';
+import { ShellSyntaxEditor } from '@/components/ui/shell-syntax-editor';
+import {
+  GitBranch,
+  Terminal,
+  FileCode,
+  Save,
+  RotateCcw,
+  Trash2,
+  Loader2,
+  PanelBottomClose,
+} from 'lucide-react';
+import { cn } from '@/lib/utils';
+import { apiGet, apiPut, apiDelete } from '@/lib/api-fetch';
+import { toast } from 'sonner';
+import { useAppStore } from '@/store/app-store';
+import { getHttpApiClient } from '@/lib/http-api-client';
+
+interface WorktreesSectionProps {
+  useWorktrees: boolean;
+  onUseWorktreesChange: (value: boolean) => void;
+}
+
+interface InitScriptResponse {
+  success: boolean;
+  exists: boolean;
+  content: string;
+  path: string;
+  error?: string;
+}
+
+export function WorktreesSection({ useWorktrees, onUseWorktreesChange }: WorktreesSectionProps) {
+  const currentProject = useAppStore((s) => s.currentProject);
+  const getShowInitScriptIndicator = useAppStore((s) => s.getShowInitScriptIndicator);
+  const setShowInitScriptIndicator = useAppStore((s) => s.setShowInitScriptIndicator);
+  const getDefaultDeleteBranch = useAppStore((s) => s.getDefaultDeleteBranch);
+  const setDefaultDeleteBranch = useAppStore((s) => s.setDefaultDeleteBranch);
+  const getAutoDismissInitScriptIndicator = useAppStore((s) => s.getAutoDismissInitScriptIndicator);
+  const setAutoDismissInitScriptIndicator = useAppStore((s) => s.setAutoDismissInitScriptIndicator);
+  const [scriptContent, setScriptContent] = useState('');
+  const [originalContent, setOriginalContent] = useState('');
+  const [scriptExists, setScriptExists] = useState(false);
+  const [isLoading, setIsLoading] = useState(true);
+  const [isSaving, setIsSaving] = useState(false);
+  const [isDeleting, setIsDeleting] = useState(false);
+
+  // Get the current show indicator setting
+  const showIndicator = currentProject?.path
+    ? getShowInitScriptIndicator(currentProject.path)
+    : true;
+
+  // Get the default delete branch setting
+  const defaultDeleteBranch = currentProject?.path
+    ? getDefaultDeleteBranch(currentProject.path)
+    : false;
+
+  // Get the auto-dismiss setting
+  const autoDismiss = currentProject?.path
+    ? getAutoDismissInitScriptIndicator(currentProject.path)
+    : true;
+
+  // Check if there are unsaved changes
+  const hasChanges = scriptContent !== originalContent;
+
+  // Load init script content when project changes
+  useEffect(() => {
+    if (!currentProject?.path) {
+      setScriptContent('');
+      setOriginalContent('');
+      setScriptExists(false);
+      setIsLoading(false);
+      return;
+    }
+
+    const loadInitScript = async () => {
+      setIsLoading(true);
+      try {
+        const response = await apiGet<InitScriptResponse>(
+          `/api/worktree/init-script?projectPath=${encodeURIComponent(currentProject.path)}`
+        );
+        if (response.success) {
+          const content = response.content || '';
+          setScriptContent(content);
+          setOriginalContent(content);
+          setScriptExists(response.exists);
+        }
+      } catch (error) {
+        console.error('Failed to load init script:', error);
+      } finally {
+        setIsLoading(false);
+      }
+    };
+
+    loadInitScript();
+  }, [currentProject?.path]);
+
+  // Save script
+  const handleSave = useCallback(async () => {
+    if (!currentProject?.path) return;
+
+    setIsSaving(true);
+    try {
+      const response = await apiPut<{ success: boolean; error?: string }>(
+        '/api/worktree/init-script',
+        {
+          projectPath: currentProject.path,
+          content: scriptContent,
+        }
+      );
+      if (response.success) {
+        setOriginalContent(scriptContent);
+        setScriptExists(true);
+        toast.success('Init script saved');
+      } else {
+        toast.error('Failed to save init script', {
+          description: response.error,
+        });
+      }
+    } catch (error) {
+      console.error('Failed to save init script:', error);
+      toast.error('Failed to save init script');
+    } finally {
+      setIsSaving(false);
+    }
+  }, [currentProject?.path, scriptContent]);
+
+  // Reset to original content
+  const handleReset = useCallback(() => {
+    setScriptContent(originalContent);
+  }, [originalContent]);
+
+  // Delete script
+  const handleDelete = useCallback(async () => {
+    if (!currentProject?.path) return;
+
+    setIsDeleting(true);
+    try {
+      const response = await apiDelete<{ success: boolean; error?: string }>(
+        '/api/worktree/init-script',
+        {
+          body: { projectPath: currentProject.path },
+        }
+      );
+      if (response.success) {
+        setScriptContent('');
+        setOriginalContent('');
+        setScriptExists(false);
+        toast.success('Init script deleted');
+      } else {
+        toast.error('Failed to delete init script', {
+          description: response.error,
+        });
+      }
+    } catch (error) {
+      console.error('Failed to delete init script:', error);
+      toast.error('Failed to delete init script');
+    } finally {
+      setIsDeleting(false);
+    }
+  }, [currentProject?.path]);
+
+  // Handle content change (no auto-save)
+  const handleContentChange = useCallback((value: string) => {
+    setScriptContent(value);
+  }, []);
+
+  return (
+    <div
+      className={cn(
+        'rounded-2xl overflow-hidden',
+        'border border-border/50',
+        'bg-gradient-to-br from-card/90 via-card/70 to-card/80 backdrop-blur-xl',
+        'shadow-sm shadow-black/5'
+      )}
+    >
+      <div className="p-6 border-b border-border/50 bg-gradient-to-r from-transparent via-accent/5 to-transparent">
+        <div className="flex items-center gap-3 mb-2">
+          <div className="w-9 h-9 rounded-xl bg-gradient-to-br from-brand-500/20 to-brand-600/10 flex items-center justify-center border border-brand-500/20">
+            <GitBranch className="w-5 h-5 text-brand-500" />
+          </div>
+          <h2 className="text-lg font-semibold text-foreground tracking-tight">Worktrees</h2>
+        </div>
+        <p className="text-sm text-muted-foreground/80 ml-12">
+          Configure git worktree isolation and initialization scripts.
+        </p>
+      </div>
+      <div className="p-6 space-y-5">
+        {/* Enable Worktrees Toggle */}
+        <div className="group flex items-start space-x-3 p-3 rounded-xl hover:bg-accent/30 transition-colors duration-200 -mx-3">
+          <Checkbox
+            id="use-worktrees"
+            checked={useWorktrees}
+            onCheckedChange={(checked) => onUseWorktreesChange(checked === true)}
+            className="mt-1"
+            data-testid="use-worktrees-checkbox"
+          />
+          <div className="space-y-1.5">
+            <Label
+              htmlFor="use-worktrees"
+              className="text-foreground cursor-pointer font-medium flex items-center gap-2"
+            >
+              <GitBranch className="w-4 h-4 text-brand-500" />
+              Enable Git Worktree Isolation
+            </Label>
+            <p className="text-xs text-muted-foreground/80 leading-relaxed">
+              Creates isolated git branches for each feature. When disabled, agents work directly in
+              the main project directory.
+            </p>
+          </div>
+        </div>
+
+        {/* Show Init Script Indicator Toggle */}
+        {currentProject && (
+          <div className="group flex items-start space-x-3 p-3 rounded-xl hover:bg-accent/30 transition-colors duration-200 -mx-3 mt-4">
+            <Checkbox
+              id="show-init-script-indicator"
+              checked={showIndicator}
+              onCheckedChange={async (checked) => {
+                if (currentProject?.path) {
+                  const value = checked === true;
+                  setShowInitScriptIndicator(currentProject.path, value);
+                  // Persist to server
+                  try {
+                    const httpClient = getHttpApiClient();
+                    await httpClient.settings.updateProject(currentProject.path, {
+                      showInitScriptIndicator: value,
+                    });
+                  } catch (error) {
+                    console.error('Failed to persist showInitScriptIndicator:', error);
+                  }
+                }
+              }}
+              className="mt-1"
+            />
+            <div className="space-y-1.5">
+              <Label
+                htmlFor="show-init-script-indicator"
+                className="text-foreground cursor-pointer font-medium flex items-center gap-2"
+              >
+                <PanelBottomClose className="w-4 h-4 text-brand-500" />
+                Show Init Script Indicator
+              </Label>
+              <p className="text-xs text-muted-foreground/80 leading-relaxed">
+                Display a floating panel in the bottom-right corner showing init script execution
+                status and output when a worktree is created.
+              </p>
+            </div>
+          </div>
+        )}
+
+        {/* Auto-dismiss Init Script Indicator Toggle */}
+        {currentProject && showIndicator && (
+          <div className="group flex items-start space-x-3 p-3 rounded-xl hover:bg-accent/30 transition-colors duration-200 -mx-3 ml-6">
+            <Checkbox
+              id="auto-dismiss-indicator"
+              checked={autoDismiss}
+              onCheckedChange={async (checked) => {
+                if (currentProject?.path) {
+                  const value = checked === true;
+                  setAutoDismissInitScriptIndicator(currentProject.path, value);
+                  // Persist to server
+                  try {
+                    const httpClient = getHttpApiClient();
+                    await httpClient.settings.updateProject(currentProject.path, {
+                      autoDismissInitScriptIndicator: value,
+                    });
+                  } catch (error) {
+                    console.error('Failed to persist autoDismissInitScriptIndicator:', error);
+                  }
+                }
+              }}
+              className="mt-1"
+            />
+            <div className="space-y-1.5">
+              <Label
+                htmlFor="auto-dismiss-indicator"
+                className="text-foreground cursor-pointer font-medium flex items-center gap-2"
+              >
+                Auto-dismiss After Completion
+              </Label>
+              <p className="text-xs text-muted-foreground/80 leading-relaxed">
+                Automatically hide the indicator 5 seconds after the script completes.
+              </p>
+            </div>
+          </div>
+        )}
+
+        {/* Default Delete Branch Toggle */}
+        {currentProject && (
+          <div className="group flex items-start space-x-3 p-3 rounded-xl hover:bg-accent/30 transition-colors duration-200 -mx-3">
+            <Checkbox
+              id="default-delete-branch"
+              checked={defaultDeleteBranch}
+              onCheckedChange={async (checked) => {
+                if (currentProject?.path) {
+                  const value = checked === true;
+                  setDefaultDeleteBranch(currentProject.path, value);
+                  // Persist to server
+                  try {
+                    const httpClient = getHttpApiClient();
+                    await httpClient.settings.updateProject(currentProject.path, {
+                      defaultDeleteBranch: value,
+                    });
+                  } catch (error) {
+                    console.error('Failed to persist defaultDeleteBranch:', error);
+                  }
+                }
+              }}
+              className="mt-1"
+            />
+            <div className="space-y-1.5">
+              <Label
+                htmlFor="default-delete-branch"
+                className="text-foreground cursor-pointer font-medium flex items-center gap-2"
+              >
+                <Trash2 className="w-4 h-4 text-brand-500" />
+                Delete Branch by Default
+              </Label>
+              <p className="text-xs text-muted-foreground/80 leading-relaxed">
+                When deleting a worktree, automatically check the "Also delete the branch" option.
+              </p>
+            </div>
+          </div>
+        )}
+
+        {/* Separator */}
+        <div className="border-t border-border/30" />
+
+        {/* Init Script Section */}
+        <div className="space-y-3">
+          <div className="flex items-center justify-between">
+            <div className="flex items-center gap-2">
+              <Terminal className="w-4 h-4 text-brand-500" />
+              <Label className="text-foreground font-medium">Initialization Script</Label>
+            </div>
+          </div>
+          <p className="text-xs text-muted-foreground/80 leading-relaxed">
+            Shell commands to run after a worktree is created. Runs once per worktree. Uses Git Bash
+            on Windows for cross-platform compatibility.
+          </p>
+
+          {currentProject ? (
+            <>
+              {/* File path indicator */}
+              <div className="flex items-center gap-2 text-xs text-muted-foreground/60">
+                <FileCode className="w-3.5 h-3.5" />
+                <code className="font-mono">.automaker/worktree-init.sh</code>
+                {hasChanges && (
+                  <span className="text-amber-500 font-medium">(unsaved changes)</span>
+                )}
+              </div>
+
+              {isLoading ? (
+                <div className="flex items-center justify-center py-8">
+                  <Loader2 className="w-5 h-5 animate-spin text-muted-foreground" />
+                </div>
+              ) : (
+                <>
+                  <ShellSyntaxEditor
+                    value={scriptContent}
+                    onChange={handleContentChange}
+                    placeholder={`# Example initialization commands
+npm install
+
+# Or use pnpm
+# pnpm install
+
+# Copy environment file
+# cp .env.example .env`}
+                    minHeight="200px"
+                    maxHeight="500px"
+                    data-testid="init-script-editor"
+                  />
+
+                  {/* Action buttons */}
+                  <div className="flex items-center justify-end gap-2 pt-2">
+                    <Button
+                      variant="outline"
+                      size="sm"
+                      onClick={handleReset}
+                      disabled={!hasChanges || isSaving || isDeleting}
+                      className="gap-1.5"
+                    >
+                      <RotateCcw className="w-3.5 h-3.5" />
+                      Reset
+                    </Button>
+                    <Button
+                      variant="outline"
+                      size="sm"
+                      onClick={handleDelete}
+                      disabled={!scriptExists || isSaving || isDeleting}
+                      className="gap-1.5 text-destructive hover:text-destructive hover:bg-destructive/10"
+                    >
+                      {isDeleting ? (
+                        <Loader2 className="w-3.5 h-3.5 animate-spin" />
+                      ) : (
+                        <Trash2 className="w-3.5 h-3.5" />
+                      )}
+                      Delete
+                    </Button>
+                    <Button
+                      size="sm"
+                      onClick={handleSave}
+                      disabled={!hasChanges || isSaving || isDeleting}
+                      className="gap-1.5"
+                    >
+                      {isSaving ? (
+                        <Loader2 className="w-3.5 h-3.5 animate-spin" />
+                      ) : (
+                        <Save className="w-3.5 h-3.5" />
+                      )}
+                      Save
+                    </Button>
+                  </div>
+                </>
+              )}
+            </>
+          ) : (
+            <div className="text-sm text-muted-foreground/60 py-4 text-center">
+              Select a project to configure the init script.
+            </div>
+          )}
+        </div>
+      </div>
+    </div>
+  );
+}

apps/ui/src/hooks/use-init-script-events.ts

@@ -0,0 +1,79 @@
+import { useEffect } from 'react';
+import { useAppStore } from '@/store/app-store';
+import { getHttpApiClient } from '@/lib/http-api-client';
+import { pathsEqual } from '@/lib/utils';
+
+interface InitScriptStartedPayload {
+  projectPath: string;
+  worktreePath: string;
+  branch: string;
+}
+
+interface InitScriptOutputPayload {
+  projectPath: string;
+  branch: string;
+  type: 'stdout' | 'stderr';
+  content: string;
+}
+
+interface InitScriptCompletedPayload {
+  projectPath: string;
+  worktreePath: string;
+  branch: string;
+  success: boolean;
+  exitCode?: number;
+  error?: string;
+}
+
+/**
+ * Hook to subscribe to init script WebSocket events and update the store.
+ * Should be used in a component that's always mounted (e.g., board-view).
+ */
+export function useInitScriptEvents(projectPath: string | null) {
+  const setInitScriptState = useAppStore((s) => s.setInitScriptState);
+  const appendInitScriptOutput = useAppStore((s) => s.appendInitScriptOutput);
+
+  useEffect(() => {
+    if (!projectPath) return;
+
+    const api = getHttpApiClient();
+
+    const unsubscribe = api.worktree.onInitScriptEvent((event) => {
+      const payload = event.payload as
+        | InitScriptStartedPayload
+        | InitScriptOutputPayload
+        | InitScriptCompletedPayload;
+
+      // Only handle events for the current project (use pathsEqual for cross-platform path comparison)
+      if (!pathsEqual(payload.projectPath, projectPath)) return;
+
+      switch (event.type) {
+        case 'worktree:init-started': {
+          const startPayload = payload as InitScriptStartedPayload;
+          setInitScriptState(projectPath, startPayload.branch, {
+            status: 'running',
+            branch: startPayload.branch,
+            output: [],
+            error: undefined,
+          });
+          break;
+        }
+        case 'worktree:init-output': {
+          const outputPayload = payload as InitScriptOutputPayload;
+          appendInitScriptOutput(projectPath, outputPayload.branch, outputPayload.content);
+          break;
+        }
+        case 'worktree:init-completed': {
+          const completePayload = payload as InitScriptCompletedPayload;
+          setInitScriptState(projectPath, completePayload.branch, {
+            status: completePayload.success ? 'success' : 'failed',
+            error: completePayload.error,
+          });
+          break;
+        }
+      }
+    });
+
+    return unsubscribe;
+  }, [projectPath, setInitScriptState, appendInitScriptOutput]);
+}

apps/ui/src/hooks/use-project-settings-loader.ts

@@ -18,6 +18,11 @@ export function useProjectSettingsLoader() {
   const setCardBorderOpacity = useAppStore((state) => state.setCardBorderOpacity);
   const setHideScrollbar = useAppStore((state) => state.setHideScrollbar);
   const setWorktreePanelVisible = useAppStore((state) => state.setWorktreePanelVisible);
+  const setShowInitScriptIndicator = useAppStore((state) => state.setShowInitScriptIndicator);
+  const setDefaultDeleteBranch = useAppStore((state) => state.setDefaultDeleteBranch);
+  const setAutoDismissInitScriptIndicator = useAppStore(
+    (state) => state.setAutoDismissInitScriptIndicator
+  );
 
   const loadingRef = useRef<string | null>(null);
   const currentProjectRef = useRef<string | null>(null);
@@ -78,6 +83,27 @@ export function useProjectSettingsLoader() {
           if (result.settings.worktreePanelVisible !== undefined) {
             setWorktreePanelVisible(requestedProjectPath, result.settings.worktreePanelVisible);
           }
+
+          // Apply showInitScriptIndicator if present
+          if (result.settings.showInitScriptIndicator !== undefined) {
+            setShowInitScriptIndicator(
+              requestedProjectPath,
+              result.settings.showInitScriptIndicator
+            );
+          }
+
+          // Apply defaultDeleteBranch if present
+          if (result.settings.defaultDeleteBranch !== undefined) {
+            setDefaultDeleteBranch(requestedProjectPath, result.settings.defaultDeleteBranch);
+          }
+
+          // Apply autoDismissInitScriptIndicator if present
+          if (result.settings.autoDismissInitScriptIndicator !== undefined) {
+            setAutoDismissInitScriptIndicator(
+              requestedProjectPath,
+              result.settings.autoDismissInitScriptIndicator
+            );
+          }
         }
       } catch (error) {
         console.error('Failed to load project settings:', error);

apps/ui/src/lib/electron.ts

@@ -651,7 +651,8 @@ export interface ElectronAPI {
           removedDependencies: string[];
           addedDependencies: string[];
         }>;
-      }
+      },
+      branchName?: string
     ) => Promise<{ success: boolean; appliedChanges?: string[]; error?: string }>;
     onEvent: (callback: (data: unknown) => void) => () => void;
   };
@@ -1769,6 +1770,47 @@ function createMockWorktreeAPI(): WorktreeAPI {
         },
       };
     },
+
+    getInitScript: async (projectPath: string) => {
+      console.log('[Mock] Getting init script:', { projectPath });
+      return {
+        success: true,
+        exists: false,
+        content: '',
+        path: `${projectPath}/.automaker/worktree-init.sh`,
+      };
+    },
+
+    setInitScript: async (projectPath: string, content: string) => {
+      console.log('[Mock] Setting init script:', { projectPath, content });
+      return {
+        success: true,
+        path: `${projectPath}/.automaker/worktree-init.sh`,
+      };
+    },
+
+    deleteInitScript: async (projectPath: string) => {
+      console.log('[Mock] Deleting init script:', { projectPath });
+      return {
+        success: true,
+      };
+    },
+
+    runInitScript: async (projectPath: string, worktreePath: string, branch: string) => {
+      console.log('[Mock] Running init script:', { projectPath, worktreePath, branch });
+      return {
+        success: true,
+        message: 'Init script started (mock)',
+      };
+    },
+
+    onInitScriptEvent: (callback) => {
+      console.log('[Mock] Subscribing to init script events');
+      // Return unsubscribe function
+      return () => {
+        console.log('[Mock] Unsubscribing from init script events');
+      };
+    },
   };
 }
 

apps/ui/src/lib/http-api-client.ts

@@ -507,7 +507,10 @@ type EventType =
   | 'issue-validation:event'
   | 'backlog-plan:event'
   | 'ideation:stream'
-  | 'ideation:analysis';
+  | 'ideation:analysis'
+  | 'worktree:init-started'
+  | 'worktree:init-output'
+  | 'worktree:init-completed';
 
 type EventCallback = (payload: unknown) => void;
 
@@ -846,13 +849,14 @@ export class HttpApiClient implements ElectronAPI {
     return response.json();
   }
 
-  private async httpDelete<T>(endpoint: string): Promise<T> {
+  private async httpDelete<T>(endpoint: string, body?: unknown): Promise<T> {
     // Ensure API key is initialized before making request
     await waitForApiKeyInit();
     const response = await fetch(`${this.serverUrl}${endpoint}`, {
       method: 'DELETE',
       headers: this.getHeaders(),
       credentials: 'include', // Include cookies for session auth
+      body: body ? JSON.stringify(body) : undefined,
     });
 
     if (response.status === 401 || response.status === 403) {
@@ -1647,6 +1651,37 @@ export class HttpApiClient implements ElectronAPI {
     listDevServers: () => this.post('/api/worktree/list-dev-servers', {}),
     getPRInfo: (worktreePath: string, branchName: string) =>
       this.post('/api/worktree/pr-info', { worktreePath, branchName }),
+    // Init script methods
+    getInitScript: (projectPath: string) =>
+      this.get(`/api/worktree/init-script?projectPath=${encodeURIComponent(projectPath)}`),
+    setInitScript: (projectPath: string, content: string) =>
+      this.put('/api/worktree/init-script', { projectPath, content }),
+    deleteInitScript: (projectPath: string) =>
+      this.httpDelete('/api/worktree/init-script', { projectPath }),
+    runInitScript: (projectPath: string, worktreePath: string, branch: string) =>
+      this.post('/api/worktree/run-init-script', { projectPath, worktreePath, branch }),
+    onInitScriptEvent: (
+      callback: (event: {
+        type: 'worktree:init-started' | 'worktree:init-output' | 'worktree:init-completed';
+        payload: unknown;
+      }) => void
+    ) => {
+      // Note: subscribeToEvent callback receives (payload) not (_, payload)
+      const unsub1 = this.subscribeToEvent('worktree:init-started', (payload) =>
+        callback({ type: 'worktree:init-started', payload })
+      );
+      const unsub2 = this.subscribeToEvent('worktree:init-output', (payload) =>
+        callback({ type: 'worktree:init-output', payload })
+      );
+      const unsub3 = this.subscribeToEvent('worktree:init-completed', (payload) =>
+        callback({ type: 'worktree:init-completed', payload })
+      );
+      return () => {
+        unsub1();
+        unsub2();
+        unsub3();
+      };
+    },
   };
 
   // Git API
@@ -2167,9 +2202,10 @@ export class HttpApiClient implements ElectronAPI {
           removedDependencies: string[];
           addedDependencies: string[];
         }>;
-      }
+      },
+      branchName?: string
     ): Promise<{ success: boolean; appliedChanges?: string[]; error?: string }> =>
-      this.post('/api/backlog-plan/apply', { projectPath, plan }),
+      this.post('/api/backlog-plan/apply', { projectPath, plan, branchName }),
 
     onEvent: (callback: (data: unknown) => void): (() => void) => {
       return this.subscribeToEvent('backlog-plan:event', callback as EventCallback);

apps/ui/src/store/app-store.ts

@@ -80,6 +80,9 @@ export type ThemeMode =
 // LocalStorage key for theme persistence (fallback when server settings aren't available)
 export const THEME_STORAGE_KEY = 'automaker:theme';
 
+// Maximum number of output lines to keep in init script state (prevents unbounded memory growth)
+export const MAX_INIT_OUTPUT_LINES = 500;
+
 /**
  * Get the theme from localStorage as a fallback
  * Used before server settings are loaded (e.g., on login/setup pages)
@@ -469,6 +472,14 @@ export interface PersistedTerminalSettings {
   maxSessions: number;
 }
 
+/** State for worktree init script execution */
+export interface InitScriptState {
+  status: 'idle' | 'running' | 'success' | 'failed';
+  branch: string;
+  output: string[];
+  error?: string;
+}
+
 export interface AppState {
   // Project state
   projects: Project[];
@@ -522,6 +533,8 @@ export interface AppState {
   defaultSkipTests: boolean; // Default value for skip tests when creating new features
   enableDependencyBlocking: boolean; // When true, show blocked badges and warnings for features with incomplete dependencies (default: true)
   skipVerificationInAutoMode: boolean; // When true, auto-mode grabs features even if dependencies are not verified (only checks they're not running)
+  planUseSelectedWorktreeBranch: boolean; // When true, Plan dialog creates features on the currently selected worktree branch
+  addFeatureUseSelectedWorktreeBranch: boolean; // When true, Add Feature dialog defaults to custom mode with selected worktree branch
 
   // Worktree Settings
   useWorktrees: boolean; // Whether to use git worktree isolation for features (default: true)
@@ -670,6 +683,18 @@ export interface AppState {
   // Whether the worktree panel row is visible (default: true)
   worktreePanelVisibleByProject: Record<string, boolean>;
 
+  // Init Script Indicator Visibility (per-project, keyed by project path)
+  // Whether to show the floating init script indicator panel (default: true)
+  showInitScriptIndicatorByProject: Record<string, boolean>;
+
+  // Default Delete Branch With Worktree (per-project, keyed by project path)
+  // Whether to default the "delete branch" checkbox when deleting a worktree (default: false)
+  defaultDeleteBranchByProject: Record<string, boolean>;
+
+  // Auto-dismiss Init Script Indicator (per-project, keyed by project path)
+  // Whether to auto-dismiss the indicator after completion (default: true)
+  autoDismissInitScriptIndicatorByProject: Record<string, boolean>;
+
   // UI State (previously in localStorage, now synced via API)
   /** Whether worktree panel is collapsed in board view */
   worktreePanelCollapsed: boolean;
@@ -677,6 +702,9 @@ export interface AppState {
   lastProjectDir: string;
   /** Recently accessed folders for quick access */
   recentFolders: string[];
+
+  // Init Script State (keyed by "projectPath::branch" to support concurrent scripts)
+  initScriptState: Record<string, InitScriptState>;
 }
 
 // Claude Usage interface matching the server response
@@ -890,6 +918,8 @@ export interface AppActions {
   setDefaultSkipTests: (skip: boolean) => void;
   setEnableDependencyBlocking: (enabled: boolean) => void;
   setSkipVerificationInAutoMode: (enabled: boolean) => Promise<void>;
+  setPlanUseSelectedWorktreeBranch: (enabled: boolean) => Promise<void>;
+  setAddFeatureUseSelectedWorktreeBranch: (enabled: boolean) => Promise<void>;
 
   // Worktree Settings actions
   setUseWorktrees: (enabled: boolean) => void;
@@ -1083,6 +1113,18 @@ export interface AppActions {
   setWorktreePanelVisible: (projectPath: string, visible: boolean) => void;
   getWorktreePanelVisible: (projectPath: string) => boolean;
 
+  // Init Script Indicator Visibility actions (per-project)
+  setShowInitScriptIndicator: (projectPath: string, visible: boolean) => void;
+  getShowInitScriptIndicator: (projectPath: string) => boolean;
+
+  // Default Delete Branch actions (per-project)
+  setDefaultDeleteBranch: (projectPath: string, deleteBranch: boolean) => void;
+  getDefaultDeleteBranch: (projectPath: string) => boolean;
+
+  // Auto-dismiss Init Script Indicator actions (per-project)
+  setAutoDismissInitScriptIndicator: (projectPath: string, autoDismiss: boolean) => void;
+  getAutoDismissInitScriptIndicator: (projectPath: string) => boolean;
+
   // UI State actions (previously in localStorage, now synced via API)
   setWorktreePanelCollapsed: (collapsed: boolean) => void;
   setLastProjectDir: (dir: string) => void;
@@ -1111,6 +1153,19 @@ export interface AppActions {
     }>
   ) => void;
 
+  // Init Script State actions (keyed by projectPath::branch to support concurrent scripts)
+  setInitScriptState: (
+    projectPath: string,
+    branch: string,
+    state: Partial<InitScriptState>
+  ) => void;
+  appendInitScriptOutput: (projectPath: string, branch: string, content: string) => void;
+  clearInitScriptState: (projectPath: string, branch: string) => void;
+  getInitScriptState: (projectPath: string, branch: string) => InitScriptState | null;
+  getInitScriptStatesForProject: (
+    projectPath: string
+  ) => Array<{ key: string; state: InitScriptState }>;
+
   // Reset
   reset: () => void;
 }
@@ -1143,6 +1198,8 @@ const initialState: AppState = {
   defaultSkipTests: true, // Default to manual verification (tests disabled)
   enableDependencyBlocking: true, // Default to enabled (show dependency blocking UI)
   skipVerificationInAutoMode: false, // Default to disabled (require dependencies to be verified)
+  planUseSelectedWorktreeBranch: true, // Default to enabled (Plan creates features on selected worktree branch)
+  addFeatureUseSelectedWorktreeBranch: false, // Default to disabled (Add Feature uses normal defaults)
   useWorktrees: true, // Default to enabled (git worktree isolation)
   currentWorktreeByProject: {},
   worktreesByProject: {},
@@ -1208,10 +1265,14 @@ const initialState: AppState = {
   codexModelsLastFetched: null,
   pipelineConfigByProject: {},
   worktreePanelVisibleByProject: {},
+  showInitScriptIndicatorByProject: {},
+  defaultDeleteBranchByProject: {},
+  autoDismissInitScriptIndicatorByProject: {},
   // UI State (previously in localStorage, now synced via API)
   worktreePanelCollapsed: false,
   lastProjectDir: '',
   recentFolders: [],
+  initScriptState: {},
 };
 
 export const useAppStore = create<AppState & AppActions>()((set, get) => ({
@@ -1764,6 +1825,30 @@ export const useAppStore = create<AppState & AppActions>()((set, get) => ({
     const { syncSettingsToServer } = await import('@/hooks/use-settings-migration');
     await syncSettingsToServer();
   },
+  setPlanUseSelectedWorktreeBranch: async (enabled) => {
+    const previous = get().planUseSelectedWorktreeBranch;
+    set({ planUseSelectedWorktreeBranch: enabled });
+    // Sync to server settings file
+    const { syncSettingsToServer } = await import('@/hooks/use-settings-migration');
+    const ok = await syncSettingsToServer();
+    if (!ok) {
+      logger.error('Failed to sync planUseSelectedWorktreeBranch setting to server - reverting');
+      set({ planUseSelectedWorktreeBranch: previous });
+    }
+  },
+  setAddFeatureUseSelectedWorktreeBranch: async (enabled) => {
+    const previous = get().addFeatureUseSelectedWorktreeBranch;
+    set({ addFeatureUseSelectedWorktreeBranch: enabled });
+    // Sync to server settings file
+    const { syncSettingsToServer } = await import('@/hooks/use-settings-migration');
+    const ok = await syncSettingsToServer();
+    if (!ok) {
+      logger.error(
+        'Failed to sync addFeatureUseSelectedWorktreeBranch setting to server - reverting'
+      );
+      set({ addFeatureUseSelectedWorktreeBranch: previous });
+    }
+  },
 
   // Worktree Settings actions
   setUseWorktrees: (enabled) => set({ useWorktrees: enabled }),
@@ -3136,6 +3221,51 @@ export const useAppStore = create<AppState & AppActions>()((set, get) => ({
     return get().worktreePanelVisibleByProject[projectPath] ?? true;
   },
 
+  // Init Script Indicator Visibility actions (per-project)
+  setShowInitScriptIndicator: (projectPath, visible) => {
+    set({
+      showInitScriptIndicatorByProject: {
+        ...get().showInitScriptIndicatorByProject,
+        [projectPath]: visible,
+      },
+    });
+  },
+
+  getShowInitScriptIndicator: (projectPath) => {
+    // Default to true (visible) if not set
+    return get().showInitScriptIndicatorByProject[projectPath] ?? true;
+  },
+
+  // Default Delete Branch actions (per-project)
+  setDefaultDeleteBranch: (projectPath, deleteBranch) => {
+    set({
+      defaultDeleteBranchByProject: {
+        ...get().defaultDeleteBranchByProject,
+        [projectPath]: deleteBranch,
+      },
+    });
+  },
+
+  getDefaultDeleteBranch: (projectPath) => {
+    // Default to false (don't delete branch) if not set
+    return get().defaultDeleteBranchByProject[projectPath] ?? false;
+  },
+
+  // Auto-dismiss Init Script Indicator actions (per-project)
+  setAutoDismissInitScriptIndicator: (projectPath, autoDismiss) => {
+    set({
+      autoDismissInitScriptIndicatorByProject: {
+        ...get().autoDismissInitScriptIndicatorByProject,
+        [projectPath]: autoDismiss,
+      },
+    });
+  },
+
+  getAutoDismissInitScriptIndicator: (projectPath) => {
+    // Default to true (auto-dismiss enabled) if not set
+    return get().autoDismissInitScriptIndicatorByProject[projectPath] ?? true;
+  },
+
   // UI State actions (previously in localStorage, now synced via API)
   setWorktreePanelCollapsed: (collapsed) => set({ worktreePanelCollapsed: collapsed }),
   setLastProjectDir: (dir) => set({ lastProjectDir: dir }),
@@ -3149,6 +3279,62 @@ export const useAppStore = create<AppState & AppActions>()((set, get) => ({
     set({ recentFolders: updated });
   },
 
+  // Init Script State actions (keyed by "projectPath::branch")
+  setInitScriptState: (projectPath, branch, state) => {
+    const key = `${projectPath}::${branch}`;
+    const current = get().initScriptState[key] || {
+      status: 'idle',
+      branch,
+      output: [],
+    };
+    set({
+      initScriptState: {
+        ...get().initScriptState,
+        [key]: { ...current, ...state },
+      },
+    });
+  },
+
+  appendInitScriptOutput: (projectPath, branch, content) => {
+    const key = `${projectPath}::${branch}`;
+    // Initialize state if absent to avoid dropping output due to event-order races
+    const current = get().initScriptState[key] || {
+      status: 'idle' as const,
+      branch,
+      output: [],
+    };
+    // Append new content and enforce fixed-size buffer to prevent memory bloat
+    const newOutput = [...current.output, content].slice(-MAX_INIT_OUTPUT_LINES);
+    set({
+      initScriptState: {
+        ...get().initScriptState,
+        [key]: {
+          ...current,
+          output: newOutput,
+        },
+      },
+    });
+  },
+
+  clearInitScriptState: (projectPath, branch) => {
+    const key = `${projectPath}::${branch}`;
+    const { [key]: _, ...rest } = get().initScriptState;
+    set({ initScriptState: rest });
+  },
+
+  getInitScriptState: (projectPath, branch) => {
+    const key = `${projectPath}::${branch}`;
+    return get().initScriptState[key] || null;
+  },
+
+  getInitScriptStatesForProject: (projectPath) => {
+    const prefix = `${projectPath}::`;
+    const states = get().initScriptState;
+    return Object.entries(states)
+      .filter(([key]) => key.startsWith(prefix))
+      .map(([key, state]) => ({ key, state }));
+  },
+
   // Reset
   reset: () => set(initialState),
 }));

apps/ui/src/types/electron.d.ts

@@ -1015,6 +1015,50 @@ export interface WorktreeAPI {
     };
     error?: string;
   }>;
+
+  // Get init script content for a project
+  getInitScript: (projectPath: string) => Promise<{
+    success: boolean;
+    exists: boolean;
+    content: string;
+    path: string;
+    error?: string;
+  }>;
+
+  // Set init script content for a project
+  setInitScript: (
+    projectPath: string,
+    content: string
+  ) => Promise<{
+    success: boolean;
+    path?: string;
+    error?: string;
+  }>;
+
+  // Delete init script for a project
+  deleteInitScript: (projectPath: string) => Promise<{
+    success: boolean;
+    error?: string;
+  }>;
+
+  // Run (or re-run) init script for a worktree
+  runInitScript: (
+    projectPath: string,
+    worktreePath: string,
+    branch: string
+  ) => Promise<{
+    success: boolean;
+    message?: string;
+    error?: string;
+  }>;
+
+  // Subscribe to init script events
+  onInitScriptEvent: (
+    callback: (event: {
+      type: 'worktree:init-started' | 'worktree:init-output' | 'worktree:init-completed';
+      payload: unknown;
+    }) => void
+  ) => () => void;
 }
 
 export interface GitAPI {

docs/worktree-init-script-example.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+# Example worktree init script for Automaker
+# Copy this content to Settings > Worktrees > Init Script
+# Or save directly as .automaker/worktree-init.sh in your project
+
+echo "=========================================="
+echo "  Worktree Init Script Starting..."
+echo "=========================================="
+echo ""
+echo "Current directory: $(pwd)"
+echo "Branch: $(git branch --show-current 2>/dev/null || echo 'unknown')"
+echo ""
+
+# Install dependencies
+echo "[1/1] Installing npm dependencies..."
+if [ -f "package.json" ]; then
+    if npm install; then
+        echo "Dependencies installed successfully!"
+    else
+        echo "ERROR: npm install failed with exit code $?"
+        exit 1
+    fi
+else
+    echo "No package.json found, skipping npm install"
+fi
+echo ""
+
+echo "=========================================="
+echo "  Worktree initialization complete!"
+echo "=========================================="

libs/platform/src/index.ts

@@ -97,6 +97,7 @@ export {
   getCodexCliPaths,
   getCodexConfigDir,
   getCodexAuthPath,
+  getGitBashPaths,
   getOpenCodeCliPaths,
   getOpenCodeConfigDir,
   getOpenCodeAuthPath,
@@ -130,6 +131,7 @@ export {
   findCodexCliPath,
   getCodexAuthIndicators,
   type CodexAuthIndicators,
+  findGitBashPath,
   findOpenCodeCliPath,
   getOpenCodeAuthIndicators,
   type OpenCodeAuthIndicators,

libs/platform/src/system-paths.ts

@@ -232,6 +232,87 @@ export function getClaudeProjectsDir(): string {
   return path.join(getClaudeConfigDir(), 'projects');
 }
 
+/**
+ * Enumerate directories matching a prefix pattern and return full paths
+ * Used to resolve dynamic directory names like version numbers
+ */
+function enumerateMatchingPaths(
+  parentDir: string,
+  prefix: string,
+  ...subPathParts: string[]
+): string[] {
+  try {
+    if (!fsSync.existsSync(parentDir)) {
+      return [];
+    }
+    const entries = fsSync.readdirSync(parentDir);
+    const matching = entries.filter((entry) => entry.startsWith(prefix));
+    return matching.map((entry) => path.join(parentDir, entry, ...subPathParts));
+  } catch {
+    return [];
+  }
+}
+
+/**
+ * Get common Git Bash installation paths on Windows
+ * Git Bash is needed for running shell scripts cross-platform
+ */
+export function getGitBashPaths(): string[] {
+  if (process.platform !== 'win32') {
+    return [];
+  }
+
+  const homeDir = os.homedir();
+  const localAppData = process.env.LOCALAPPDATA || '';
+
+  // Dynamic paths that require directory enumeration
+  // winget installs to: LocalAppData\Microsoft\WinGet\Packages\Git.Git_<hash>\bin\bash.exe
+  const wingetGitPaths = localAppData
+    ? enumerateMatchingPaths(
+        path.join(localAppData, 'Microsoft', 'WinGet', 'Packages'),
+        'Git.Git_',
+        'bin',
+        'bash.exe'
+      )
+    : [];
+
+  // GitHub Desktop bundles Git at: LocalAppData\GitHubDesktop\app-<version>\resources\app\git\cmd\bash.exe
+  const githubDesktopPaths = localAppData
+    ? enumerateMatchingPaths(
+        path.join(localAppData, 'GitHubDesktop'),
+        'app-',
+        'resources',
+        'app',
+        'git',
+        'cmd',
+        'bash.exe'
+      )
+    : [];
+
+  return [
+    // Standard Git for Windows installations
+    'C:\\Program Files\\Git\\bin\\bash.exe',
+    'C:\\Program Files (x86)\\Git\\bin\\bash.exe',
+    // User-local installations
+    path.join(localAppData, 'Programs', 'Git', 'bin', 'bash.exe'),
+    // Scoop package manager
+    path.join(homeDir, 'scoop', 'apps', 'git', 'current', 'bin', 'bash.exe'),
+    // Chocolatey
+    path.join(
+      process.env.ChocolateyInstall || 'C:\\ProgramData\\chocolatey',
+      'lib',
+      'git',
+      'tools',
+      'bin',
+      'bash.exe'
+    ),
+    // winget installations (dynamically resolved)
+    ...wingetGitPaths,
+    // GitHub Desktop bundled Git (dynamically resolved)
+    ...githubDesktopPaths,
+  ].filter(Boolean);
+}
+
 /**
  * Get common shell paths for shell detection
  * Includes both full paths and short names to match $SHELL or PATH entries
@@ -550,6 +631,8 @@ function getAllAllowedSystemPaths(): string[] {
     getOpenCodeAuthPath(),
     // Shell paths
     ...getShellPaths(),
+    // Git Bash paths (for Windows cross-platform shell script execution)
+    ...getGitBashPaths(),
     // Node.js system paths
     ...getNodeSystemPaths(),
     getScoopNodePath(),
@@ -883,6 +966,13 @@ export async function findCodexCliPath(): Promise<string | null> {
   return findFirstExistingPath(getCodexCliPaths());
 }
 
+/**
+ * Find Git Bash on Windows and return its path
+ */
+export async function findGitBashPath(): Promise<string | null> {
+  return findFirstExistingPath(getGitBashPaths());
+}
+
 /**
  * Get Claude authentication status by checking various indicators
  */

libs/types/src/event.ts

@@ -39,6 +39,9 @@ export type EventType =
   | 'ideation:idea-created'
   | 'ideation:idea-updated'
   | 'ideation:idea-deleted'
-  | 'ideation:idea-converted';
+  | 'ideation:idea-converted'
+  | 'worktree:init-started'
+  | 'worktree:init-output'
+  | 'worktree:init-completed';
 
 export type EventCallback = (type: EventType, payload: unknown) => void;

libs/types/src/settings.ts

@@ -599,6 +599,14 @@ export interface ProjectSettings {
   // UI Visibility
   /** Whether the worktree panel row is visible (default: true) */
   worktreePanelVisible?: boolean;
+  /** Whether to show the init script indicator panel (default: true) */
+  showInitScriptIndicator?: boolean;
+
+  // Worktree Behavior
+  /** Default value for "delete branch" checkbox when deleting a worktree (default: false) */
+  defaultDeleteBranchWithWorktree?: boolean;
+  /** Auto-dismiss init script indicator after completion (default: true) */
+  autoDismissInitScriptIndicator?: boolean;
 
   // Session Tracking
   /** Last chat session selected in this project */

package-lock.json

@@ -87,6 +87,8 @@
         "@automaker/dependency-resolver": "1.0.0",
         "@automaker/types": "1.0.0",
         "@codemirror/lang-xml": "6.1.0",
+        "@codemirror/language": "^6.12.1",
+        "@codemirror/legacy-modes": "^6.5.2",
         "@codemirror/theme-one-dark": "6.1.3",
         "@dnd-kit/core": "6.3.1",
         "@dnd-kit/sortable": "10.0.0",
@@ -1199,19 +1201,28 @@
       }
     },
     "node_modules/@codemirror/language": {
-      "version": "6.11.3",
+      "version": "6.12.1",
-      "resolved": "https://registry.npmjs.org/@codemirror/language/-/language-6.11.3.tgz",
+      "resolved": "https://registry.npmjs.org/@codemirror/language/-/language-6.12.1.tgz",
-      "integrity": "sha512-9HBM2XnwDj7fnu0551HkGdrUrrqmYq/WC5iv6nbY2WdicXdGbhR/gfbZOH73Aqj4351alY1+aoG9rCNfiwS1RA==",
+      "integrity": "sha512-Fa6xkSiuGKc8XC8Cn96T+TQHYj4ZZ7RdFmXA3i9xe/3hLHfwPZdM+dqfX0Cp0zQklBKhVD8Yzc8LS45rkqcwpQ==",
       "license": "MIT",
       "dependencies": {
         "@codemirror/state": "^6.0.0",
         "@codemirror/view": "^6.23.0",
-        "@lezer/common": "^1.1.0",
+        "@lezer/common": "^1.5.0",
         "@lezer/highlight": "^1.0.0",
         "@lezer/lr": "^1.0.0",
         "style-mod": "^4.0.0"
       }
     },
+    "node_modules/@codemirror/legacy-modes": {
+      "version": "6.5.2",
+      "resolved": "https://registry.npmjs.org/@codemirror/legacy-modes/-/legacy-modes-6.5.2.tgz",
+      "integrity": "sha512-/jJbwSTazlQEDOQw2FJ8LEEKVS72pU0lx6oM54kGpL8t/NJ2Jda3CZ4pcltiKTdqYSRk3ug1B3pil1gsjA6+8Q==",
+      "license": "MIT",
+      "dependencies": {
+        "@codemirror/language": "^6.0.0"
+      }
+    },
     "node_modules/@codemirror/lint": {
       "version": "6.9.2",
       "resolved": "https://registry.npmjs.org/@codemirror/lint/-/lint-6.9.2.tgz",
@@ -3604,9 +3615,9 @@
       }
     },
     "node_modules/@lezer/common": {
-      "version": "1.4.0",
+      "version": "1.5.0",
-      "resolved": "https://registry.npmjs.org/@lezer/common/-/common-1.4.0.tgz",
+      "resolved": "https://registry.npmjs.org/@lezer/common/-/common-1.5.0.tgz",
-      "integrity": "sha512-DVeMRoGrgn/k45oQNu189BoW4SZwgZFzJ1+1TV5j2NJ/KFC83oa/enRqZSGshyeMk5cPWMhsKs9nx+8o0unwGg==",
+      "integrity": "sha512-PNGcolp9hr4PJdXR4ix7XtixDrClScvtSCYW3rQG106oVMOOI+jFb+0+J3mbeL/53g1Zd6s0kJzaw6Ri68GmAA==",
       "license": "MIT"
     },
     "node_modules/@lezer/highlight": {