Implement branch selection and worktree management features

- Added a new BranchAutocomplete component for selecting branches in feature dialogs.
- Enhanced BoardView to fetch and display branch suggestions.
- Updated CreateWorktreeDialog and EditFeatureDialog to include branch selection.
- Modified worktree management to ensure proper handling of branch-specific worktrees.
- Refactored related components and hooks to support the new branch management functionality.
- Removed unused revert and merge handlers from Kanban components for cleaner code.

apps/server/src/routes/app-spec/generate-features-from-spec.ts

@@ -3,13 +3,13 @@
  */
 
 import { query } from "@anthropic-ai/claude-agent-sdk";
-import path from "path";
 import fs from "fs/promises";
 import type { EventEmitter } from "../../lib/events.js";
 import { createLogger } from "../../lib/logger.js";
 import { createFeatureGenerationOptions } from "../../lib/sdk-options.js";
 import { logAuthStatus } from "./common.js";
 import { parseAndCreateFeatures } from "./parse-and-create-features.js";
+import { getAppSpecPath } from "../../lib/automaker-paths.js";
 
 const logger = createLogger("SpecRegeneration");
 
@@ -26,8 +26,8 @@ export async function generateFeaturesFromSpec(
   logger.debug("projectPath:", projectPath);
   logger.debug("maxFeatures:", featureCount);
 
-  // Read existing spec
-  const specPath = path.join(projectPath, ".automaker", "app_spec.txt");
+  // Read existing spec from external automaker directory
+  const specPath = await getAppSpecPath(projectPath);
   let spec: string;
 
   logger.debug("Reading spec from:", specPath);

apps/server/src/routes/app-spec/generate-spec.ts

@@ -11,6 +11,7 @@ import { createLogger } from "../../lib/logger.js";
 import { createSpecGenerationOptions } from "../../lib/sdk-options.js";
 import { logAuthStatus } from "./common.js";
 import { generateFeaturesFromSpec } from "./generate-features-from-spec.js";
+import { ensureAutomakerDir, getAppSpecPath } from "../../lib/automaker-paths.js";
 
 const logger = createLogger("SpecRegeneration");
 
@@ -209,14 +210,13 @@ ${getAppSpecFormatInstruction()}`;
     logger.error("❌ WARNING: responseText is empty! Nothing to save.");
   }
 
-  // Save spec
-  const specDir = path.join(projectPath, ".automaker");
-  const specPath = path.join(specDir, "app_spec.txt");
+  // Save spec to external automaker directory
+  const specDir = await ensureAutomakerDir(projectPath);
+  const specPath = await getAppSpecPath(projectPath);
 
   logger.info("Saving spec to:", specPath);
   logger.info(`Content to save (${responseText.length} chars)`);
 
-  await fs.mkdir(specDir, { recursive: true });
   await fs.writeFile(specPath, responseText);
 
   // Verify the file was written

apps/server/src/routes/app-spec/parse-and-create-features.ts

@@ -6,6 +6,7 @@ import path from "path";
 import fs from "fs/promises";
 import type { EventEmitter } from "../../lib/events.js";
 import { createLogger } from "../../lib/logger.js";
+import { getFeaturesDir } from "../../lib/automaker-paths.js";
 
 const logger = createLogger("SpecRegeneration");
 
@@ -41,7 +42,7 @@ export async function parseAndCreateFeatures(
     logger.info(`Parsed ${parsed.features?.length || 0} features`);
     logger.info("Parsed features:", JSON.stringify(parsed.features, null, 2));
 
-    const featuresDir = path.join(projectPath, ".automaker", "features");
+    const featuresDir = await getFeaturesDir(projectPath);
     await fs.mkdir(featuresDir, { recursive: true });
 
     const createdFeatures: Array<{ id: string; title: string }> = [];

apps/server/src/routes/auto-mode/routes/commit-feature.ts

@@ -9,9 +9,10 @@ import { getErrorMessage, logError } from "../common.js";
 export function createCommitFeatureHandler(autoModeService: AutoModeService) {
   return async (req: Request, res: Response): Promise<void> => {
     try {
-      const { projectPath, featureId } = req.body as {
+      const { projectPath, featureId, worktreePath } = req.body as {
         projectPath: string;
         featureId: string;
+        worktreePath?: string;
       };
 
       if (!projectPath || !featureId) {
@@ -26,7 +27,8 @@ export function createCommitFeatureHandler(autoModeService: AutoModeService) {
 
       const commitHash = await autoModeService.commitFeature(
         projectPath,
-        featureId
+        featureId,
+        worktreePath
       );
       res.json({ success: true, commitHash });
     } catch (error) {

apps/server/src/routes/auto-mode/routes/follow-up-feature.ts

@@ -12,11 +12,12 @@ const logger = createLogger("AutoMode");
 export function createFollowUpFeatureHandler(autoModeService: AutoModeService) {
   return async (req: Request, res: Response): Promise<void> => {
     try {
-      const { projectPath, featureId, prompt, imagePaths } = req.body as {
+      const { projectPath, featureId, prompt, imagePaths, worktreePath } = req.body as {
         projectPath: string;
         featureId: string;
         prompt: string;
         imagePaths?: string[];
+        worktreePath?: string;
       };
 
       if (!projectPath || !featureId || !prompt) {
@@ -27,9 +28,9 @@ export function createFollowUpFeatureHandler(autoModeService: AutoModeService) {
         return;
       }
 
-      // Start follow-up in background
+      // Start follow-up in background, using the feature's worktreePath for correct branch
       autoModeService
-        .followUpFeature(projectPath, featureId, prompt, imagePaths)
+        .followUpFeature(projectPath, featureId, prompt, imagePaths, worktreePath)
         .catch((error) => {
           logger.error(
             `[AutoMode] Follow up feature ${featureId} error:`,

apps/server/src/routes/auto-mode/routes/run-feature.ts

@@ -12,10 +12,11 @@ const logger = createLogger("AutoMode");
 export function createRunFeatureHandler(autoModeService: AutoModeService) {
   return async (req: Request, res: Response): Promise<void> => {
     try {
-      const { projectPath, featureId, useWorktrees } = req.body as {
+      const { projectPath, featureId, useWorktrees, worktreePath } = req.body as {
         projectPath: string;
         featureId: string;
         useWorktrees?: boolean;
+        worktreePath?: string;
       };
 
       if (!projectPath || !featureId) {
@@ -29,8 +30,9 @@ export function createRunFeatureHandler(autoModeService: AutoModeService) {
       }
 
       // Start execution in background
+      // If worktreePath is provided, use it directly; otherwise let the service decide
       autoModeService
-        .executeFeature(projectPath, featureId, useWorktrees ?? true, false)
+        .executeFeature(projectPath, featureId, useWorktrees ?? true, false, worktreePath)
         .catch((error) => {
           logger.error(`[AutoMode] Feature ${featureId} error:`, error);
         });

apps/server/src/routes/fs/routes/delete-board-background.ts

@@ -6,6 +6,7 @@ import type { Request, Response } from "express";
 import fs from "fs/promises";
 import path from "path";
 import { getErrorMessage, logError } from "../common.js";
+import { getBoardDir } from "../../../lib/automaker-paths.js";
 
 export function createDeleteBoardBackgroundHandler() {
   return async (req: Request, res: Response): Promise<void> => {
@@ -20,10 +21,11 @@ export function createDeleteBoardBackgroundHandler() {
         return;
       }
 
-      const boardDir = path.join(projectPath, ".automaker", "board");
+      // Get external board directory
+      const boardDir = await getBoardDir(projectPath);
 
       try {
-        // Try to remove all files in the board directory
+        // Try to remove all background files in the board directory
         const files = await fs.readdir(boardDir);
         for (const file of files) {
           if (file.startsWith("background")) {

apps/server/src/routes/fs/routes/mkdir.ts

@@ -1,5 +1,6 @@
 /**
  * POST /mkdir endpoint - Create directory
+ * Handles symlinks safely to avoid ELOOP errors
  */
 
 import type { Request, Response } from "express";
@@ -20,13 +21,46 @@ export function createMkdirHandler() {
 
       const resolvedPath = path.resolve(dirPath);
 
+      // Check if path already exists using lstat (doesn't follow symlinks)
+      try {
+        const stats = await fs.lstat(resolvedPath);
+        // Path exists - if it's a directory or symlink, consider it success
+        if (stats.isDirectory() || stats.isSymbolicLink()) {
+          addAllowedPath(resolvedPath);
+          res.json({ success: true });
+          return;
+        }
+        // It's a file - can't create directory
+        res.status(400).json({
+          success: false,
+          error: "Path exists and is not a directory",
+        });
+        return;
+      } catch (statError: any) {
+        // ENOENT means path doesn't exist - we should create it
+        if (statError.code !== "ENOENT") {
+          // Some other error (could be ELOOP in parent path)
+          throw statError;
+        }
+      }
+
+      // Path doesn't exist, create it
       await fs.mkdir(resolvedPath, { recursive: true });
 
       // Add the new directory to allowed paths for tracking
       addAllowedPath(resolvedPath);
 
       res.json({ success: true });
-    } catch (error) {
+    } catch (error: any) {
+      // Handle ELOOP specifically
+      if (error.code === "ELOOP") {
+        logError(error, "Create directory failed - symlink loop detected");
+        res.status(400).json({
+          success: false,
+          error: "Cannot create directory: symlink loop detected in path",
+        });
+        return;
+      }
       logError(error, "Create directory failed");
       res.status(500).json({ success: false, error: getErrorMessage(error) });
     }

apps/server/src/routes/fs/routes/save-board-background.ts

@@ -7,6 +7,7 @@ import fs from "fs/promises";
 import path from "path";
 import { addAllowedPath } from "../../../lib/security.js";
 import { getErrorMessage, logError } from "../common.js";
+import { getBoardDir } from "../../../lib/automaker-paths.js";
 
 export function createSaveBoardBackgroundHandler() {
   return async (req: Request, res: Response): Promise<void> => {
@@ -26,8 +27,8 @@ export function createSaveBoardBackgroundHandler() {
         return;
       }
 
-      // Create .automaker/board directory if it doesn't exist
-      const boardDir = path.join(projectPath, ".automaker", "board");
+      // Get external board directory
+      const boardDir = await getBoardDir(projectPath);
       await fs.mkdir(boardDir, { recursive: true });
 
       // Decode base64 data (remove data URL prefix if present)
@@ -42,12 +43,11 @@ export function createSaveBoardBackgroundHandler() {
       // Write file
       await fs.writeFile(filePath, buffer);
 
-      // Add project path to allowed paths if not already
-      addAllowedPath(projectPath);
+      // Add board directory to allowed paths
+      addAllowedPath(boardDir);
 
-      // Return the relative path for storage
-      const relativePath = `.automaker/board/${uniqueFilename}`;
-      res.json({ success: true, path: relativePath });
+      // Return the absolute path
+      res.json({ success: true, path: filePath });
     } catch (error) {
       logError(error, "Save board background failed");
       res.status(500).json({ success: false, error: getErrorMessage(error) });

apps/server/src/routes/fs/routes/save-image.ts

@@ -1,5 +1,5 @@
 /**
- * POST /save-image endpoint - Save image to .automaker/images directory
+ * POST /save-image endpoint - Save image to external automaker images directory
  */
 
 import type { Request, Response } from "express";
@@ -7,6 +7,7 @@ import fs from "fs/promises";
 import path from "path";
 import { addAllowedPath } from "../../../lib/security.js";
 import { getErrorMessage, logError } from "../common.js";
+import { getImagesDir } from "../../../lib/automaker-paths.js";
 
 export function createSaveImageHandler() {
   return async (req: Request, res: Response): Promise<void> => {
@@ -26,8 +27,8 @@ export function createSaveImageHandler() {
         return;
       }
 
-      // Create .automaker/images directory if it doesn't exist
-      const imagesDir = path.join(projectPath, ".automaker", "images");
+      // Get external images directory
+      const imagesDir = await getImagesDir(projectPath);
       await fs.mkdir(imagesDir, { recursive: true });
 
       // Decode base64 data (remove data URL prefix if present)
@@ -44,9 +45,10 @@ export function createSaveImageHandler() {
       // Write file
       await fs.writeFile(filePath, buffer);
 
-      // Add project path to allowed paths if not already
-      addAllowedPath(projectPath);
+      // Add automaker directory to allowed paths
+      addAllowedPath(imagesDir);
 
+      // Return the absolute path
       res.json({ success: true, path: filePath });
     } catch (error) {
       logError(error, "Save image failed");

apps/server/src/routes/fs/routes/write.ts

@@ -7,6 +7,7 @@ import fs from "fs/promises";
 import path from "path";
 import { validatePath } from "../../../lib/security.js";
 import { getErrorMessage, logError } from "../common.js";
+import { mkdirSafe } from "../../../lib/fs-utils.js";
 
 export function createWriteHandler() {
   return async (req: Request, res: Response): Promise<void> => {
@@ -23,8 +24,8 @@ export function createWriteHandler() {
 
       const resolvedPath = validatePath(filePath);
 
-      // Ensure parent directory exists
-      await fs.mkdir(path.dirname(resolvedPath), { recursive: true });
+      // Ensure parent directory exists (symlink-safe)
+      await mkdirSafe(path.dirname(resolvedPath));
       await fs.writeFile(resolvedPath, content, "utf-8");
 
       res.json({ success: true });

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

@@ -19,6 +19,13 @@ import { createPullHandler } from "./routes/pull.js";
 import { createCheckoutBranchHandler } from "./routes/checkout-branch.js";
 import { createListBranchesHandler } from "./routes/list-branches.js";
 import { createSwitchBranchHandler } from "./routes/switch-branch.js";
+import { createOpenInEditorHandler } from "./routes/open-in-editor.js";
+import { createInitGitHandler } from "./routes/init-git.js";
+import { createActivateHandler } from "./routes/activate.js";
+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";
 
 export function createWorktreeRoutes(): Router {
   const router = Router();
@@ -39,6 +46,13 @@ export function createWorktreeRoutes(): Router {
   router.post("/checkout-branch", createCheckoutBranchHandler());
   router.post("/list-branches", createListBranchesHandler());
   router.post("/switch-branch", createSwitchBranchHandler());
+  router.post("/open-in-editor", createOpenInEditorHandler());
+  router.post("/init-git", createInitGitHandler());
+  router.post("/activate", createActivateHandler());
+  router.post("/migrate", createMigrateHandler());
+  router.post("/start-dev", createStartDevHandler());
+  router.post("/stop-dev", createStopDevHandler());
+  router.post("/list-dev-servers", createListDevServersHandler());
 
   return router;
 }

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

@@ -0,0 +1,149 @@
+/**
+ * POST /activate endpoint - Switch main project to a worktree's branch
+ *
+ * This allows users to "activate" a worktree so their running dev server
+ * (like Vite) shows the worktree's files. It does this by:
+ * 1. Checking for uncommitted changes (fails if found)
+ * 2. Removing the worktree (unlocks the branch)
+ * 3. Checking out that branch in the main directory
+ *
+ * Users should commit their changes before activating a worktree.
+ */
+
+import type { Request, Response } from "express";
+import { exec } from "child_process";
+import { promisify } from "util";
+import { getErrorMessage, logError } from "../common.js";
+
+const execAsync = promisify(exec);
+
+async function hasUncommittedChanges(cwd: string): Promise<boolean> {
+  try {
+    const { stdout } = await execAsync("git status --porcelain", { cwd });
+    // Filter out our own .worktrees directory from the check
+    const lines = stdout.trim().split("\n").filter((line) => {
+      if (!line.trim()) return false;
+      // Exclude .worktrees/ directory (created by automaker)
+      if (line.includes(".worktrees/") || line.endsWith(".worktrees")) return false;
+      return true;
+    });
+    return lines.length > 0;
+  } catch {
+    return false;
+  }
+}
+
+async function getCurrentBranch(cwd: string): Promise<string> {
+  const { stdout } = await execAsync("git branch --show-current", { cwd });
+  return stdout.trim();
+}
+
+async function getWorktreeBranch(worktreePath: string): Promise<string> {
+  const { stdout } = await execAsync("git branch --show-current", {
+    cwd: worktreePath,
+  });
+  return stdout.trim();
+}
+
+async function getChangesSummary(cwd: string): Promise<string> {
+  try {
+    const { stdout } = await execAsync("git status --short", { cwd });
+    const lines = stdout.trim().split("\n").filter((line) => {
+      if (!line.trim()) return false;
+      // Exclude .worktrees/ directory
+      if (line.includes(".worktrees/") || line.endsWith(".worktrees")) return false;
+      return true;
+    });
+    if (lines.length === 0) return "";
+    if (lines.length <= 5) return lines.join(", ");
+    return `${lines.slice(0, 5).join(", ")} and ${lines.length - 5} more files`;
+  } catch {
+    return "unknown changes";
+  }
+}
+
+export function createActivateHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, worktreePath } = req.body as {
+        projectPath: string;
+        worktreePath: string | null; // null means switch back to main branch
+      };
+
+      if (!projectPath) {
+        res.status(400).json({
+          success: false,
+          error: "projectPath is required",
+        });
+        return;
+      }
+
+      const currentBranch = await getCurrentBranch(projectPath);
+      let targetBranch: string;
+
+      // Check for uncommitted changes in main directory
+      if (await hasUncommittedChanges(projectPath)) {
+        const summary = await getChangesSummary(projectPath);
+        res.status(400).json({
+          success: false,
+          error: `Cannot switch: you have uncommitted changes in the main directory (${summary}). Please commit your changes first.`,
+          code: "UNCOMMITTED_CHANGES",
+        });
+        return;
+      }
+
+      if (worktreePath) {
+        // Switching to a worktree's branch
+        targetBranch = await getWorktreeBranch(worktreePath);
+
+        // Check for uncommitted changes in the worktree
+        if (await hasUncommittedChanges(worktreePath)) {
+          const summary = await getChangesSummary(worktreePath);
+          res.status(400).json({
+            success: false,
+            error: `Cannot switch: you have uncommitted changes in the worktree (${summary}). Please commit your changes first.`,
+            code: "UNCOMMITTED_CHANGES",
+          });
+          return;
+        }
+
+        // Remove the worktree (unlocks the branch)
+        console.log(`[activate] Removing worktree at ${worktreePath}...`);
+        await execAsync(`git worktree remove "${worktreePath}" --force`, {
+          cwd: projectPath,
+        });
+
+        // Checkout the branch in main directory
+        console.log(`[activate] Checking out branch ${targetBranch}...`);
+        await execAsync(`git checkout "${targetBranch}"`, { cwd: projectPath });
+      } else {
+        // Switching back to main branch
+        try {
+          const { stdout: mainBranch } = await execAsync(
+            "git symbolic-ref refs/remotes/origin/HEAD --short 2>/dev/null | sed 's@origin/@@' || echo 'main'",
+            { cwd: projectPath }
+          );
+          targetBranch = mainBranch.trim() || "main";
+        } catch {
+          targetBranch = "main";
+        }
+
+        // Checkout main branch
+        console.log(`[activate] Checking out main branch ${targetBranch}...`);
+        await execAsync(`git checkout "${targetBranch}"`, { cwd: projectPath });
+      }
+
+      res.json({
+        success: true,
+        result: {
+          previousBranch: currentBranch,
+          currentBranch: targetBranch,
+          message: `Switched from ${currentBranch} to ${targetBranch}`,
+        },
+      });
+    } catch (error) {
+      logError(error, "Activate worktree failed");
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/worktree/routes/branch-tracking.ts

@@ -0,0 +1,125 @@
+/**
+ * Branch tracking utilities
+ *
+ * Tracks active branches in external automaker storage so users
+ * can switch between branches even after worktrees are removed.
+ *
+ * Data is stored outside the git repo to avoid worktree/symlink conflicts.
+ */
+
+import { readFile, writeFile } from "fs/promises";
+import path from "path";
+import {
+  getBranchTrackingPath,
+  ensureAutomakerDir,
+} from "../../../lib/automaker-paths.js";
+
+export interface TrackedBranch {
+  name: string;
+  createdAt: string;
+  lastActivatedAt?: string;
+}
+
+interface BranchTrackingData {
+  branches: TrackedBranch[];
+}
+
+/**
+ * Read tracked branches from file
+ */
+export async function getTrackedBranches(
+  projectPath: string
+): Promise<TrackedBranch[]> {
+  try {
+    const filePath = await getBranchTrackingPath(projectPath);
+    const content = await readFile(filePath, "utf-8");
+    const data: BranchTrackingData = JSON.parse(content);
+    return data.branches || [];
+  } catch (error: any) {
+    if (error.code === "ENOENT") {
+      return [];
+    }
+    console.warn("[branch-tracking] Failed to read tracked branches:", error);
+    return [];
+  }
+}
+
+/**
+ * Save tracked branches to file
+ */
+async function saveTrackedBranches(
+  projectPath: string,
+  branches: TrackedBranch[]
+): Promise<void> {
+  const automakerDir = await ensureAutomakerDir(projectPath);
+  const filePath = path.join(automakerDir, "active-branches.json");
+  const data: BranchTrackingData = { branches };
+  await writeFile(filePath, JSON.stringify(data, null, 2), "utf-8");
+}
+
+/**
+ * Add a branch to tracking
+ */
+export async function trackBranch(
+  projectPath: string,
+  branchName: string
+): Promise<void> {
+  const branches = await getTrackedBranches(projectPath);
+
+  // Check if already tracked
+  const existing = branches.find((b) => b.name === branchName);
+  if (existing) {
+    return; // Already tracked
+  }
+
+  branches.push({
+    name: branchName,
+    createdAt: new Date().toISOString(),
+  });
+
+  await saveTrackedBranches(projectPath, branches);
+  console.log(`[branch-tracking] Now tracking branch: ${branchName}`);
+}
+
+/**
+ * Remove a branch from tracking
+ */
+export async function untrackBranch(
+  projectPath: string,
+  branchName: string
+): Promise<void> {
+  const branches = await getTrackedBranches(projectPath);
+  const filtered = branches.filter((b) => b.name !== branchName);
+
+  if (filtered.length !== branches.length) {
+    await saveTrackedBranches(projectPath, filtered);
+    console.log(`[branch-tracking] Stopped tracking branch: ${branchName}`);
+  }
+}
+
+/**
+ * Update last activated timestamp for a branch
+ */
+export async function updateBranchActivation(
+  projectPath: string,
+  branchName: string
+): Promise<void> {
+  const branches = await getTrackedBranches(projectPath);
+  const branch = branches.find((b) => b.name === branchName);
+
+  if (branch) {
+    branch.lastActivatedAt = new Date().toISOString();
+    await saveTrackedBranches(projectPath, branches);
+  }
+}
+
+/**
+ * Check if a branch is tracked
+ */
+export async function isBranchTracked(
+  projectPath: string,
+  branchName: string
+): Promise<boolean> {
+  const branches = await getTrackedBranches(projectPath);
+  return branches.some((b) => b.name === branchName);
+}

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

@@ -6,8 +6,9 @@ import type { Request, Response } from "express";
 import { exec } from "child_process";
 import { promisify } from "util";
 import path from "path";
-import fs from "fs/promises";
+import { mkdir, access } from "fs/promises";
 import { isGitRepo, getErrorMessage, logError } from "../common.js";
+import { trackBranch } from "./branch-tracking.js";
 
 const execAsync = promisify(exec);
 
@@ -42,14 +43,19 @@ export function createCreateHandler() {
       const worktreePath = path.join(worktreesDir, sanitizedName);
 
       // Create worktrees directory if it doesn't exist
-      await fs.mkdir(worktreesDir, { recursive: true });
+      await mkdir(worktreesDir, { recursive: true });
 
       // Check if worktree already exists
       try {
-        await fs.access(worktreePath);
-        res.status(400).json({
-          success: false,
-          error: `Worktree for branch '${branchName}' already exists`,
+        await access(worktreePath);
+        // Worktree already exists, return it instead of error
+        res.json({
+          success: true,
+          worktree: {
+            path: worktreePath,
+            branch: branchName,
+            isNew: false,
+          },
         });
         return;
       } catch {
@@ -80,22 +86,12 @@ export function createCreateHandler() {
 
       await execAsync(createCmd, { cwd: projectPath });
 
-      // Symlink .automaker directory to worktree so features are shared
-      const mainAutomaker = path.join(projectPath, ".automaker");
-      const worktreeAutomaker = path.join(worktreePath, ".automaker");
+      // 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
 
-      try {
-        // Check if .automaker exists in main project
-        await fs.access(mainAutomaker);
-        // Create symlink in worktree pointing to main .automaker
-        // Use 'junction' on Windows, 'dir' on other platforms
-        const symlinkType = process.platform === "win32" ? "junction" : "dir";
-        await fs.symlink(mainAutomaker, worktreeAutomaker, symlinkType);
-      } catch (symlinkError) {
-        // .automaker doesn't exist or symlink failed
-        // Log but don't fail - worktree is still usable without shared .automaker
-        console.warn("[Worktree] Could not create .automaker symlink:", symlinkError);
-      }
+      // Track the branch so it persists in the UI even after worktree is removed
+      await trackBranch(projectPath, branchName);
 
       res.json({
         success: true,

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

@@ -29,12 +29,8 @@ export function createDiffsHandler() {
         return;
       }
 
-      const worktreePath = path.join(
-        projectPath,
-        ".automaker",
-        "worktrees",
-        featureId
-      );
+      // Git worktrees are stored in project directory
+      const worktreePath = path.join(projectPath, ".worktrees", featureId);
 
       try {
         await fs.access(worktreePath);

apps/server/src/routes/worktree/routes/file-diff.ts

@@ -28,12 +28,8 @@ export function createFileDiffHandler() {
         return;
       }
 
-      const worktreePath = path.join(
-        projectPath,
-        ".automaker",
-        "worktrees",
-        featureId
-      );
+      // Git worktrees are stored in project directory
+      const worktreePath = path.join(projectPath, ".worktrees", featureId);
 
       try {
         await fs.access(worktreePath);

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

@@ -29,13 +29,8 @@ export function createInfoHandler() {
         return;
       }
 
-      // Check if worktree exists
-      const worktreePath = path.join(
-        projectPath,
-        ".automaker",
-        "worktrees",
-        featureId
-      );
+      // Check if worktree exists (git worktrees are stored in project directory)
+      const worktreePath = path.join(projectPath, ".worktrees", featureId);
       try {
         await fs.access(worktreePath);
         const { stdout } = await execAsync("git rev-parse --abbrev-ref HEAD", {

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

@@ -0,0 +1,60 @@
+/**
+ * POST /init-git endpoint - Initialize a git repository in a directory
+ */
+
+import type { Request, Response } from "express";
+import { exec } from "child_process";
+import { promisify } from "util";
+import { existsSync } from "fs";
+import { join } from "path";
+import { getErrorMessage, logError } from "../common.js";
+
+const execAsync = promisify(exec);
+
+export function createInitGitHandler() {
+  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 required",
+        });
+        return;
+      }
+
+      // Check if .git already exists
+      const gitDirPath = join(projectPath, ".git");
+      if (existsSync(gitDirPath)) {
+        res.json({
+          success: true,
+          result: {
+            initialized: false,
+            message: "Git repository already exists",
+          },
+        });
+        return;
+      }
+
+      // Initialize git and create an initial empty commit
+      await execAsync(
+        `git init && git commit --allow-empty -m "Initial commit"`,
+        { cwd: projectPath }
+      );
+
+      res.json({
+        success: true,
+        result: {
+          initialized: true,
+          message: "Git repository initialized with initial commit",
+        },
+      });
+    } catch (error) {
+      logError(error, "Init git failed");
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/worktree/routes/list-dev-servers.ts

@@ -0,0 +1,29 @@
+/**
+ * POST /list-dev-servers endpoint - List all running dev servers
+ *
+ * Returns information about all worktree dev servers currently running,
+ * including their ports and URLs.
+ */
+
+import type { Request, Response } from "express";
+import { getDevServerService } from "../../../services/dev-server-service.js";
+import { getErrorMessage, logError } from "../common.js";
+
+export function createListDevServersHandler() {
+  return async (_req: Request, res: Response): Promise<void> => {
+    try {
+      const devServerService = getDevServerService();
+      const result = devServerService.listDevServers();
+
+      res.json({
+        success: true,
+        result: {
+          servers: result.result.servers,
+        },
+      });
+    } catch (error) {
+      logError(error, "List dev servers failed");
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

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

@@ -1,5 +1,8 @@
 /**
- * POST /list endpoint - List all worktrees
+ * POST /list endpoint - List all git worktrees
+ *
+ * Returns actual git worktrees from `git worktree list`.
+ * Does NOT include tracked branches - only real worktrees with separate directories.
  */
 
 import type { Request, Response } from "express";
@@ -13,10 +16,21 @@ interface WorktreeInfo {
   path: string;
   branch: string;
   isMain: boolean;
+  isCurrent: boolean; // Is this the currently checked out branch in main?
+  hasWorktree: boolean; // Always true for items in this list
   hasChanges?: boolean;
   changedFilesCount?: number;
 }
 
+async function getCurrentBranch(cwd: string): Promise<string> {
+  try {
+    const { stdout } = await execAsync("git branch --show-current", { cwd });
+    return stdout.trim();
+  } catch {
+    return "";
+  }
+}
+
 export function createListHandler() {
   return async (req: Request, res: Response): Promise<void> => {
     try {
@@ -35,6 +49,10 @@ export function createListHandler() {
         return;
       }
 
+      // Get current branch in main directory
+      const currentBranch = await getCurrentBranch(projectPath);
+
+      // Get actual worktrees from git
       const { stdout } = await execAsync("git worktree list --porcelain", {
         cwd: projectPath,
       });
@@ -51,11 +69,12 @@ export function createListHandler() {
           current.branch = line.slice(7).replace("refs/heads/", "");
         } else if (line === "") {
           if (current.path && current.branch) {
-            // The first worktree in the list is always the main worktree
             worktrees.push({
               path: current.path,
               branch: current.branch,
-              isMain: isFirst
+              isMain: isFirst,
+              isCurrent: current.branch === currentBranch,
+              hasWorktree: true,
             });
             isFirst = false;
           }
@@ -71,11 +90,13 @@ export function createListHandler() {
               "git status --porcelain",
               { cwd: worktree.path }
             );
-            const changedFiles = statusOutput.trim().split("\n").filter(line => line.trim());
+            const changedFiles = statusOutput
+              .trim()
+              .split("\n")
+              .filter((line) => line.trim());
             worktree.hasChanges = changedFiles.length > 0;
             worktree.changedFilesCount = changedFiles.length;
           } catch {
-            // If we can't get status, assume no changes
             worktree.hasChanges = false;
             worktree.changedFilesCount = 0;
           }

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

@@ -30,12 +30,8 @@ export function createMergeHandler() {
       }
 
       const branchName = `feature/${featureId}`;
-      const worktreePath = path.join(
-        projectPath,
-        ".automaker",
-        "worktrees",
-        featureId
-      );
+      // Git worktrees are stored in project directory
+      const worktreePath = path.join(projectPath, ".worktrees", featureId);
 
       // Get current branch
       const { stdout: currentBranch } = await execAsync(

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

@@ -0,0 +1,63 @@
+/**
+ * POST /migrate endpoint - Migrate legacy .automaker data to external storage
+ *
+ * This endpoint checks if there's legacy .automaker data in the project directory
+ * and migrates it to the external ~/.automaker/projects/{project-id}/ location.
+ */
+
+import type { Request, Response } from "express";
+import { getErrorMessage, logError } from "../common.js";
+import {
+  hasLegacyAutomakerDir,
+  migrateLegacyData,
+  getAutomakerDir,
+  getLegacyAutomakerDir,
+} from "../../../lib/automaker-paths.js";
+
+export function createMigrateHandler() {
+  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;
+      }
+
+      // Check if migration is needed
+      const hasLegacy = await hasLegacyAutomakerDir(projectPath);
+
+      if (!hasLegacy) {
+        const automakerDir = await getAutomakerDir(projectPath);
+        res.json({
+          success: true,
+          migrated: false,
+          message: "No legacy .automaker directory found - nothing to migrate",
+          externalPath: automakerDir,
+        });
+        return;
+      }
+
+      // Perform migration
+      console.log(`[migrate] Starting migration for project: ${projectPath}`);
+      const legacyPath = await getLegacyAutomakerDir(projectPath);
+      const externalPath = await getAutomakerDir(projectPath);
+
+      await migrateLegacyData(projectPath);
+
+      res.json({
+        success: true,
+        migrated: true,
+        message: "Successfully migrated .automaker data to external storage",
+        legacyPath,
+        externalPath,
+      });
+    } catch (error) {
+      logError(error, "Migration failed");
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/worktree/routes/open-in-editor.ts

@@ -0,0 +1,73 @@
+/**
+ * POST /open-in-editor endpoint - Open a worktree directory in VS Code
+ */
+
+import type { Request, Response } from "express";
+import { exec } from "child_process";
+import { promisify } from "util";
+import { getErrorMessage, logError } from "../common.js";
+
+const execAsync = promisify(exec);
+
+export function createOpenInEditorHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { worktreePath } = req.body as {
+        worktreePath: string;
+      };
+
+      if (!worktreePath) {
+        res.status(400).json({
+          success: false,
+          error: "worktreePath required",
+        });
+        return;
+      }
+
+      // Try to open in VS Code
+      try {
+        await execAsync(`code "${worktreePath}"`);
+        res.json({
+          success: true,
+          result: {
+            message: `Opened ${worktreePath} in VS Code`,
+          },
+        });
+      } catch {
+        // If 'code' command fails, try 'cursor' (for Cursor editor)
+        try {
+          await execAsync(`cursor "${worktreePath}"`);
+          res.json({
+            success: true,
+            result: {
+              message: `Opened ${worktreePath} in Cursor`,
+            },
+          });
+        } catch {
+          // If both fail, try opening in default file manager
+          const platform = process.platform;
+          let openCommand: string;
+
+          if (platform === "darwin") {
+            openCommand = `open "${worktreePath}"`;
+          } else if (platform === "win32") {
+            openCommand = `explorer "${worktreePath}"`;
+          } else {
+            openCommand = `xdg-open "${worktreePath}"`;
+          }
+
+          await execAsync(openCommand);
+          res.json({
+            success: true,
+            result: {
+              message: `Opened ${worktreePath} in file manager`,
+            },
+          });
+        }
+      }
+    } catch (error) {
+      logError(error, "Open in editor failed");
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

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

@@ -43,7 +43,7 @@ export function createPullHandler() {
       if (hasLocalChanges) {
         res.status(400).json({
           success: false,
-          error: "You have local changes. Please commit or stash them before pulling.",
+          error: "You have local changes. Please commit them before pulling.",
         });
         return;
       }

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

@@ -28,12 +28,8 @@ export function createRevertHandler() {
         return;
       }
 
-      const worktreePath = path.join(
-        projectPath,
-        ".automaker",
-        "worktrees",
-        featureId
-      );
+      // Git worktrees are stored in project directory
+      const worktreePath = path.join(projectPath, ".worktrees", featureId);
 
       try {
         // Remove worktree

apps/server/src/routes/worktree/routes/start-dev.ts

@@ -0,0 +1,61 @@
+/**
+ * POST /start-dev endpoint - Start a dev server for a worktree
+ *
+ * Spins up a development server (npm run dev) in the worktree directory
+ * on a unique port, allowing preview of the worktree's changes without
+ * affecting the main dev server.
+ */
+
+import type { Request, Response } from "express";
+import { getDevServerService } from "../../../services/dev-server-service.js";
+import { getErrorMessage, logError } from "../common.js";
+
+export function createStartDevHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, worktreePath } = req.body as {
+        projectPath: string;
+        worktreePath: 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;
+      }
+
+      const devServerService = getDevServerService();
+      const result = await devServerService.startDevServer(projectPath, worktreePath);
+
+      if (result.success && result.result) {
+        res.json({
+          success: true,
+          result: {
+            worktreePath: result.result.worktreePath,
+            port: result.result.port,
+            url: result.result.url,
+            message: result.result.message,
+          },
+        });
+      } else {
+        res.status(400).json({
+          success: false,
+          error: result.error || "Failed to start dev server",
+        });
+      }
+    } catch (error) {
+      logError(error, "Start dev server failed");
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

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

@@ -29,12 +29,8 @@ export function createStatusHandler() {
         return;
       }
 
-      const worktreePath = path.join(
-        projectPath,
-        ".automaker",
-        "worktrees",
-        featureId
-      );
+      // Git worktrees are stored in project directory
+      const worktreePath = path.join(projectPath, ".worktrees", featureId);
 
       try {
         await fs.access(worktreePath);

apps/server/src/routes/worktree/routes/stop-dev.ts

@@ -0,0 +1,49 @@
+/**
+ * POST /stop-dev endpoint - Stop a dev server for a worktree
+ *
+ * Stops the development server running for a specific worktree,
+ * freeing up the ports for reuse.
+ */
+
+import type { Request, Response } from "express";
+import { getDevServerService } from "../../../services/dev-server-service.js";
+import { getErrorMessage, logError } from "../common.js";
+
+export function createStopDevHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { worktreePath } = req.body as {
+        worktreePath: string;
+      };
+
+      if (!worktreePath) {
+        res.status(400).json({
+          success: false,
+          error: "worktreePath is required",
+        });
+        return;
+      }
+
+      const devServerService = getDevServerService();
+      const result = await devServerService.stopDevServer(worktreePath);
+
+      if (result.success && result.result) {
+        res.json({
+          success: true,
+          result: {
+            worktreePath: result.result.worktreePath,
+            message: result.result.message,
+          },
+        });
+      } else {
+        res.status(400).json({
+          success: false,
+          error: result.error || "Failed to stop dev server",
+        });
+      }
+    } catch (error) {
+      logError(error, "Stop dev server failed");
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/worktree/routes/switch-branch.ts

@@ -1,6 +1,9 @@
 /**
  * POST /switch-branch endpoint - Switch to an existing branch
- * Automatically stashes uncommitted changes and pops them after switching
+ *
+ * Simple branch switching.
+ * If there are uncommitted changes, the switch will fail and
+ * the user should commit first.
  */
 
 import type { Request, Response } from "express";
@@ -10,6 +13,46 @@ import { getErrorMessage, logError } from "../common.js";
 
 const execAsync = promisify(exec);
 
+/**
+ * Check if there are uncommitted changes in the working directory
+ * Excludes .worktrees/ directory which is created by automaker
+ */
+async function hasUncommittedChanges(cwd: string): Promise<boolean> {
+  try {
+    const { stdout } = await execAsync("git status --porcelain", { cwd });
+    const lines = stdout.trim().split("\n").filter((line) => {
+      if (!line.trim()) return false;
+      // Exclude .worktrees/ directory (created by automaker)
+      if (line.includes(".worktrees/") || line.endsWith(".worktrees")) return false;
+      return true;
+    });
+    return lines.length > 0;
+  } catch {
+    return false;
+  }
+}
+
+/**
+ * Get a summary of uncommitted changes for user feedback
+ * Excludes .worktrees/ directory
+ */
+async function getChangesSummary(cwd: string): Promise<string> {
+  try {
+    const { stdout } = await execAsync("git status --short", { cwd });
+    const lines = stdout.trim().split("\n").filter((line) => {
+      if (!line.trim()) return false;
+      // Exclude .worktrees/ directory
+      if (line.includes(".worktrees/") || line.endsWith(".worktrees")) return false;
+      return true;
+    });
+    if (lines.length === 0) return "";
+    if (lines.length <= 5) return lines.join(", ");
+    return `${lines.slice(0, 5).join(", ")} and ${lines.length - 5} more files`;
+  } catch {
+    return "unknown changes";
+  }
+}
+
 export function createSwitchBranchHandler() {
   return async (req: Request, res: Response): Promise<void> => {
     try {
@@ -34,7 +77,7 @@ export function createSwitchBranchHandler() {
         return;
       }
 
-      // Get current branch for reference
+      // Get current branch
       const { stdout: currentBranchOutput } = await execAsync(
         "git rev-parse --abbrev-ref HEAD",
         { cwd: worktreePath }
@@ -48,7 +91,6 @@ export function createSwitchBranchHandler() {
             previousBranch,
             currentBranch: branchName,
             message: `Already on branch '${branchName}'`,
-            stashed: false,
           },
         });
         return;
@@ -68,81 +110,27 @@ export function createSwitchBranchHandler() {
       }
 
       // Check for uncommitted changes
-      const { stdout: statusOutput } = await execAsync(
-        "git status --porcelain",
-        { cwd: worktreePath }
-      );
-
-      const hasChanges = statusOutput.trim().length > 0;
-      let stashed = false;
-
-      // Stash changes if there are any
-      if (hasChanges) {
-        await execAsync("git stash push -m \"auto-stash before branch switch\"", {
-          cwd: worktreePath,
+      if (await hasUncommittedChanges(worktreePath)) {
+        const summary = await getChangesSummary(worktreePath);
+        res.status(400).json({
+          success: false,
+          error: `Cannot switch branches: you have uncommitted changes (${summary}). Please commit your changes first.`,
+          code: "UNCOMMITTED_CHANGES",
         });
-        stashed = true;
+        return;
       }
 
-      try {
-        // Switch to the branch
-        await execAsync(`git checkout ${branchName}`, {
-          cwd: worktreePath,
-        });
+      // Switch to the target branch
+      await execAsync(`git checkout "${branchName}"`, { cwd: worktreePath });
 
-        // Pop the stash if we stashed changes
-        if (stashed) {
-          try {
-            await execAsync("git stash pop", {
-              cwd: worktreePath,
-            });
-          } catch (stashPopError) {
-            // Stash pop might fail due to conflicts
-            const err = stashPopError as { stderr?: string; message?: string };
-            const errorMsg = err.stderr || err.message || "";
-
-            if (errorMsg.includes("CONFLICT") || errorMsg.includes("conflict")) {
-              res.json({
-                success: true,
-                result: {
-                  previousBranch,
-                  currentBranch: branchName,
-                  message: `Switched to '${branchName}' but stash had conflicts. Please resolve manually.`,
-                  stashed: true,
-                  stashConflict: true,
-                },
-              });
-              return;
-            }
-            // Re-throw if it's not a conflict error
-            throw stashPopError;
-          }
-        }
-
-        const message = stashed
-          ? `Switched to branch '${branchName}' (changes stashed and restored)`
-          : `Switched to branch '${branchName}'`;
-
-        res.json({
-          success: true,
-          result: {
-            previousBranch,
-            currentBranch: branchName,
-            message,
-            stashed,
-          },
-        });
-      } catch (checkoutError) {
-        // If checkout fails and we stashed, try to restore the stash
-        if (stashed) {
-          try {
-            await execAsync("git stash pop", { cwd: worktreePath });
-          } catch {
-            // Ignore stash pop errors during recovery
-          }
-        }
-        throw checkoutError;
-      }
+      res.json({
+        success: true,
+        result: {
+          previousBranch,
+          currentBranch: branchName,
+          message: `Switched to branch '${branchName}'`,
+        },
+      });
     } catch (error) {
       logError(error, "Switch branch failed");
       res.status(500).json({ success: false, error: getErrorMessage(error) });