Fix concurrency limits and remote branch fetching issues (#788)

* Changes from fix/bug-fixes

* feat: Refactor worktree iteration and improve error logging across services

* feat: Extract URL/port patterns to module level and fix abort condition

* fix: Improve IPv6 loopback handling, select component layout, and terminal UI

* feat: Add thinking level defaults and adjust list row padding

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

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

* feat: Add worktree-aware terminal creation and split options, fix npm security issues from audit

* feat: Add tracked remote detection to pull dialog flow

* feat: Add merge state tracking to git operations

* feat: Improve merge detection and add post-merge action preferences

* Update apps/ui/src/components/views/board-view/dialogs/git-pull-dialog.tsx

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

* Update apps/ui/src/components/views/board-view/dialogs/git-pull-dialog.tsx

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

* fix: Pass merge detection info to stash reapplication and handle merge state consistently

* fix: Call onPulled callback in merge handlers and add validation checks

---------

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

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

@@ -26,23 +26,9 @@ export function createRunFeatureHandler(autoModeService: AutoModeServiceCompat)
         return;
       }
 
-      // Check per-worktree capacity before starting
+      // Note: No concurrency limit check here. Manual feature starts always run
-      const capacity = await autoModeService.checkWorktreeCapacity(projectPath, featureId);
+      // immediately and bypass the concurrency limit. Their presence IS counted
-      if (!capacity.hasCapacity) {
+      // by the auto-loop coordinator when deciding whether to dispatch new auto-mode tasks.
-        const worktreeDesc = capacity.branchName
-          ? `worktree "${capacity.branchName}"`
-          : 'main worktree';
-        res.status(429).json({
-          success: false,
-          error: `Agent limit reached for ${worktreeDesc} (${capacity.currentAgents}/${capacity.maxAgents}). Wait for running tasks to complete or increase the limit.`,
-          details: {
-            currentAgents: capacity.currentAgents,
-            maxAgents: capacity.maxAgents,
-            branchName: capacity.branchName,
-          },
-        });
-        return;
-      }
 
       // Start execution in background
       // executeFeature derives workDir from feature.branchName

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

@@ -23,6 +23,7 @@ export function createDiffsHandler() {
           diff: result.diff,
           files: result.files,
           hasChanges: result.hasChanges,
+          ...(result.mergeState ? { mergeState: result.mergeState } : {}),
         });
       } catch (innerError) {
         logError(innerError, 'Git diff failed');

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

@@ -22,6 +22,36 @@ import { getErrorMessage, logError, isValidBranchName } from '../common.js';
 import { execGitCommand } from '../../../lib/git.js';
 import type { EventEmitter } from '../../../lib/events.js';
 import { performCheckoutBranch } from '../../../services/checkout-branch-service.js';
+import { createLogger } from '@automaker/utils';
+
+const logger = createLogger('CheckoutBranchRoute');
+
+/** Timeout for git fetch operations (30 seconds) */
+const FETCH_TIMEOUT_MS = 30_000;
+
+/**
+ * Fetch latest from all remotes (silently, with timeout).
+ * Non-fatal: fetch errors are logged and swallowed so the workflow continues.
+ */
+async function fetchRemotes(cwd: string): Promise<void> {
+  const controller = new AbortController();
+  const timerId = setTimeout(() => controller.abort(), FETCH_TIMEOUT_MS);
+
+  try {
+    await execGitCommand(['fetch', '--all', '--quiet'], cwd, undefined, controller);
+  } catch (error) {
+    if (error instanceof Error && error.message === 'Process aborted') {
+      logger.warn(
+        `fetchRemotes timed out after ${FETCH_TIMEOUT_MS}ms - continuing without latest remote refs`
+      );
+    } else {
+      logger.warn(`fetchRemotes failed: ${getErrorMessage(error)} - continuing with local refs`);
+    }
+    // Non-fatal: continue with locally available refs
+  } finally {
+    clearTimeout(timerId);
+  }
+}
 
 export function createCheckoutBranchHandler(events?: EventEmitter) {
   return async (req: Request, res: Response): Promise<void> => {
@@ -127,6 +157,10 @@ export function createCheckoutBranchHandler(events?: EventEmitter) {
       }
 
       // Original simple flow (no stash handling)
+      // Fetch latest remote refs before creating the branch so that
+      // base branch validation works for remote references like "origin/main"
+      await fetchRemotes(resolvedPath);
+
       const currentBranchOutput = await execGitCommand(
         ['rev-parse', '--abbrev-ref', 'HEAD'],
         resolvedPath

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

@@ -30,6 +30,9 @@ import { runInitScript } from '../../../services/init-script-service.js';
 
 const logger = createLogger('Worktree');
 
+/** Timeout for git fetch operations (30 seconds) */
+const FETCH_TIMEOUT_MS = 30_000;
+
 const execAsync = promisify(exec);
 
 /**
@@ -83,41 +86,6 @@ async function findExistingWorktreeForBranch(
   }
 }
 
-/**
- * Detect whether a base branch reference is a remote branch (e.g. "origin/main").
- * Returns the remote name if it matches a known remote, otherwise null.
- */
-async function detectRemoteBranch(
-  projectPath: string,
-  baseBranch: string
-): Promise<{ remote: string; branch: string } | null> {
-  const slashIndex = baseBranch.indexOf('/');
-  if (slashIndex <= 0) return null;
-
-  const possibleRemote = baseBranch.substring(0, slashIndex);
-
-  try {
-    // Check if this is actually a remote name by listing remotes
-    const stdout = await execGitCommand(['remote'], projectPath);
-    const remotes = stdout
-      .trim()
-      .split('\n')
-      .map((r: string) => r.trim())
-      .filter(Boolean);
-
-    if (remotes.includes(possibleRemote)) {
-      return {
-        remote: possibleRemote,
-        branch: baseBranch.substring(slashIndex + 1),
-      };
-    }
-  } catch {
-    // Not a git repo or no remotes — fall through
-  }
-
-  return null;
-}
-
 export function createCreateHandler(events: EventEmitter, settingsService?: SettingsService) {
   const worktreeService = new WorktreeService();
 
@@ -206,26 +174,23 @@ export function createCreateHandler(events: EventEmitter, settingsService?: Sett
       // Create worktrees directory if it doesn't exist
       await secureFs.mkdir(worktreesDir, { recursive: true });
 
-      // If a base branch is specified and it's a remote branch, fetch from that remote first
+      // Fetch latest from all remotes before creating the worktree.
-      // This ensures we have the latest refs before creating the worktree
+      // This ensures remote refs are up-to-date for:
-      if (baseBranch && baseBranch !== 'HEAD') {
+      // - Remote base branches (e.g. "origin/main")
-        const remoteBranchInfo = await detectRemoteBranch(projectPath, baseBranch);
+      // - Existing remote branches being checked out as worktrees
-        if (remoteBranchInfo) {
+      // - Branch existence checks against fresh remote state
-          logger.info(
+      logger.info('Fetching from all remotes before creating worktree');
-            `Fetching from remote "${remoteBranchInfo.remote}" before creating worktree (base: ${baseBranch})`
+      try {
-          );
+        const controller = new AbortController();
-          try {
+        const timerId = setTimeout(() => controller.abort(), FETCH_TIMEOUT_MS);
-            await execGitCommand(
+        try {
-              ['fetch', remoteBranchInfo.remote, remoteBranchInfo.branch],
+          await execGitCommand(['fetch', '--all', '--quiet'], projectPath, undefined, controller);
-              projectPath
+        } finally {
-            );
+          clearTimeout(timerId);
-          } catch (fetchErr) {
-            // Non-fatal: log but continue — the ref might already be cached locally
-            logger.warn(
-              `Failed to fetch from remote "${remoteBranchInfo.remote}": ${getErrorMessage(fetchErr)}`
-            );
-          }
         }
+      } catch (fetchErr) {
+        // Non-fatal: log but continue — refs might already be cached locally
+        logger.warn(`Failed to fetch from remotes: ${getErrorMessage(fetchErr)}`);
       }
 
       // Check if branch exists (using array arguments to prevent injection)

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

@@ -34,6 +34,7 @@ export function createDiffsHandler() {
           diff: result.diff,
           files: result.files,
           hasChanges: result.hasChanges,
+          ...(result.mergeState ? { mergeState: result.mergeState } : {}),
         });
         return;
       }
@@ -55,6 +56,7 @@ export function createDiffsHandler() {
           diff: result.diff,
           files: result.files,
           hasChanges: result.hasChanges,
+          ...(result.mergeState ? { mergeState: result.mergeState } : {}),
         });
       } catch (innerError) {
         // Worktree doesn't exist - fallback to main project path
@@ -71,6 +73,7 @@ export function createDiffsHandler() {
             diff: result.diff,
             files: result.files,
             hasChanges: result.hasChanges,
+            ...(result.mergeState ? { mergeState: result.mergeState } : {}),
           });
         } catch (fallbackError) {
           logError(fallbackError, 'Fallback to main project also failed');

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

@@ -83,6 +83,9 @@ function mapResultToResponse(res: Response, result: PullResult): void {
       stashed: result.stashed,
       stashRestored: result.stashRestored,
       message: result.message,
+      isMerge: result.isMerge,
+      isFastForward: result.isFastForward,
+      mergeAffectedFiles: result.mergeAffectedFiles,
     },
   });
 }

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

@@ -9,7 +9,7 @@
  * For remote branches (e.g., "origin/feature"), automatically creates a
  * local tracking branch and checks it out.
  *
- * Also fetches the latest remote refs after switching.
+ * Also fetches the latest remote refs before switching to ensure accurate branch detection.
  *
  * Git business logic is delegated to worktree-branch-service.ts.
  * Events are emitted at key lifecycle points for WebSocket subscribers.

apps/server/src/services/auto-loop-coordinator.ts

@@ -163,6 +163,10 @@ export class AutoLoopCoordinator {
     const { projectPath, branchName } = projectState.config;
     while (projectState.isRunning && !projectState.abortController.signal.aborted) {
       try {
+        // Count ALL running features (both auto and manual) against the concurrency limit.
+        // This ensures auto mode is aware of the total system load and does not over-subscribe
+        // resources. Manual tasks always bypass the limit and run immediately, but their
+        // presence is accounted for when deciding whether to dispatch new auto-mode tasks.
         const runningCount = await this.getRunningCountForWorktree(projectPath, branchName);
         if (runningCount >= projectState.config.maxConcurrency) {
           await this.sleep(5000, projectState.abortController.signal);
@@ -298,11 +302,17 @@ export class AutoLoopCoordinator {
     return Array.from(activeProjects);
   }
 
+  /**
+   * Get the number of running features for a worktree.
+   * By default counts ALL running features (both auto-mode and manual).
+   * Pass `autoModeOnly: true` to count only auto-mode features.
+   */
   async getRunningCountForWorktree(
     projectPath: string,
-    branchName: string | null
+    branchName: string | null,
+    options?: { autoModeOnly?: boolean }
   ): Promise<number> {
-    return this.concurrencyManager.getRunningCountForWorktree(projectPath, branchName);
+    return this.concurrencyManager.getRunningCountForWorktree(projectPath, branchName, options);
   }
 
   trackFailureAndCheckPauseForProject(

apps/server/src/services/auto-mode/facade.ts

@@ -334,6 +334,23 @@ export class AutoModeServiceFacade {
       async (pPath) => featureLoader.getAll(pPath)
     );
 
+    /**
+     * Iterate all active worktrees for this project, falling back to the
+     * main worktree (null) when none are active.
+     */
+    const forEachProjectWorktree = (fn: (branchName: string | null) => void): void => {
+      const projectWorktrees = autoLoopCoordinator
+        .getActiveWorktrees()
+        .filter((w) => w.projectPath === projectPath);
+      if (projectWorktrees.length === 0) {
+        fn(null);
+      } else {
+        for (const w of projectWorktrees) {
+          fn(w.branchName);
+        }
+      }
+    };
+
     // ExecutionService - runAgentFn delegates to AgentExecutor via shared helper
     const executionService = new ExecutionService(
       eventBus,
@@ -357,11 +374,36 @@ export class AutoModeServiceFacade {
       (pPath, featureId) => getFacade().contextExists(featureId),
       (pPath, featureId, useWorktrees, _calledInternally) =>
         getFacade().resumeFeature(featureId, useWorktrees, _calledInternally),
-      (errorInfo) =>
+      (errorInfo) => {
-        autoLoopCoordinator.trackFailureAndCheckPauseForProject(projectPath, null, errorInfo),
+        // Track failure against ALL active worktrees for this project.
-      (errorInfo) => autoLoopCoordinator.signalShouldPauseForProject(projectPath, null, errorInfo),
+        // The ExecutionService callbacks don't receive branchName, so we
+        // iterate all active worktrees. Uses a for-of loop (not .some()) to
+        // ensure every worktree's failure counter is incremented.
+        let shouldPause = false;
+        forEachProjectWorktree((branchName) => {
+          if (
+            autoLoopCoordinator.trackFailureAndCheckPauseForProject(
+              projectPath,
+              branchName,
+              errorInfo
+            )
+          ) {
+            shouldPause = true;
+          }
+        });
+        return shouldPause;
+      },
+      (errorInfo) => {
+        forEachProjectWorktree((branchName) =>
+          autoLoopCoordinator.signalShouldPauseForProject(projectPath, branchName, errorInfo)
+        );
+      },
       () => {
-        /* recordSuccess - no-op */
+        // Record success to clear failure tracking. This prevents failures
+        // from accumulating over time and incorrectly pausing auto mode.
+        forEachProjectWorktree((branchName) =>
+          autoLoopCoordinator.recordSuccessForProject(projectPath, branchName)
+        );
       },
       (_pPath) => getFacade().saveExecutionState(),
       loadContextFiles

apps/server/src/services/checkout-branch-service.ts

@@ -10,6 +10,7 @@
  * Follows the same pattern as worktree-branch-service.ts (performSwitchBranch).
  *
  * The workflow:
+ * 0. Fetch latest from all remotes (ensures remote refs are up-to-date)
  * 1. Validate inputs (branch name, base branch)
  * 2. Get current branch name
  * 3. Check if target branch already exists
@@ -19,11 +20,51 @@
  * 7. Handle error recovery (restore stash if checkout fails)
  */
 
-import { getErrorMessage } from '@automaker/utils';
+import { createLogger, getErrorMessage } from '@automaker/utils';
 import { execGitCommand } from '../lib/git.js';
 import type { EventEmitter } from '../lib/events.js';
 import { hasAnyChanges, stashChanges, popStash, localBranchExists } from './branch-utils.js';
 
+const logger = createLogger('CheckoutBranchService');
+
+// ============================================================================
+// Local Helpers
+// ============================================================================
+
+/** Timeout for git fetch operations (30 seconds) */
+const FETCH_TIMEOUT_MS = 30_000;
+
+/**
+ * Fetch latest from all remotes (silently, with timeout).
+ *
+ * A process-level timeout is enforced via an AbortController so that a
+ * slow or unresponsive remote does not block the branch creation flow
+ * indefinitely.  Timeout errors are logged and treated as non-fatal
+ * (the same as network-unavailable errors) so the rest of the workflow
+ * continues normally.  This is called before creating the new branch to
+ * ensure remote refs are up-to-date when a remote base branch is used.
+ */
+async function fetchRemotes(cwd: string): Promise<void> {
+  const controller = new AbortController();
+  const timerId = setTimeout(() => controller.abort(), FETCH_TIMEOUT_MS);
+
+  try {
+    await execGitCommand(['fetch', '--all', '--quiet'], cwd, undefined, controller);
+  } catch (error) {
+    if (controller.signal.aborted) {
+      // Fetch timed out - log and continue; callers should not be blocked by a slow remote
+      logger.warn(
+        `fetchRemotes timed out after ${FETCH_TIMEOUT_MS}ms - continuing without latest remote refs`
+      );
+    } else {
+      logger.warn(`fetchRemotes failed: ${getErrorMessage(error)} - continuing with local refs`);
+    }
+    // Non-fatal: continue with locally available refs regardless of failure type
+  } finally {
+    clearTimeout(timerId);
+  }
+}
+
 // ============================================================================
 // Types
 // ============================================================================
@@ -78,6 +119,11 @@ export async function performCheckoutBranch(
   // Emit start event
   events?.emit('switch:start', { worktreePath, branchName, operation: 'checkout' });
 
+  // 0. Fetch latest from all remotes before creating the branch
+  //    This ensures remote refs are up-to-date so that base branch validation
+  //    works correctly for remote branch references (e.g. "origin/main").
+  await fetchRemotes(worktreePath);
+
   // 1. Get current branch
   let previousBranch: string;
   try {

apps/server/src/services/concurrency-manager.ts

@@ -170,17 +170,28 @@ export class ConcurrencyManager {
    * @param projectPath - The project path
    * @param branchName - The branch name, or null for main worktree
    *                     (features without branchName or matching primary branch)
+   * @param options.autoModeOnly - If true, only count features started by auto mode.
+   *                               Note: The auto-loop coordinator now counts ALL
+   *                               running features (not just auto-mode) to ensure
+   *                               total system load is respected. This option is
+   *                               retained for other callers that may need filtered counts.
    * @returns Number of running features for the worktree
    */
   async getRunningCountForWorktree(
     projectPath: string,
-    branchName: string | null
+    branchName: string | null,
+    options?: { autoModeOnly?: boolean }
   ): Promise<number> {
     // Get the actual primary branch name for the project
     const primaryBranch = await this.getCurrentBranch(projectPath);
 
     let count = 0;
     for (const [, feature] of this.runningFeatures) {
+      // If autoModeOnly is set, skip manually started features
+      if (options?.autoModeOnly && !feature.isAutoMode) {
+        continue;
+      }
+
       // Filter by project path AND branchName to get accurate worktree-specific count
       const featureBranch = feature.branchName ?? null;
       if (branchName === null) {

apps/server/src/services/dev-server-service.ts

@@ -19,6 +19,69 @@ const logger = createLogger('DevServerService');
 // Maximum scrollback buffer size (characters) - matches TerminalService pattern
 const MAX_SCROLLBACK_SIZE = 50000; // ~50KB per dev server
 
+// URL patterns for detecting full URLs from dev server output.
+// Defined once at module level to avoid reallocation on every call to detectUrlFromOutput.
+// Ordered from most specific (framework-specific) to least specific.
+const URL_PATTERNS: Array<{ pattern: RegExp; description: string }> = [
+  // Vite / Nuxt / SvelteKit / Astro / Angular CLI format: "Local:  http://..."
+  {
+    pattern: /(?:Local|Network|External):\s+(https?:\/\/[^\s]+)/i,
+    description: 'Vite/Nuxt/SvelteKit/Astro/Angular format',
+  },
+  // Next.js format: "ready - started server on 0.0.0.0:3000, url: http://localhost:3000"
+  // Next.js 14+: "▲ Next.js 14.0.0\n- Local: http://localhost:3000"
+  {
+    pattern: /(?:ready|started server).*?(?:url:\s*)?(https?:\/\/[^\s,]+)/i,
+    description: 'Next.js format',
+  },
+  // Remix format: "started at http://localhost:3000"
+  // Django format: "Starting development server at http://127.0.0.1:8000/"
+  // Rails / Puma: "Listening on http://127.0.0.1:3000"
+  // Generic: "listening at http://...", "available at http://...", "running at http://..."
+  {
+    pattern:
+      /(?:starting|started|listening|running|available|serving|accessible)\s+(?:at|on)\s+(https?:\/\/[^\s,)]+)/i,
+    description: 'Generic "starting/started/listening at" format',
+  },
+  // PHP built-in server: "Development Server (http://localhost:8000) started"
+  {
+    pattern: /(?:server|development server)\s*\(\s*(https?:\/\/[^\s)]+)\s*\)/i,
+    description: 'PHP server format',
+  },
+  // Webpack Dev Server: "Project is running at http://localhost:8080/"
+  {
+    pattern: /(?:project|app|application)\s+(?:is\s+)?running\s+(?:at|on)\s+(https?:\/\/[^\s,]+)/i,
+    description: 'Webpack/generic "running at" format',
+  },
+  // Go / Rust / generic: "Serving on http://...", "Server on http://..."
+  {
+    pattern: /(?:serving|server)\s+(?:on|at)\s+(https?:\/\/[^\s,]+)/i,
+    description: 'Generic "serving on" format',
+  },
+  // Localhost URL with port (conservative - must be localhost/127.0.0.1/[::]/0.0.0.0)
+  // This catches anything that looks like a dev server URL
+  {
+    pattern: /(https?:\/\/(?:localhost|127\.0\.0\.1|\[::\]|0\.0\.0\.0):\d+\S*)/i,
+    description: 'Generic localhost URL with port',
+  },
+];
+
+// Port-only patterns for detecting port numbers from dev server output
+// when a full URL is not present in the output.
+// Defined once at module level to avoid reallocation on every call to detectUrlFromOutput.
+const PORT_PATTERNS: Array<{ pattern: RegExp; description: string }> = [
+  // "listening on port 3000", "server on port 3000", "started on port 3000"
+  {
+    pattern: /(?:listening|running|started|serving|available)\s+on\s+port\s+(\d+)/i,
+    description: '"listening on port" format',
+  },
+  // "Port: 3000", "port 3000" (at start of line or after whitespace)
+  {
+    pattern: /(?:^|\s)port[:\s]+(\d{4,5})(?:\s|$|[.,;])/im,
+    description: '"port:" format',
+  },
+];
+
 // Throttle output to prevent overwhelming WebSocket under heavy load
 const OUTPUT_THROTTLE_MS = 4; // ~250fps max update rate for responsive feedback
 const OUTPUT_BATCH_SIZE = 4096; // Smaller batches for lower latency
@@ -105,9 +168,52 @@ class DevServerService {
     }
   }
 
+  /**
+   * Strip ANSI escape codes from a string
+   * Dev server output often contains color codes that can interfere with URL detection
+   */
+  private stripAnsi(str: string): string {
+    // Matches ANSI escape sequences: CSI sequences, OSC sequences, and simple escapes
+    // eslint-disable-next-line no-control-regex
+    return str.replace(/\x1B(?:\[[0-9;]*[a-zA-Z]|\].*?(?:\x07|\x1B\\)|\[[?]?[0-9;]*[hl])/g, '');
+  }
+
+  /**
+   * Extract port number from a URL string.
+   * Returns the explicit port if present, or null if no port is specified.
+   * Default protocol ports (80/443) are intentionally NOT returned to avoid
+   * overwriting allocated dev server ports with protocol defaults.
+   */
+  private extractPortFromUrl(url: string): number | null {
+    try {
+      const parsed = new URL(url);
+      if (parsed.port) {
+        return parseInt(parsed.port, 10);
+      }
+      return null;
+    } catch {
+      return null;
+    }
+  }
+
   /**
    * Detect actual server URL from output
-   * Parses stdout/stderr for common URL patterns from dev servers
+   * Parses stdout/stderr for common URL patterns from dev servers.
+   *
+   * Supports detection of URLs from:
+   * - Vite: "Local:   http://localhost:5173/"
+   * - Next.js: "ready - started server on 0.0.0.0:3000, url: http://localhost:3000"
+   * - Nuxt: "Local:    http://localhost:3000/"
+   * - Remix: "started at http://localhost:3000"
+   * - Astro: "Local    http://localhost:4321/"
+   * - SvelteKit: "Local:   http://localhost:5173/"
+   * - CRA/Webpack: "On Your Network: http://192.168.1.1:3000"
+   * - Angular: "Local:   http://localhost:4200/"
+   * - Express/Fastify/Koa: "Server listening on port 3000"
+   * - Django: "Starting development server at http://127.0.0.1:8000/"
+   * - Rails: "Listening on http://127.0.0.1:3000"
+   * - PHP: "Development Server (http://localhost:8000) started"
+   * - Generic: Any localhost URL with a port
    */
   private detectUrlFromOutput(server: DevServerInfo, content: string): void {
     // Skip if URL already detected
@@ -115,39 +221,95 @@ class DevServerService {
       return;
     }
 
-    // Common URL patterns from various dev servers:
+    // Strip ANSI escape codes to prevent color codes from breaking regex matching
-    // - Vite: "Local:   http://localhost:5173/"
+    const cleanContent = this.stripAnsi(content);
-    // - Next.js: "ready - started server on 0.0.0.0:3000, url: http://localhost:3000"
-    // - CRA/Webpack: "On Your Network:  http://192.168.1.1:3000"
-    // - Generic: Any http:// or https:// URL
-    const urlPatterns = [
-      /(?:Local|Network):\s+(https?:\/\/[^\s]+)/i, // Vite format
-      /(?:ready|started server).*?(?:url:\s*)?(https?:\/\/[^\s,]+)/i, // Next.js format
-      /(https?:\/\/(?:localhost|127\.0\.0\.1|\[::\]):\d+)/i, // Generic localhost URL
-      /(https?:\/\/[^\s<>"{}|\\^`[\]]+)/i, // Any HTTP(S) URL
-    ];
 
-    for (const pattern of urlPatterns) {
+    // Phase 1: Try to detect a full URL from output
-      const match = content.match(pattern);
+    // Patterns are defined at module level (URL_PATTERNS) and reused across calls
+    for (const { pattern, description } of URL_PATTERNS) {
+      const match = cleanContent.match(pattern);
       if (match && match[1]) {
-        const detectedUrl = match[1].trim();
+        let detectedUrl = match[1].trim();
-        // Validate it looks like a reasonable URL
+        // Remove trailing punctuation that might have been captured
+        detectedUrl = detectedUrl.replace(/[.,;:!?)\]}>]+$/, '');
+
         if (detectedUrl.startsWith('http://') || detectedUrl.startsWith('https://')) {
+          // Normalize 0.0.0.0 to localhost for browser accessibility
+          detectedUrl = detectedUrl.replace(
+            /\/\/0\.0\.0\.0(:\d+)?/,
+            (_, port) => `//localhost${port || ''}`
+          );
+          // Normalize [::] to localhost for browser accessibility
+          detectedUrl = detectedUrl.replace(
+            /\/\/\[::\](:\d+)?/,
+            (_, port) => `//localhost${port || ''}`
+          );
+          // Normalize [::1] (IPv6 loopback) to localhost for browser accessibility
+          detectedUrl = detectedUrl.replace(
+            /\/\/\[::1\](:\d+)?/,
+            (_, port) => `//localhost${port || ''}`
+          );
+
           server.url = detectedUrl;
           server.urlDetected = true;
-          logger.info(
+
-            `Detected actual server URL: ${detectedUrl} (allocated port was ${server.port})`
+          // Update the port to match the detected URL's actual port
-          );
+          const detectedPort = this.extractPortFromUrl(detectedUrl);
+          if (detectedPort && detectedPort !== server.port) {
+            logger.info(
+              `Port mismatch: allocated ${server.port}, detected ${detectedPort} from ${description}`
+            );
+            server.port = detectedPort;
+          }
+
+          logger.info(`Detected server URL via ${description}: ${detectedUrl}`);
 
           // Emit URL update event
           if (this.emitter) {
             this.emitter.emit('dev-server:url-detected', {
               worktreePath: server.worktreePath,
               url: detectedUrl,
+              port: server.port,
               timestamp: new Date().toISOString(),
             });
           }
-          break;
+          return;
+        }
+      }
+    }
+
+    // Phase 2: Try to detect just a port number from output (no full URL)
+    // Some servers only print "listening on port 3000" without a full URL
+    // Patterns are defined at module level (PORT_PATTERNS) and reused across calls
+    for (const { pattern, description } of PORT_PATTERNS) {
+      const match = cleanContent.match(pattern);
+      if (match && match[1]) {
+        const detectedPort = parseInt(match[1], 10);
+        // Sanity check: port should be in a reasonable range
+        if (detectedPort > 0 && detectedPort <= 65535) {
+          const detectedUrl = `http://localhost:${detectedPort}`;
+          server.url = detectedUrl;
+          server.urlDetected = true;
+
+          if (detectedPort !== server.port) {
+            logger.info(
+              `Port mismatch: allocated ${server.port}, detected ${detectedPort} from ${description}`
+            );
+            server.port = detectedPort;
+          }
+
+          logger.info(`Detected server port via ${description}: ${detectedPort} → ${detectedUrl}`);
+
+          // Emit URL update event
+          if (this.emitter) {
+            this.emitter.emit('dev-server:url-detected', {
+              worktreePath: server.worktreePath,
+              url: detectedUrl,
+              port: server.port,
+              timestamp: new Date().toISOString(),
+            });
+          }
+          return;
         }
       }
     }
@@ -673,6 +835,7 @@ class DevServerService {
         worktreePath: string;
         port: number;
         url: string;
+        urlDetected: boolean;
       }>;
     };
   } {
@@ -680,6 +843,7 @@ class DevServerService {
       worktreePath: s.worktreePath,
       port: s.port,
       url: s.url,
+      urlDetected: s.urlDetected,
     }));
 
     return {

apps/server/src/services/pull-service.ts

@@ -46,6 +46,12 @@ export interface PullResult {
   conflictSource?: 'pull' | 'stash';
   conflictFiles?: string[];
   message?: string;
+  /** Whether the pull resulted in a merge commit (not fast-forward) */
+  isMerge?: boolean;
+  /** Whether the pull was a fast-forward (no merge commit needed) */
+  isFastForward?: boolean;
+  /** Files affected by the merge (only present when isMerge is true) */
+  mergeAffectedFiles?: string[];
 }
 
 // ============================================================================
@@ -178,6 +184,31 @@ function isConflictError(errorOutput: string): boolean {
   return errorOutput.includes('CONFLICT') || errorOutput.includes('Automatic merge failed');
 }
 
+/**
+ * Determine whether the current HEAD commit is a merge commit by checking
+ * whether it has two or more parent hashes.
+ *
+ * Runs `git show -s --pretty=%P HEAD` which prints the parent SHAs separated
+ * by spaces.  A merge commit has at least two parents; a regular commit has one.
+ *
+ * @param worktreePath - Path to the git worktree
+ * @returns true if HEAD is a merge commit, false otherwise
+ */
+async function isMergeCommit(worktreePath: string): Promise<boolean> {
+  try {
+    const output = await execGitCommand(['show', '-s', '--pretty=%P', 'HEAD'], worktreePath);
+    // Each parent SHA is separated by a space; two or more means it's a merge
+    const parents = output
+      .trim()
+      .split(/\s+/)
+      .filter((p) => p.length > 0);
+    return parents.length >= 2;
+  } catch {
+    // If the check fails for any reason, assume it is not a merge commit
+    return false;
+  }
+}
+
 /**
  * Check whether an output string indicates a stash conflict.
  */
@@ -302,10 +333,39 @@ export async function performPull(
   const pullArgs = upstreamStatus === 'tracking' ? ['pull'] : ['pull', targetRemote, branchName];
   let pullConflict = false;
   let pullConflictFiles: string[] = [];
+
+  // Declare merge detection variables before the try block so they are accessible
+  // in the stash reapplication path even when didStash is true.
+  let isMerge = false;
+  let isFastForward = false;
+  let mergeAffectedFiles: string[] = [];
+
   try {
     const pullOutput = await execGitCommand(pullArgs, worktreePath);
 
     const alreadyUpToDate = pullOutput.includes('Already up to date');
+    // Detect fast-forward from git pull output
+    isFastForward = pullOutput.includes('Fast-forward') || pullOutput.includes('fast-forward');
+    // Detect merge by checking whether the new HEAD has two parents (more reliable
+    // than string-matching localised pull output which may not contain 'Merge').
+    isMerge = !alreadyUpToDate && !isFastForward ? await isMergeCommit(worktreePath) : false;
+
+    // If it was a real merge (not fast-forward), get the affected files
+    if (isMerge) {
+      try {
+        // Get files changed in the merge commit
+        const diffOutput = await execGitCommand(
+          ['diff', '--name-only', 'HEAD~1', 'HEAD'],
+          worktreePath
+        );
+        mergeAffectedFiles = diffOutput
+          .trim()
+          .split('\n')
+          .filter((f: string) => f.trim().length > 0);
+      } catch {
+        // Ignore errors - this is best-effort
+      }
+    }
 
     // If no stash to reapply, return success
     if (!didStash) {
@@ -317,6 +377,8 @@ export async function performPull(
         stashed: false,
         stashRestored: false,
         message: alreadyUpToDate ? 'Already up to date' : 'Pulled latest changes',
+        ...(isMerge ? { isMerge: true, mergeAffectedFiles } : {}),
+        ...(isFastForward ? { isFastForward: true } : {}),
       };
     }
   } catch (pullError: unknown) {
@@ -374,7 +436,11 @@ export async function performPull(
 
   // 10. Pull succeeded, now try to reapply stash
   if (didStash) {
-    return await reapplyStash(worktreePath, branchName);
+    return await reapplyStash(worktreePath, branchName, {
+      isMerge,
+      isFastForward,
+      mergeAffectedFiles,
+    });
   }
 
   // Shouldn't reach here, but return a safe default
@@ -392,9 +458,21 @@ export async function performPull(
  *
  * @param worktreePath - Path to the git worktree
  * @param branchName - Current branch name
+ * @param mergeInfo - Merge/fast-forward detection info from the pull step
  * @returns PullResult reflecting stash reapplication status
  */
-async function reapplyStash(worktreePath: string, branchName: string): Promise<PullResult> {
+async function reapplyStash(
+  worktreePath: string,
+  branchName: string,
+  mergeInfo: { isMerge: boolean; isFastForward: boolean; mergeAffectedFiles: string[] }
+): Promise<PullResult> {
+  const mergeFields: Partial<PullResult> = {
+    ...(mergeInfo.isMerge
+      ? { isMerge: true, mergeAffectedFiles: mergeInfo.mergeAffectedFiles }
+      : {}),
+    ...(mergeInfo.isFastForward ? { isFastForward: true } : {}),
+  };
+
   try {
     await popStash(worktreePath);
 
@@ -406,6 +484,7 @@ async function reapplyStash(worktreePath: string, branchName: string): Promise<P
       hasConflicts: false,
       stashed: true,
       stashRestored: true,
+      ...mergeFields,
       message: 'Pulled latest changes and restored your stashed changes.',
     };
   } catch (stashPopError: unknown) {
@@ -431,6 +510,7 @@ async function reapplyStash(worktreePath: string, branchName: string): Promise<P
         conflictFiles: stashConflictFiles,
         stashed: true,
         stashRestored: false,
+        ...mergeFields,
         message: 'Pull succeeded but reapplying your stashed changes resulted in merge conflicts.',
       };
     }
@@ -445,6 +525,7 @@ async function reapplyStash(worktreePath: string, branchName: string): Promise<P
       hasConflicts: false,
       stashed: true,
       stashRestored: false,
+      ...mergeFields,
       message:
         'Pull succeeded but failed to reapply stashed changes. Your changes are still in the stash list.',
     };

apps/server/src/services/worktree-branch-service.ts

@@ -9,7 +9,8 @@
  * For remote branches (e.g., "origin/feature"), automatically creates a
  * local tracking branch and checks it out.
  *
- * Also fetches the latest remote refs after switching.
+ * Fetches the latest remote refs before switching to ensure remote branch
+ * references are up-to-date for accurate detection and checkout.
  *
  * Extracted from the worktree switch-branch route to improve organization
  * and testability. Follows the same pattern as pull-service.ts and
@@ -57,7 +58,8 @@ const FETCH_TIMEOUT_MS = 30_000;
  * slow or unresponsive remote does not block the branch-switch flow
  * indefinitely.  Timeout errors are logged and treated as non-fatal
  * (the same as network-unavailable errors) so the rest of the workflow
- * continues normally.
+ * continues normally.  This is called before the branch switch to
+ * ensure remote refs are up-to-date for branch detection and checkout.
  */
 async function fetchRemotes(cwd: string): Promise<void> {
   const controller = new AbortController();
@@ -66,15 +68,15 @@ async function fetchRemotes(cwd: string): Promise<void> {
   try {
     await execGitCommand(['fetch', '--all', '--quiet'], cwd, undefined, controller);
   } catch (error) {
-    if (error instanceof Error && error.message === 'Process aborted') {
+    if (controller.signal.aborted) {
       // Fetch timed out - log and continue; callers should not be blocked by a slow remote
       logger.warn(
         `fetchRemotes timed out after ${FETCH_TIMEOUT_MS}ms - continuing without latest remote refs`
       );
+    } else {
+      logger.warn(`fetchRemotes failed: ${getErrorMessage(error)} - continuing with local refs`);
     }
-    // Ignore all fetch errors (timeout or otherwise) - we may be offline or the
+    // Non-fatal: continue with locally available refs regardless of failure type
-    // remote may be temporarily unavailable.  The branch switch itself has
-    // already succeeded at this point.
   } finally {
     clearTimeout(timerId);
   }
@@ -126,13 +128,13 @@ async function isRemoteBranch(cwd: string, branchName: string): Promise<boolean>
  * Perform a full branch switch workflow on the given worktree.
  *
  * The workflow:
- * 1. Get current branch name
+ * 1. Fetch latest from all remotes (ensures remote refs are up-to-date)
- * 2. Detect remote vs local branch and determine target
+ * 2. Get current branch name
- * 3. Return early if already on target branch
+ * 3. Detect remote vs local branch and determine target
- * 4. Validate branch existence
+ * 4. Return early if already on target branch
- * 5. Stash local changes if any
+ * 5. Validate branch existence
- * 6. Checkout the target branch
+ * 6. Stash local changes if any
- * 7. Fetch latest from remotes
+ * 7. Checkout the target branch
  * 8. Reapply stashed changes (detect conflicts)
  * 9. Handle error recovery (restore stash if checkout fails)
  *
@@ -149,14 +151,20 @@ export async function performSwitchBranch(
   // Emit start event
   events?.emit('switch:start', { worktreePath, branchName });
 
-  // 1. Get current branch
+  // 1. Fetch latest from all remotes before switching
+  //    This ensures remote branch refs are up-to-date so that isRemoteBranch()
+  //    can detect newly created remote branches and local tracking branches
+  //    are aware of upstream changes.
+  await fetchRemotes(worktreePath);
+
+  // 2. Get current branch
   const currentBranchOutput = await execGitCommand(
     ['rev-parse', '--abbrev-ref', 'HEAD'],
     worktreePath
   );
   const previousBranch = currentBranchOutput.trim();
 
-  // 2. Determine the actual target branch name for checkout
+  // 3. Determine the actual target branch name for checkout
   let targetBranch = branchName;
   let isRemote = false;
 
@@ -180,7 +188,7 @@ export async function performSwitchBranch(
     }
   }
 
-  // 3. Return early if already on the target branch
+  // 4. Return early if already on the target branch
   if (previousBranch === targetBranch) {
     events?.emit('switch:done', {
       worktreePath,
@@ -198,7 +206,7 @@ export async function performSwitchBranch(
     };
   }
 
-  // 4. Check if target branch exists as a local branch
+  // 5. Check if target branch exists as a local branch
   if (!isRemote) {
     if (!(await localBranchExists(worktreePath, branchName))) {
       events?.emit('switch:error', {
@@ -213,7 +221,7 @@ export async function performSwitchBranch(
     }
   }
 
-  // 5. Stash local changes if any exist
+  // 6. Stash local changes if any exist
   const hadChanges = await hasAnyChanges(worktreePath, { excludeWorktreePaths: true });
   let didStash = false;
 
@@ -242,7 +250,7 @@ export async function performSwitchBranch(
   }
 
   try {
-    // 6. Switch to the target branch
+    // 7. Switch to the target branch
     events?.emit('switch:checkout', {
       worktreePath,
       targetBranch,
@@ -265,9 +273,6 @@ export async function performSwitchBranch(
       await execGitCommand(['checkout', targetBranch], worktreePath);
     }
 
-    // 7. Fetch latest from remotes after switching
-    await fetchRemotes(worktreePath);
-
     // 8. Reapply stashed changes if we stashed earlier
     let hasConflicts = false;
     let conflictMessage = '';
@@ -347,7 +352,7 @@ export async function performSwitchBranch(
       };
     }
   } catch (checkoutError) {
-    // 9. If checkout failed and we stashed, try to restore the stash
+    // 9. Error recovery: if checkout failed and we stashed, try to restore the stash
     if (didStash) {
       const popResult = await popStash(worktreePath);
       if (popResult.hasConflicts) {

apps/server/tests/unit/services/auto-loop-coordinator.test.ts

@@ -328,6 +328,86 @@ describe('auto-loop-coordinator.ts', () => {
       // Should not have executed features because at capacity
       expect(mockExecuteFeature).not.toHaveBeenCalled();
     });
+
+    it('counts all running features (auto + manual) against concurrency limit', async () => {
+      vi.mocked(mockLoadPendingFeatures).mockResolvedValue([testFeature]);
+      // 2 manual features running — total count is 2
+      vi.mocked(mockConcurrencyManager.getRunningCountForWorktree).mockResolvedValue(2);
+
+      await coordinator.startAutoLoopForProject('/test/project', null, 2);
+
+      await vi.advanceTimersByTimeAsync(6000);
+
+      await coordinator.stopAutoLoopForProject('/test/project', null);
+
+      // Should NOT execute because total running count (2) meets the concurrency limit (2)
+      expect(mockExecuteFeature).not.toHaveBeenCalled();
+      // Verify it was called WITHOUT autoModeOnly (counts all tasks)
+      // The coordinator's wrapper passes options through as undefined when not specified
+      expect(mockConcurrencyManager.getRunningCountForWorktree).toHaveBeenCalledWith(
+        '/test/project',
+        null,
+        undefined
+      );
+    });
+
+    it('allows auto dispatch when manual tasks finish and capacity becomes available', async () => {
+      vi.mocked(mockLoadPendingFeatures).mockResolvedValue([testFeature]);
+      // First call: at capacity (2 manual features running)
+      // Second call: capacity freed (1 feature running)
+      vi.mocked(mockConcurrencyManager.getRunningCountForWorktree)
+        .mockResolvedValueOnce(2) // at capacity
+        .mockResolvedValueOnce(1); // capacity available after manual task completes
+
+      await coordinator.startAutoLoopForProject('/test/project', null, 2);
+
+      // First iteration: at capacity, should wait
+      await vi.advanceTimersByTimeAsync(5000);
+
+      // Second iteration: capacity available, should execute
+      await vi.advanceTimersByTimeAsync(6000);
+
+      await coordinator.stopAutoLoopForProject('/test/project', null);
+
+      // Should execute after capacity freed
+      expect(mockExecuteFeature).toHaveBeenCalledWith('/test/project', 'feature-1', true, true);
+    });
+
+    it('waits when manually started tasks already fill concurrency limit at auto mode activation', async () => {
+      vi.mocked(mockLoadPendingFeatures).mockResolvedValue([testFeature]);
+      // Manual tasks already fill the limit
+      vi.mocked(mockConcurrencyManager.getRunningCountForWorktree).mockResolvedValue(3);
+
+      await coordinator.startAutoLoopForProject('/test/project', null, 3);
+
+      await vi.advanceTimersByTimeAsync(6000);
+
+      await coordinator.stopAutoLoopForProject('/test/project', null);
+
+      // Auto mode should remain waiting, not dispatch
+      expect(mockExecuteFeature).not.toHaveBeenCalled();
+    });
+
+    it('resumes dispatching when all running tasks complete simultaneously', async () => {
+      vi.mocked(mockLoadPendingFeatures).mockResolvedValue([testFeature]);
+      // First check: all 3 slots occupied
+      // Second check: all tasks completed simultaneously
+      vi.mocked(mockConcurrencyManager.getRunningCountForWorktree)
+        .mockResolvedValueOnce(3) // all slots full
+        .mockResolvedValueOnce(0); // all tasks completed at once
+
+      await coordinator.startAutoLoopForProject('/test/project', null, 3);
+
+      // First iteration: at capacity
+      await vi.advanceTimersByTimeAsync(5000);
+      // Second iteration: all freed
+      await vi.advanceTimersByTimeAsync(6000);
+
+      await coordinator.stopAutoLoopForProject('/test/project', null);
+
+      // Should execute after all tasks freed capacity
+      expect(mockExecuteFeature).toHaveBeenCalledWith('/test/project', 'feature-1', true, true);
+    });
   });
 
   describe('priority-based feature selection', () => {
@@ -788,7 +868,23 @@ describe('auto-loop-coordinator.ts', () => {
       expect(count).toBe(3);
       expect(mockConcurrencyManager.getRunningCountForWorktree).toHaveBeenCalledWith(
         '/test/project',
-        null
+        null,
+        undefined
+      );
+    });
+
+    it('passes autoModeOnly option to ConcurrencyManager', async () => {
+      vi.mocked(mockConcurrencyManager.getRunningCountForWorktree).mockResolvedValue(1);
+
+      const count = await coordinator.getRunningCountForWorktree('/test/project', null, {
+        autoModeOnly: true,
+      });
+
+      expect(count).toBe(1);
+      expect(mockConcurrencyManager.getRunningCountForWorktree).toHaveBeenCalledWith(
+        '/test/project',
+        null,
+        { autoModeOnly: true }
       );
     });
   });

apps/server/tests/unit/services/concurrency-manager.test.ts

@@ -416,6 +416,90 @@ describe('ConcurrencyManager', () => {
       expect(mainCount).toBe(2);
     });
 
+    it('should count only auto-mode features when autoModeOnly is true', async () => {
+      // Auto-mode feature on main worktree
+      manager.acquire({
+        featureId: 'feature-auto',
+        projectPath: '/test/project',
+        isAutoMode: true,
+      });
+
+      // Manual feature on main worktree
+      manager.acquire({
+        featureId: 'feature-manual',
+        projectPath: '/test/project',
+        isAutoMode: false,
+      });
+
+      // Without autoModeOnly: counts both
+      const totalCount = await manager.getRunningCountForWorktree('/test/project', null);
+      expect(totalCount).toBe(2);
+
+      // With autoModeOnly: counts only auto-mode features
+      const autoModeCount = await manager.getRunningCountForWorktree('/test/project', null, {
+        autoModeOnly: true,
+      });
+      expect(autoModeCount).toBe(1);
+    });
+
+    it('should count only auto-mode features on specific worktree when autoModeOnly is true', async () => {
+      // Auto-mode feature on feature branch
+      manager.acquire({
+        featureId: 'feature-auto',
+        projectPath: '/test/project',
+        isAutoMode: true,
+      });
+      manager.updateRunningFeature('feature-auto', { branchName: 'feature-branch' });
+
+      // Manual feature on same feature branch
+      manager.acquire({
+        featureId: 'feature-manual',
+        projectPath: '/test/project',
+        isAutoMode: false,
+      });
+      manager.updateRunningFeature('feature-manual', { branchName: 'feature-branch' });
+
+      // Another auto-mode feature on different branch (should not be counted)
+      manager.acquire({
+        featureId: 'feature-other',
+        projectPath: '/test/project',
+        isAutoMode: true,
+      });
+      manager.updateRunningFeature('feature-other', { branchName: 'other-branch' });
+
+      const autoModeCount = await manager.getRunningCountForWorktree(
+        '/test/project',
+        'feature-branch',
+        { autoModeOnly: true }
+      );
+      expect(autoModeCount).toBe(1);
+
+      const totalCount = await manager.getRunningCountForWorktree(
+        '/test/project',
+        'feature-branch'
+      );
+      expect(totalCount).toBe(2);
+    });
+
+    it('should return 0 when autoModeOnly is true and only manual features are running', async () => {
+      manager.acquire({
+        featureId: 'feature-manual-1',
+        projectPath: '/test/project',
+        isAutoMode: false,
+      });
+
+      manager.acquire({
+        featureId: 'feature-manual-2',
+        projectPath: '/test/project',
+        isAutoMode: false,
+      });
+
+      const autoModeCount = await manager.getRunningCountForWorktree('/test/project', null, {
+        autoModeOnly: true,
+      });
+      expect(autoModeCount).toBe(0);
+    });
+
     it('should filter by both projectPath and branchName', async () => {
       manager.acquire({
         featureId: 'feature-1',

apps/server/tests/unit/services/dev-server-service.test.ts

@@ -486,7 +486,7 @@ describe('dev-server-service.ts', () => {
       await service.startDevServer(testDir, testDir);
 
       // Simulate HTTPS dev server
-      mockProcess.stdout.emit('data', Buffer.from('Server at https://localhost:3443\n'));
+      mockProcess.stdout.emit('data', Buffer.from('Server listening at https://localhost:3443\n'));
 
       await new Promise((resolve) => setTimeout(resolve, 50));
 
@@ -521,6 +521,368 @@ describe('dev-server-service.ts', () => {
       expect(serverInfo?.url).toBe(firstUrl);
       expect(serverInfo?.url).toBe('http://localhost:5173/');
     });
+
+    it('should detect Astro format URL', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      await service.startDevServer(testDir, testDir);
+
+      // Astro uses the same "Local:" prefix as Vite
+      mockProcess.stdout.emit('data', Buffer.from('  🚀  astro  v4.0.0 started in 200ms\n'));
+      mockProcess.stdout.emit('data', Buffer.from('  ┃ Local    http://localhost:4321/\n'));
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      // Astro doesn't use "Local:" with colon, so it should be caught by the localhost URL pattern
+      expect(serverInfo?.url).toBe('http://localhost:4321/');
+      expect(serverInfo?.urlDetected).toBe(true);
+    });
+
+    it('should detect Remix format URL', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      await service.startDevServer(testDir, testDir);
+
+      mockProcess.stdout.emit(
+        'data',
+        Buffer.from('Remix App Server started at http://localhost:3000\n')
+      );
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      expect(serverInfo?.url).toBe('http://localhost:3000');
+      expect(serverInfo?.urlDetected).toBe(true);
+    });
+
+    it('should detect Django format URL', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      await service.startDevServer(testDir, testDir);
+
+      mockProcess.stdout.emit(
+        'data',
+        Buffer.from('Starting development server at http://127.0.0.1:8000/\n')
+      );
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      expect(serverInfo?.url).toBe('http://127.0.0.1:8000/');
+      expect(serverInfo?.urlDetected).toBe(true);
+    });
+
+    it('should detect Webpack Dev Server format URL', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      await service.startDevServer(testDir, testDir);
+
+      mockProcess.stdout.emit(
+        'data',
+        Buffer.from('<i> [webpack-dev-server] Project is running at http://localhost:8080/\n')
+      );
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      expect(serverInfo?.url).toBe('http://localhost:8080/');
+      expect(serverInfo?.urlDetected).toBe(true);
+    });
+
+    it('should detect PHP built-in server format URL', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      await service.startDevServer(testDir, testDir);
+
+      mockProcess.stdout.emit(
+        'data',
+        Buffer.from('Development Server (http://localhost:8000) started\n')
+      );
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      expect(serverInfo?.url).toBe('http://localhost:8000');
+      expect(serverInfo?.urlDetected).toBe(true);
+    });
+
+    it('should detect "listening on port" format (port-only detection)', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      await service.startDevServer(testDir, testDir);
+
+      // Some servers only print the port number, not a full URL
+      mockProcess.stdout.emit('data', Buffer.from('Server listening on port 4000\n'));
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      expect(serverInfo?.url).toBe('http://localhost:4000');
+      expect(serverInfo?.urlDetected).toBe(true);
+    });
+
+    it('should detect "running on port" format (port-only detection)', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      await service.startDevServer(testDir, testDir);
+
+      mockProcess.stdout.emit('data', Buffer.from('Application running on port 9000\n'));
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      expect(serverInfo?.url).toBe('http://localhost:9000');
+      expect(serverInfo?.urlDetected).toBe(true);
+    });
+
+    it('should strip ANSI escape codes before detecting URL', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      await service.startDevServer(testDir, testDir);
+
+      // Simulate Vite output with ANSI color codes
+      mockProcess.stdout.emit(
+        'data',
+        Buffer.from(
+          '  \x1B[32m➜\x1B[0m  \x1B[1mLocal:\x1B[0m   \x1B[36mhttp://localhost:5173/\x1B[0m\n'
+        )
+      );
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      expect(serverInfo?.url).toBe('http://localhost:5173/');
+      expect(serverInfo?.urlDetected).toBe(true);
+    });
+
+    it('should normalize 0.0.0.0 to localhost', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      await service.startDevServer(testDir, testDir);
+
+      mockProcess.stdout.emit('data', Buffer.from('Server listening at http://0.0.0.0:3000\n'));
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      expect(serverInfo?.url).toBe('http://localhost:3000');
+      expect(serverInfo?.urlDetected).toBe(true);
+    });
+
+    it('should normalize [::] to localhost', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      await service.startDevServer(testDir, testDir);
+
+      mockProcess.stdout.emit('data', Buffer.from('Local: http://[::]:4000/\n'));
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      expect(serverInfo?.url).toBe('http://localhost:4000/');
+      expect(serverInfo?.urlDetected).toBe(true);
+    });
+
+    it('should update port field when detected URL has different port', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      const result = await service.startDevServer(testDir, testDir);
+      const allocatedPort = result.result?.port;
+
+      // Server starts on a completely different port (ignoring PORT env var)
+      mockProcess.stdout.emit('data', Buffer.from('Local: http://localhost:9999/\n'));
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      expect(serverInfo?.url).toBe('http://localhost:9999/');
+      expect(serverInfo?.port).toBe(9999);
+      // The port should be different from what was initially allocated
+      if (allocatedPort !== 9999) {
+        expect(serverInfo?.port).not.toBe(allocatedPort);
+      }
+    });
+
+    it('should detect URL from stderr output', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      await service.startDevServer(testDir, testDir);
+
+      // Some servers output URL info to stderr
+      mockProcess.stderr.emit('data', Buffer.from('Local: http://localhost:3000/\n'));
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      expect(serverInfo?.url).toBe('http://localhost:3000/');
+      expect(serverInfo?.urlDetected).toBe(true);
+    });
+
+    it('should not match URLs without a port (non-dev-server URLs)', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      const result = await service.startDevServer(testDir, testDir);
+
+      // CDN/external URLs should not be detected
+      mockProcess.stdout.emit(
+        'data',
+        Buffer.from('Downloading from https://cdn.example.com/bundle.js\n')
+      );
+      mockProcess.stdout.emit('data', Buffer.from('Fetching https://registry.npmjs.org/package\n'));
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      // Should keep the initial allocated URL since external URLs don't match
+      expect(serverInfo?.url).toBe(result.result?.url);
+      expect(serverInfo?.urlDetected).toBe(false);
+    });
+
+    it('should handle URLs with trailing punctuation', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      await service.startDevServer(testDir, testDir);
+
+      // URL followed by punctuation
+      mockProcess.stdout.emit('data', Buffer.from('Server started at http://localhost:3000.\n'));
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      expect(serverInfo?.url).toBe('http://localhost:3000');
+      expect(serverInfo?.urlDetected).toBe(true);
+    });
+
+    it('should detect Express/Fastify format URL', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      await service.startDevServer(testDir, testDir);
+
+      mockProcess.stdout.emit('data', Buffer.from('Server listening on http://localhost:3000\n'));
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      expect(serverInfo?.url).toBe('http://localhost:3000');
+      expect(serverInfo?.urlDetected).toBe(true);
+    });
+
+    it('should detect Angular CLI format URL', async () => {
+      vi.mocked(secureFs.access).mockResolvedValue(undefined);
+
+      const mockProcess = createMockProcess();
+      vi.mocked(spawn).mockReturnValue(mockProcess as any);
+
+      const { getDevServerService } = await import('@/services/dev-server-service.js');
+      const service = getDevServerService();
+
+      await service.startDevServer(testDir, testDir);
+
+      // Angular CLI output
+      mockProcess.stderr.emit(
+        'data',
+        Buffer.from(
+          '** Angular Live Development Server is listening on localhost:4200, open your browser on http://localhost:4200/ **\n'
+        )
+      );
+
+      await new Promise((resolve) => setTimeout(resolve, 50));
+
+      const serverInfo = service.getServerInfo(testDir);
+      expect(serverInfo?.url).toBe('http://localhost:4200/');
+      expect(serverInfo?.urlDetected).toBe(true);
+    });
   });
 });
 
@@ -531,6 +893,7 @@ function createMockProcess() {
   mockProcess.stderr = new EventEmitter();
   mockProcess.kill = vi.fn();
   mockProcess.killed = false;
+  mockProcess.pid = 12345;
 
   // Don't exit immediately - let the test control the lifecycle
   return mockProcess;

apps/ui/src/components/ui/git-diff-panel.tsx

@@ -10,6 +10,7 @@ import {
   ChevronRight,
   RefreshCw,
   GitBranch,
+  GitMerge,
   AlertCircle,
   Plus,
   Minus,
@@ -20,7 +21,7 @@ import { Button } from './button';
 import { useWorktreeDiffs, useGitDiffs } from '@/hooks/queries';
 import { getElectronAPI } from '@/lib/electron';
 import { toast } from 'sonner';
-import type { FileStatus } from '@/types/electron';
+import type { FileStatus, MergeStateInfo } from '@/types/electron';
 
 interface GitDiffPanelProps {
   projectPath: string;
@@ -318,6 +319,86 @@ function StagingBadge({ state }: { state: 'staged' | 'unstaged' | 'partial' }) {
   );
 }
 
+function MergeBadge({ mergeType }: { mergeType?: string }) {
+  if (!mergeType) return null;
+
+  const label = (() => {
+    switch (mergeType) {
+      case 'both-modified':
+        return 'Both Modified';
+      case 'added-by-us':
+        return 'Added by Us';
+      case 'added-by-them':
+        return 'Added by Them';
+      case 'deleted-by-us':
+        return 'Deleted by Us';
+      case 'deleted-by-them':
+        return 'Deleted by Them';
+      case 'both-added':
+        return 'Both Added';
+      case 'both-deleted':
+        return 'Both Deleted';
+      case 'merged':
+        return 'Merged';
+      default:
+        return 'Merge';
+    }
+  })();
+
+  return (
+    <span className="text-[10px] px-1.5 py-0.5 rounded border font-medium bg-purple-500/15 text-purple-400 border-purple-500/30 inline-flex items-center gap-1">
+      <GitMerge className="w-2.5 h-2.5" />
+      {label}
+    </span>
+  );
+}
+
+function MergeStateBanner({ mergeState }: { mergeState: MergeStateInfo }) {
+  // Completed merge commit (HEAD is a merge)
+  if (mergeState.isMergeCommit && !mergeState.isMerging) {
+    return (
+      <div className="mx-4 mt-3 flex items-start gap-2 p-3 rounded-md bg-purple-500/10 border border-purple-500/20">
+        <GitMerge className="w-4 h-4 text-purple-500 mt-0.5 flex-shrink-0" />
+        <div className="text-sm">
+          <span className="font-medium text-purple-400">Merge commit</span>
+          <span className="text-purple-400/80 ml-1">
+            &mdash; {mergeState.mergeAffectedFiles.length} file
+            {mergeState.mergeAffectedFiles.length !== 1 ? 's' : ''} changed in merge
+          </span>
+        </div>
+      </div>
+    );
+  }
+
+  // In-progress merge/rebase/cherry-pick
+  const operationLabel =
+    mergeState.mergeOperationType === 'cherry-pick'
+      ? 'Cherry-pick'
+      : mergeState.mergeOperationType === 'rebase'
+        ? 'Rebase'
+        : 'Merge';
+
+  return (
+    <div className="mx-4 mt-3 flex items-start gap-2 p-3 rounded-md bg-purple-500/10 border border-purple-500/20">
+      <GitMerge className="w-4 h-4 text-purple-500 mt-0.5 flex-shrink-0" />
+      <div className="text-sm">
+        <span className="font-medium text-purple-400">{operationLabel} in progress</span>
+        {mergeState.conflictFiles.length > 0 ? (
+          <span className="text-purple-400/80 ml-1">
+            &mdash; {mergeState.conflictFiles.length} file
+            {mergeState.conflictFiles.length !== 1 ? 's' : ''} with conflicts
+          </span>
+        ) : mergeState.isCleanMerge ? (
+          <span className="text-purple-400/80 ml-1">
+            &mdash; Clean merge, {mergeState.mergeAffectedFiles.length} file
+            {mergeState.mergeAffectedFiles.length !== 1 ? 's' : ''} affected
+          </span>
+        ) : null}
+      </div>
+    </div>
+  );
+}
+
 function FileDiffSection({
   fileDiff,
   isExpanded,
@@ -348,9 +429,21 @@ function FileDiffSection({
 
   const stagingState = fileStatus ? getStagingState(fileStatus) : undefined;
 
+  const isMergeFile = fileStatus?.isMergeAffected;
+
   return (
-    <div className="border border-border rounded-lg overflow-hidden">
+    <div
-      <div className="w-full px-3 py-2 flex flex-col gap-1 text-left bg-card hover:bg-accent/50 transition-colors sm:flex-row sm:items-center sm:gap-2">
+      className={cn(
+        'border rounded-lg overflow-hidden',
+        isMergeFile ? 'border-purple-500/40' : 'border-border'
+      )}
+    >
+      <div
+        className={cn(
+          'w-full px-3 py-2 flex flex-col gap-1 text-left transition-colors sm:flex-row sm:items-center sm:gap-2',
+          isMergeFile ? 'bg-purple-500/5 hover:bg-purple-500/10' : 'bg-card hover:bg-accent/50'
+        )}
+      >
         {/* File name row */}
         <button onClick={onToggle} className="flex items-center gap-2 flex-1 min-w-0 text-left">
           {isExpanded ? (
@@ -358,7 +451,9 @@ function FileDiffSection({
           ) : (
             <ChevronRight className="w-4 h-4 text-muted-foreground flex-shrink-0" />
           )}
-          {fileStatus ? (
+          {isMergeFile ? (
+            <GitMerge className="w-4 h-4 text-purple-500 flex-shrink-0" />
+          ) : fileStatus ? (
             getFileIcon(fileStatus.status)
           ) : (
             <FileText className="w-4 h-4 text-muted-foreground flex-shrink-0" />
@@ -370,6 +465,7 @@ function FileDiffSection({
         </button>
         {/* Indicators & staging row */}
         <div className="flex items-center gap-2 flex-shrink-0 pl-6 sm:pl-0">
+          {fileStatus?.isMergeAffected && <MergeBadge mergeType={fileStatus.mergeType} />}
           {enableStaging && stagingState && <StagingBadge state={stagingState} />}
           {fileDiff.isNew && (
             <span className="text-xs px-1.5 py-0.5 rounded bg-green-500/20 text-green-400">
@@ -483,9 +579,10 @@ export function GitDiffPanel({
   const isLoading = useWorktrees ? isLoadingWorktree : isLoadingGit;
   const queryError = useWorktrees ? worktreeError : gitError;
 
-  // Extract files and diff content from the data
+  // Extract files, diff content, and merge state from the data
   const files: FileStatus[] = diffsData?.files ?? [];
   const diffContent = diffsData?.diff ?? '';
+  const mergeState: MergeStateInfo | undefined = diffsData?.mergeState;
   const error = queryError
     ? queryError instanceof Error
       ? queryError.message
@@ -495,8 +592,6 @@ export function GitDiffPanel({
   // Refetch function
   const loadDiffs = useWorktrees ? refetchWorktree : refetchGit;
 
-  const parsedDiffs = useMemo(() => parseDiff(diffContent), [diffContent]);
-
   // Build a map from file path to FileStatus for quick lookup
   const fileStatusMap = useMemo(() => {
     const map = new Map<string, FileStatus>();
@@ -506,6 +601,24 @@ export function GitDiffPanel({
     return map;
   }, [files]);
 
+  const parsedDiffs = useMemo(() => {
+    const diffs = parseDiff(diffContent);
+    // Sort: merge-affected files first, then preserve original order
+    if (mergeState?.isMerging || mergeState?.isMergeCommit) {
+      const mergeSet = new Set(mergeState.mergeAffectedFiles);
+      diffs.sort((a, b) => {
+        const aIsMerge =
+          mergeSet.has(a.filePath) || (fileStatusMap.get(a.filePath)?.isMergeAffected ?? false);
+        const bIsMerge =
+          mergeSet.has(b.filePath) || (fileStatusMap.get(b.filePath)?.isMergeAffected ?? false);
+        if (aIsMerge && !bIsMerge) return -1;
+        if (!aIsMerge && bIsMerge) return 1;
+        return 0;
+      });
+    }
+    return diffs;
+  }, [diffContent, mergeState, fileStatusMap]);
+
   const toggleFile = (filePath: string) => {
     setExpandedFiles((prev) => {
       const next = new Set(prev);
@@ -682,6 +795,18 @@ export function GitDiffPanel({
     );
   }, [worktreePath, projectPath, useWorktrees, enableStaging, files, executeStagingAction]);
 
+  // Compute merge summary
+  const mergeSummary = useMemo(() => {
+    const mergeFiles = files.filter((f) => f.isMergeAffected);
+    if (mergeFiles.length === 0) return null;
+    return {
+      total: mergeFiles.length,
+      conflicted: mergeFiles.filter(
+        (f) => f.mergeType === 'both-modified' || f.mergeType === 'both-added'
+      ).length,
+    };
+  }, [files]);
+
   // Compute staging summary
   const stagingSummary = useMemo(() => {
     if (!enableStaging) return null;
@@ -776,6 +901,11 @@ export function GitDiffPanel({
             </div>
           ) : (
             <div>
+              {/* Merge state banner */}
+              {(mergeState?.isMerging || mergeState?.isMergeCommit) && (
+                <MergeStateBanner mergeState={mergeState} />
+              )}
+
               {/* Summary bar */}
               <div className="p-4 pb-2 border-b border-border-glass">
                 <div className="flex flex-col gap-2 sm:flex-row sm:items-center sm:justify-between">
@@ -799,7 +929,7 @@ export function GitDiffPanel({
                         {} as Record<string, { count: number; statusText: string; files: string[] }>
                       );
 
-                      return Object.entries(statusGroups).map(([status, group]) => (
+                      const groups = Object.entries(statusGroups).map(([status, group]) => (
                         <div
                           key={status}
                           className="flex items-center gap-1.5"
@@ -817,6 +947,24 @@ export function GitDiffPanel({
                           </span>
                         </div>
                       ));
+
+                      // Add merge group indicator if merge files exist
+                      if (mergeSummary) {
+                        groups.unshift(
+                          <div
+                            key="merge"
+                            className="flex items-center gap-1.5"
+                            data-testid="git-status-group-merge"
+                          >
+                            <GitMerge className="w-4 h-4 text-purple-500" />
+                            <span className="text-xs px-1.5 py-0.5 rounded border font-medium bg-purple-500/20 text-purple-400 border-purple-500/30">
+                              {mergeSummary.total} Merge
+                            </span>
+                          </div>
+                        );
+                      }
+
+                      return groups;
                     })()}
                   </div>
                   <div className="flex items-center gap-1 flex-wrap">
@@ -907,7 +1055,7 @@ export function GitDiffPanel({
                     fileDiff={fileDiff}
                     isExpanded={expandedFiles.has(fileDiff.filePath)}
                     onToggle={() => toggleFile(fileDiff.filePath)}
-                    fileStatus={enableStaging ? fileStatusMap.get(fileDiff.filePath) : undefined}
+                    fileStatus={fileStatusMap.get(fileDiff.filePath)}
                     enableStaging={enableStaging}
                     onStage={enableStaging ? handleStageFile : undefined}
                     onUnstage={enableStaging ? handleUnstageFile : undefined}
@@ -919,15 +1067,28 @@ export function GitDiffPanel({
                   <div className="space-y-2">
                     {files.map((file) => {
                       const stagingState = getStagingState(file);
+                      const isFileMerge = file.isMergeAffected;
                       return (
                         <div
                           key={file.path}
-                          className="border border-border rounded-lg overflow-hidden"
+                          className={cn(
+                            'border rounded-lg overflow-hidden',
+                            isFileMerge ? 'border-purple-500/40' : 'border-border'
+                          )}
                         >
-                          <div className="w-full px-3 py-2 flex flex-col gap-1 text-left bg-card sm:flex-row sm:items-center sm:gap-2">
+                          <div
+                            className={cn(
+                              'w-full px-3 py-2 flex flex-col gap-1 text-left sm:flex-row sm:items-center sm:gap-2',
+                              isFileMerge ? 'bg-purple-500/5 hover:bg-purple-500/10' : 'bg-card'
+                            )}
+                          >
                             {/* File name row */}
                             <div className="flex items-center gap-2 flex-1 min-w-0">
-                              {getFileIcon(file.status)}
+                              {isFileMerge ? (
+                                <GitMerge className="w-4 h-4 text-purple-500 flex-shrink-0" />
+                              ) : (
+                                getFileIcon(file.status)
+                              )}
                               <TruncatedFilePath
                                 path={file.path}
                                 className="flex-1 text-sm font-mono text-foreground"
@@ -935,6 +1096,7 @@ export function GitDiffPanel({
                             </div>
                             {/* Indicators & staging row */}
                             <div className="flex items-center gap-2 flex-shrink-0 pl-6 sm:pl-0">
+                              {isFileMerge && <MergeBadge mergeType={file.mergeType} />}
                               {enableStaging && <StagingBadge state={stagingState} />}
                               <span
                                 className={cn(

apps/ui/src/components/ui/select.tsx

@@ -126,7 +126,7 @@ const SelectItem = React.forwardRef<
     </span>
 
     {description ? (
-      <div className="flex flex-col items-start">
+      <div className="flex flex-col items-start w-full min-w-0">
         <SelectPrimitive.ItemText>{children}</SelectPrimitive.ItemText>
         {description}
       </div>

apps/ui/src/components/ui/test-logs-panel.tsx

@@ -215,7 +215,7 @@ function TestLogsPanelContent({
   return (
     <>
       {/* Header */}
-      <DialogHeader className="shrink-0 px-4 py-3 border-b border-border/50 pr-12">
+      <DialogHeader className="shrink-0 px-4 py-3 border-b border-border/50 pr-12 dialog-compact-header-mobile">
         <div className="flex items-center justify-between">
           <DialogTitle className="flex items-center gap-2 text-base">
             <FlaskConical className="w-4 h-4 text-primary" />

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

@@ -375,10 +375,20 @@ export function BoardView() {
       return specificTargetCollisions;
     }
 
-    // Priority 2: Columns
+    // Priority 2: Columns (including column headers and pipeline columns)
-    const columnCollisions = pointerCollisions.filter((collision: Collision) =>
+    const columnCollisions = pointerCollisions.filter((collision: Collision) => {
-      COLUMNS.some((col) => col.id === collision.id)
+      const colId = String(collision.id);
-    );
+      // Direct column ID match (e.g. 'backlog', 'in_progress')
+      if (COLUMNS.some((col) => col.id === colId)) return true;
+      // Column header droppable (e.g. 'column-header-backlog')
+      if (colId.startsWith('column-header-')) {
+        const baseId = colId.replace('column-header-', '');
+        return COLUMNS.some((col) => col.id === baseId) || baseId.startsWith('pipeline_');
+      }
+      // Pipeline column IDs (e.g. 'pipeline_tests')
+      if (colId.startsWith('pipeline_')) return true;
+      return false;
+    });
 
     // If we found a column collision, use that
     if (columnCollisions.length > 0) {
@@ -1426,13 +1436,12 @@ export function BoardView() {
               },
             });
 
-            // Also update backend if auto mode is running
+            // Also update backend if auto mode is running.
+            // Use restartWithConcurrency to avoid toggle flickering - it restarts
+            // the backend without toggling isRunning off/on in the UI.
             if (autoMode.isRunning) {
-              // Restart auto mode with new concurrency (backend will handle this)
+              autoMode.restartWithConcurrency().catch((error) => {
-              autoMode.stop().then(() => {
+                logger.error('[AutoMode] Failed to restart with new concurrency:', error);
-                autoMode.start().catch((error) => {
-                  logger.error('[AutoMode] Failed to restart with new concurrency:', error);
-                });
               });
             }
           }

apps/ui/src/components/views/board-view/components/kanban-card/card-actions.tsx

@@ -17,6 +17,8 @@ import {
 interface CardActionsProps {
   feature: Feature;
   isCurrentAutoTask: boolean;
+  /** Whether this feature is tracked as a running task (may be true even before status updates to in_progress) */
+  isRunningTask?: boolean;
   hasContext?: boolean;
   shortcutKey?: string;
   isSelectionMode?: boolean;
@@ -36,6 +38,7 @@ interface CardActionsProps {
 export const CardActions = memo(function CardActions({
   feature,
   isCurrentAutoTask,
+  isRunningTask = false,
   hasContext: _hasContext,
   shortcutKey,
   isSelectionMode = false,
@@ -340,7 +343,57 @@ export const CardActions = memo(function CardActions({
           ) : null}
         </>
       )}
+      {/* Running task with stale status: feature is tracked as running but status hasn't updated yet.
+          Show Logs/Stop controls instead of Make to avoid confusing UI. */}
       {!isCurrentAutoTask &&
+        isRunningTask &&
+        (feature.status === 'backlog' ||
+          feature.status === 'interrupted' ||
+          feature.status === 'ready') && (
+          <>
+            {onViewOutput && (
+              <Button
+                variant="secondary"
+                size="sm"
+                className="flex-1 h-7 text-[11px]"
+                onClick={(e) => {
+                  e.stopPropagation();
+                  onViewOutput();
+                }}
+                onPointerDown={(e) => e.stopPropagation()}
+                data-testid={`view-output-${feature.id}`}
+              >
+                <FileText className="w-3 h-3 mr-1 shrink-0" />
+                <span className="truncate">Logs</span>
+                {shortcutKey && (
+                  <span
+                    className="ml-1.5 px-1 py-0.5 text-[9px] font-mono rounded bg-foreground/10"
+                    data-testid={`shortcut-key-${feature.id}`}
+                  >
+                    {shortcutKey}
+                  </span>
+                )}
+              </Button>
+            )}
+            {onForceStop && (
+              <Button
+                variant="destructive"
+                size="sm"
+                className="h-7 text-[11px] px-2 shrink-0"
+                onClick={(e) => {
+                  e.stopPropagation();
+                  onForceStop();
+                }}
+                onPointerDown={(e) => e.stopPropagation()}
+                data-testid={`force-stop-${feature.id}`}
+              >
+                <StopCircle className="w-3 h-3" />
+              </Button>
+            )}
+          </>
+        )}
+      {!isCurrentAutoTask &&
+        !isRunningTask &&
         (feature.status === 'backlog' ||
           feature.status === 'interrupted' ||
           feature.status === 'ready') && (

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

@@ -114,15 +114,27 @@ export const KanbanCard = memo(function KanbanCard({
       currentProject: state.currentProject,
     }))
   );
-  // A card should only display as "actively running" if it's both in the
+  // A card should display as "actively running" if it's in the runningAutoTasks list
-  // runningAutoTasks list AND in an execution-compatible status. Cards in resting
+  // AND in an execution-compatible status. However, there's a race window where a feature
-  // states (backlog, ready, waiting_approval, verified, completed) should never
+  // is tracked as running (in runningAutoTasks) but its disk/UI status hasn't caught up yet
-  // show running controls, even if they appear in runningAutoTasks due to stale
+  // (still 'backlog', 'ready', or 'interrupted'). In this case, we still want to show
-  // state (e.g., after a server restart that reconciled features back to backlog).
+  // running controls (Logs/Stop) and animated border, but not the full "actively running"
+  // state that gates all UI behavior.
   const isInExecutionState =
     feature.status === 'in_progress' ||
     (typeof feature.status === 'string' && feature.status.startsWith('pipeline_'));
   const isActivelyRunning = !!isCurrentAutoTask && isInExecutionState;
+  // isRunningWithStaleStatus: feature is tracked as running but status hasn't updated yet.
+  // This happens during the timing gap between when the server starts a feature and when
+  // the UI receives the status update. Show running UI to prevent "Make" button flash.
+  const isRunningWithStaleStatus =
+    !!isCurrentAutoTask &&
+    !isInExecutionState &&
+    (feature.status === 'backlog' ||
+      feature.status === 'ready' ||
+      feature.status === 'interrupted');
+  // Show running visual treatment for both fully confirmed and stale-status running tasks
+  const showRunningVisuals = isActivelyRunning || isRunningWithStaleStatus;
   const [isLifted, setIsLifted] = useState(false);
 
   useLayoutEffect(() => {
@@ -135,6 +147,7 @@ export const KanbanCard = memo(function KanbanCard({
 
   const isDraggable =
     !isSelectionMode &&
+    !isRunningWithStaleStatus &&
     (feature.status === 'backlog' ||
       feature.status === 'interrupted' ||
       feature.status === 'ready' ||
@@ -198,13 +211,13 @@ export const KanbanCard = memo(function KanbanCard({
     'kanban-card-content h-full relative',
     reduceEffects ? 'shadow-none' : 'shadow-sm',
     'transition-all duration-200 ease-out',
-    // Disable hover translate for in-progress cards to prevent gap showing gradient
+    // Disable hover translate for running cards to prevent gap showing gradient
     isInteractive &&
       !reduceEffects &&
-      !isActivelyRunning &&
+      !showRunningVisuals &&
       'hover:-translate-y-0.5 hover:shadow-md hover:shadow-black/10 bg-transparent',
     !glassmorphism && 'backdrop-blur-[0px]!',
-    !isActivelyRunning &&
+    !showRunningVisuals &&
       cardBorderEnabled &&
       (cardBorderOpacity === 100 ? 'border-border/50' : 'border'),
     hasError && 'border-[var(--status-error)] border-2 shadow-[var(--status-error-bg)] shadow-lg',
@@ -221,7 +234,7 @@ export const KanbanCard = memo(function KanbanCard({
 
   const renderCardContent = () => (
     <Card
-      style={isActivelyRunning ? undefined : cardStyle}
+      style={showRunningVisuals ? undefined : cardStyle}
       className={innerCardClasses}
       onDoubleClick={isSelectionMode ? undefined : onEdit}
       onClick={handleCardClick}
@@ -290,6 +303,7 @@ export const KanbanCard = memo(function KanbanCard({
         <CardActions
           feature={feature}
           isCurrentAutoTask={isActivelyRunning}
+          isRunningTask={!!isCurrentAutoTask}
           hasContext={hasContext}
           shortcutKey={shortcutKey}
           isSelectionMode={isSelectionMode}
@@ -316,7 +330,7 @@ export const KanbanCard = memo(function KanbanCard({
       className={wrapperClasses}
       data-testid={`kanban-card-${feature.id}`}
     >
-      {isActivelyRunning ? (
+      {showRunningVisuals ? (
         <div className="animated-border-wrapper">{renderCardContent()}</div>
       ) : (
         renderCardContent()

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

@@ -42,7 +42,12 @@ export const KanbanColumn = memo(function KanbanColumn({
   contentStyle,
   disableItemSpacing = false,
 }: KanbanColumnProps) {
-  const { setNodeRef, isOver } = useDroppable({ id });
+  const { setNodeRef, isOver: isColumnOver } = useDroppable({ id });
+  // Also make the header explicitly a drop target so dragging to the top of the column works
+  const { setNodeRef: setHeaderDropRef, isOver: isHeaderOver } = useDroppable({
+    id: `column-header-${id}`,
+  });
+  const isOver = isColumnOver || isHeaderOver;
 
   // Use inline style for width if provided, otherwise use default w-72
   const widthStyle = width ? { width: `${width}px`, flexShrink: 0 } : undefined;
@@ -70,8 +75,9 @@ export const KanbanColumn = memo(function KanbanColumn({
         style={{ opacity: opacity / 100 }}
       />
 
-      {/* Column Header */}
+      {/* Column Header - also registered as a drop target so dragging to the header area works */}
       <div
+        ref={setHeaderDropRef}
         className={cn(
           'relative z-10 flex items-center gap-3 px-3 py-2.5',
           showBorder && 'border-b border-border/40'

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

@@ -209,15 +209,22 @@ export const ListRow = memo(function ListRow({
   blockingDependencies = [],
   className,
 }: ListRowProps) {
-  // A row should only display as "actively running" if it's both in the
+  // A row should display as "actively running" if it's in the runningAutoTasks list
-  // runningAutoTasks list AND in an execution-compatible status. Features in resting
+  // AND in an execution-compatible status. However, there's a race window where a feature
-  // states (backlog, ready, waiting_approval, verified, completed) should never
+  // is tracked as running but its status hasn't caught up yet (still 'backlog', 'ready',
-  // show running controls, even if they appear in runningAutoTasks due to stale
+  // or 'interrupted'). We handle this with isRunningWithStaleStatus.
-  // state (e.g., after a server restart that reconciled features back to backlog).
   const isInExecutionState =
     feature.status === 'in_progress' ||
     (typeof feature.status === 'string' && feature.status.startsWith('pipeline_'));
   const isActivelyRunning = isCurrentAutoTask && isInExecutionState;
+  // Feature is tracked as running but status hasn't updated yet - show running UI
+  const isRunningWithStaleStatus =
+    isCurrentAutoTask &&
+    !isInExecutionState &&
+    (feature.status === 'backlog' ||
+      feature.status === 'ready' ||
+      feature.status === 'interrupted');
+  const showRunningVisuals = isActivelyRunning || isRunningWithStaleStatus;
 
   const handleRowClick = useCallback(
     (e: React.MouseEvent) => {
@@ -268,7 +275,7 @@ export const ListRow = memo(function ListRow({
     >
       {/* Checkbox column */}
       {showCheckbox && (
-        <div role="cell" className="flex items-center justify-center w-10 px-2 py-3 shrink-0">
+        <div role="cell" className="flex items-center justify-center w-10 px-2 py-2 shrink-0">
           <input
             type="checkbox"
             checked={isSelected}
@@ -287,7 +294,7 @@ export const ListRow = memo(function ListRow({
       <div
         role="cell"
         className={cn(
-          'flex items-center pl-3 pr-0 py-3 gap-0',
+          'flex items-center pl-3 pr-0 py-2 gap-0',
           getColumnWidth('title'),
           getColumnAlign('title')
         )}
@@ -296,7 +303,7 @@ export const ListRow = memo(function ListRow({
           <div className="flex items-center">
             <span
               className={cn(
-                'font-medium truncate',
+                'text-sm font-medium truncate',
                 feature.titleGenerating && !feature.title && 'animate-pulse text-muted-foreground'
               )}
               title={feature.title || feature.description}
@@ -325,7 +332,7 @@ export const ListRow = memo(function ListRow({
       <div
         role="cell"
         className={cn(
-          'flex items-center pl-0 pr-3 py-3 shrink-0',
+          'flex items-center pl-0 pr-3 py-2 shrink-0',
           getColumnWidth('priority'),
           getColumnAlign('priority')
         )}
@@ -358,14 +365,19 @@ export const ListRow = memo(function ListRow({
       </div>
 
       {/* Actions column */}
-      <div role="cell" className="flex items-center justify-end px-3 py-3 w-[80px] shrink-0">
+      <div role="cell" className="flex items-center justify-end px-3 py-2 w-[80px] shrink-0">
-        <RowActions feature={feature} handlers={handlers} isCurrentAutoTask={isActivelyRunning} />
+        <RowActions
+          feature={feature}
+          handlers={handlers}
+          isCurrentAutoTask={isActivelyRunning}
+          isRunningTask={!!isCurrentAutoTask}
+        />
       </div>
     </div>
   );
 
-  // Wrap with animated border for currently running auto task
+  // Wrap with animated border for currently running auto task (including stale status)
-  if (isActivelyRunning) {
+  if (showRunningVisuals) {
     return <div className="animated-border-wrapper-row">{rowContent}</div>;
   }
 

apps/ui/src/components/views/board-view/components/list-view/row-actions.tsx

@@ -60,6 +60,8 @@ export interface RowActionsProps {
   handlers: RowActionHandlers;
   /** Whether this feature is the current auto task (agent is running) */
   isCurrentAutoTask?: boolean;
+  /** Whether this feature is tracked as a running task (may be true even before status updates to in_progress) */
+  isRunningTask?: boolean;
   /** Whether the dropdown menu is open */
   isOpen?: boolean;
   /** Callback when the dropdown open state changes */
@@ -115,7 +117,8 @@ const MenuItem = memo(function MenuItem({
 function getPrimaryAction(
   feature: Feature,
   handlers: RowActionHandlers,
-  isCurrentAutoTask: boolean
+  isCurrentAutoTask: boolean,
+  isRunningTask: boolean = false
 ): {
   icon: React.ComponentType<{ className?: string }>;
   label: string;
@@ -135,6 +138,24 @@ function getPrimaryAction(
     return null;
   }
 
+  // Running task with stale status - show stop instead of Make
+  // This handles the race window where the feature is tracked as running
+  // but status hasn't updated to in_progress yet
+  if (
+    isRunningTask &&
+    (feature.status === 'backlog' ||
+      feature.status === 'ready' ||
+      feature.status === 'interrupted') &&
+    handlers.onForceStop
+  ) {
+    return {
+      icon: StopCircle,
+      label: 'Stop',
+      onClick: handlers.onForceStop,
+      variant: 'destructive',
+    };
+  }
+
   // Backlog - implement is primary
   if (feature.status === 'backlog' && handlers.onImplement) {
     return {
@@ -263,6 +284,7 @@ export const RowActions = memo(function RowActions({
   feature,
   handlers,
   isCurrentAutoTask = false,
+  isRunningTask = false,
   isOpen,
   onOpenChange,
   className,
@@ -286,7 +308,7 @@ export const RowActions = memo(function RowActions({
     [setOpen]
   );
 
-  const primaryAction = getPrimaryAction(feature, handlers, isCurrentAutoTask);
+  const primaryAction = getPrimaryAction(feature, handlers, isCurrentAutoTask, isRunningTask);
   const secondaryActions = getSecondaryActions(feature, handlers);
 
   // Helper to close menu after action
@@ -403,7 +425,7 @@ export const RowActions = memo(function RowActions({
           )}
 
           {/* Backlog actions */}
-          {!isCurrentAutoTask && feature.status === 'backlog' && (
+          {!isCurrentAutoTask && !isRunningTask && feature.status === 'backlog' && (
             <>
               <MenuItem icon={Edit} label="Edit" onClick={withClose(handlers.onEdit)} />
               {feature.planSpec?.content && handlers.onViewPlan && (

apps/ui/src/components/views/board-view/dialogs/cherry-pick-dialog.tsx

@@ -493,7 +493,7 @@ export function CherryPickDialog({
   if (step === 'select-commits') {
     return (
       <Dialog open={open} onOpenChange={onOpenChange}>
-        <DialogContent className="w-full h-full max-w-full max-h-full sm:w-[90vw] sm:max-w-[640px] sm:max-h-[100dvh] sm:h-auto sm:rounded-xl rounded-none flex flex-col dialog-fullscreen-mobile">
+        <DialogContent className="w-full h-full max-w-full max-h-full sm:w-[90vw] sm:max-w-[640px] sm:max-h-[85dvh] sm:h-auto sm:rounded-xl rounded-none flex flex-col dialog-fullscreen-mobile">
           <DialogHeader>
             <DialogTitle className="flex items-center gap-2">
               <Cherry className="w-5 h-5 text-foreground" />

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

@@ -20,6 +20,7 @@ import {
 } from '@/components/ui/select';
 import {
   GitCommit,
+  GitMerge,
   Sparkles,
   FilePlus,
   FileX,
@@ -36,7 +37,7 @@ import { toast } from 'sonner';
 import { useAppStore } from '@/store/app-store';
 import { cn } from '@/lib/utils';
 import { TruncatedFilePath } from '@/components/ui/truncated-file-path';
-import type { FileStatus } from '@/types/electron';
+import type { FileStatus, MergeStateInfo } from '@/types/electron';
 import { parseDiff, type ParsedFileDiff } from '@/lib/diff-utils';
 
 interface RemoteInfo {
@@ -116,6 +117,27 @@ const getStatusBadgeColor = (status: string) => {
   }
 };
 
+const getMergeTypeLabel = (mergeType?: string) => {
+  switch (mergeType) {
+    case 'both-modified':
+      return 'Both Modified';
+    case 'added-by-us':
+      return 'Added by Us';
+    case 'added-by-them':
+      return 'Added by Them';
+    case 'deleted-by-us':
+      return 'Deleted by Us';
+    case 'deleted-by-them':
+      return 'Deleted by Them';
+    case 'both-added':
+      return 'Both Added';
+    case 'both-deleted':
+      return 'Both Deleted';
+    default:
+      return 'Merge';
+  }
+};
+
 function DiffLine({
   type,
   content,
@@ -190,6 +212,7 @@ export function CommitWorktreeDialog({
   const [selectedFiles, setSelectedFiles] = useState<Set<string>>(new Set());
   const [expandedFile, setExpandedFile] = useState<string | null>(null);
   const [isLoadingDiffs, setIsLoadingDiffs] = useState(false);
+  const [mergeState, setMergeState] = useState<MergeStateInfo | undefined>(undefined);
 
   // Push after commit state
   const [pushAfterCommit, setPushAfterCommit] = useState(false);
@@ -274,6 +297,7 @@ export function CommitWorktreeDialog({
       setDiffContent('');
       setSelectedFiles(new Set());
       setExpandedFile(null);
+      setMergeState(undefined);
       // Reset push state
       setPushAfterCommit(false);
       setRemotes([]);
@@ -292,8 +316,20 @@ export function CommitWorktreeDialog({
             const result = await api.git.getDiffs(worktree.path);
             if (result.success) {
               const fileList = result.files ?? [];
+              // Sort merge-affected files first when a merge is in progress
+              if (result.mergeState?.isMerging) {
+                const mergeSet = new Set(result.mergeState.mergeAffectedFiles);
+                fileList.sort((a, b) => {
+                  const aIsMerge = mergeSet.has(a.path) || (a.isMergeAffected ?? false);
+                  const bIsMerge = mergeSet.has(b.path) || (b.isMergeAffected ?? false);
+                  if (aIsMerge && !bIsMerge) return -1;
+                  if (!aIsMerge && bIsMerge) return 1;
+                  return 0;
+                });
+              }
               if (!cancelled) setFiles(fileList);
               if (!cancelled) setDiffContent(result.diff ?? '');
+              if (!cancelled) setMergeState(result.mergeState);
               // If any files are already staged, pre-select only staged files
               // Otherwise select all files by default
               const stagedFiles = fileList.filter((f) => {
@@ -579,6 +615,34 @@ export function CommitWorktreeDialog({
         </DialogHeader>
 
         <div className="flex flex-col gap-3 py-2 min-h-0 flex-1 overflow-hidden">
+          {/* Merge state banner */}
+          {mergeState?.isMerging && (
+            <div className="flex items-start gap-2 p-3 rounded-md bg-purple-500/10 border border-purple-500/20">
+              <GitMerge className="w-4 h-4 text-purple-500 mt-0.5 flex-shrink-0" />
+              <div className="text-sm">
+                <span className="font-medium text-purple-400">
+                  {mergeState.mergeOperationType === 'cherry-pick'
+                    ? 'Cherry-pick'
+                    : mergeState.mergeOperationType === 'rebase'
+                      ? 'Rebase'
+                      : 'Merge'}{' '}
+                  in progress
+                </span>
+                {mergeState.conflictFiles.length > 0 ? (
+                  <span className="text-purple-400/80 ml-1">
+                    &mdash; {mergeState.conflictFiles.length} file
+                    {mergeState.conflictFiles.length !== 1 ? 's' : ''} with conflicts
+                  </span>
+                ) : mergeState.isCleanMerge ? (
+                  <span className="text-purple-400/80 ml-1">
+                    &mdash; Clean merge, {mergeState.mergeAffectedFiles.length} file
+                    {mergeState.mergeAffectedFiles.length !== 1 ? 's' : ''} affected
+                  </span>
+                ) : null}
+              </div>
+            </div>
+          )}
+
           {/* File Selection */}
           <div className="flex flex-col min-h-0">
             <div className="flex items-center justify-between mb-1.5">
@@ -625,13 +689,25 @@ export function CommitWorktreeDialog({
                   const isStaged = idx !== ' ' && idx !== '?';
                   const isUnstaged = wt !== ' ' && wt !== '?';
                   const isUntracked = idx === '?' && wt === '?';
+                  const isMergeFile =
+                    file.isMergeAffected ||
+                    (mergeState?.mergeAffectedFiles?.includes(file.path) ?? false);
 
                   return (
-                    <div key={file.path} className="border-b border-border last:border-b-0">
+                    <div
+                      key={file.path}
+                      className={cn(
+                        'border-b last:border-b-0',
+                        isMergeFile ? 'border-purple-500/30' : 'border-border'
+                      )}
+                    >
                       <div
                         className={cn(
-                          'flex items-center gap-2 px-3 py-1.5 hover:bg-accent/50 transition-colors group',
+                          'flex items-center gap-2 px-3 py-1.5 transition-colors group',
-                          isExpanded && 'bg-accent/30'
+                          isMergeFile
+                            ? 'bg-purple-500/5 hover:bg-purple-500/10'
+                            : 'hover:bg-accent/50',
+                          isExpanded && (isMergeFile ? 'bg-purple-500/10' : 'bg-accent/30')
                         )}
                       >
                         {/* Checkbox */}
@@ -651,11 +727,21 @@ export function CommitWorktreeDialog({
                           ) : (
                             <ChevronRight className="w-3 h-3 text-muted-foreground flex-shrink-0" />
                           )}
-                          {getFileIcon(file.status)}
+                          {isMergeFile ? (
+                            <GitMerge className="w-3.5 h-3.5 text-purple-500 flex-shrink-0" />
+                          ) : (
+                            getFileIcon(file.status)
+                          )}
                           <TruncatedFilePath
                             path={file.path}
                             className="text-xs font-mono flex-1 text-foreground"
                           />
+                          {isMergeFile && (
+                            <span className="text-[10px] px-1.5 py-0.5 rounded border font-medium flex-shrink-0 bg-purple-500/15 text-purple-400 border-purple-500/30 inline-flex items-center gap-0.5">
+                              <GitMerge className="w-2.5 h-2.5" />
+                              {getMergeTypeLabel(file.mergeType)}
+                            </span>
+                          )}
                           <span
                             className={cn(
                               'text-[10px] px-1.5 py-0.5 rounded border font-medium flex-shrink-0',
@@ -810,11 +896,16 @@ export function CommitWorktreeDialog({
                       </SelectTrigger>
                       <SelectContent>
                         {remotes.map((remote) => (
-                          <SelectItem key={remote.name} value={remote.name}>
+                          <SelectItem
+                            key={remote.name}
+                            value={remote.name}
+                            description={
+                              <span className="text-xs text-muted-foreground truncate w-full block">
+                                {remote.url}
+                              </span>
+                            }
+                          >
                             <span className="font-medium">{remote.name}</span>
-                            <span className="ml-2 text-muted-foreground text-xs inline-block truncate max-w-[200px] align-bottom">
-                              {remote.url}
-                            </span>
                           </SelectItem>
                         ))}
                       </SelectContent>

apps/ui/src/components/views/board-view/dialogs/git-pull-dialog.tsx

@@ -1,4 +1,4 @@
-import { useState, useEffect, useCallback } from 'react';
+import { useState, useEffect, useCallback, useRef } from 'react';
 import {
   Dialog,
   DialogContent,
@@ -17,11 +17,17 @@ import {
   FileWarning,
   Wrench,
   Sparkles,
+  GitMerge,
+  GitCommitHorizontal,
+  FileText,
+  Settings,
 } from 'lucide-react';
 import { Spinner } from '@/components/ui/spinner';
+import { Checkbox } from '@/components/ui/checkbox';
 import { getElectronAPI } from '@/lib/electron';
 import { toast } from 'sonner';
 import { cn } from '@/lib/utils';
+import { useAppStore } from '@/store/app-store';
 import type { MergeConflictInfo } from '../worktree-panel/types';
 
 interface WorktreeInfo {
@@ -37,6 +43,7 @@ type PullPhase =
   | 'local-changes' // Local changes detected, asking user what to do
   | 'pulling' // Actively pulling (with or without stash)
   | 'success' // Pull completed successfully
+  | 'merge-complete' // Pull resulted in a merge (not fast-forward, no conflicts)
   | 'conflict' // Merge conflicts detected
   | 'error'; // Something went wrong
 
@@ -53,6 +60,9 @@ interface PullResult {
   stashed?: boolean;
   stashRestored?: boolean;
   stashRecoveryFailed?: boolean;
+  isMerge?: boolean;
+  isFastForward?: boolean;
+  mergeAffectedFiles?: string[];
 }
 
 interface GitPullDialogProps {
@@ -62,6 +72,8 @@ interface GitPullDialogProps {
   remote?: string;
   onPulled?: () => void;
   onCreateConflictResolutionFeature?: (conflictInfo: MergeConflictInfo) => void;
+  /** Called when user chooses to commit the merge — opens the commit dialog */
+  onCommitMerge?: (worktree: { path: string; branch: string; isMain: boolean }) => void;
 }
 
 export function GitPullDialog({
@@ -71,10 +83,54 @@ export function GitPullDialog({
   remote,
   onPulled,
   onCreateConflictResolutionFeature,
+  onCommitMerge,
 }: GitPullDialogProps) {
   const [phase, setPhase] = useState<PullPhase>('checking');
   const [pullResult, setPullResult] = useState<PullResult | null>(null);
   const [errorMessage, setErrorMessage] = useState<string | null>(null);
+  const [rememberChoice, setRememberChoice] = useState(false);
+  const [showMergeFiles, setShowMergeFiles] = useState(false);
+
+  const mergePostAction = useAppStore((s) => s.mergePostAction);
+  const setMergePostAction = useAppStore((s) => s.setMergePostAction);
+
+  /**
+   * Determine the appropriate phase after a successful pull.
+   * If the pull resulted in a merge (not fast-forward) and no conflicts,
+   * check user preference before deciding whether to show merge prompt.
+   */
+  const handleSuccessfulPull = useCallback(
+    (result: PullResult) => {
+      setPullResult(result);
+
+      if (result.isMerge && !result.hasConflicts) {
+        // Merge happened — check user preference
+        if (mergePostAction === 'commit') {
+          // User preference: auto-commit
+          setPhase('success');
+          onPulled?.();
+          // Auto-trigger commit dialog
+          if (worktree && onCommitMerge) {
+            onCommitMerge(worktree);
+            onOpenChange(false);
+          }
+        } else if (mergePostAction === 'manual') {
+          // User preference: manual review
+          setPhase('success');
+          onPulled?.();
+        } else {
+          // No preference — show merge prompt; onPulled will be called from the
+          // user-action handlers (handleCommitMerge / handleMergeManually) once
+          // the user makes their choice, consistent with the conflict phase.
+          setPhase('merge-complete');
+        }
+      } else {
+        setPhase('success');
+        onPulled?.();
+      }
+    },
+    [mergePostAction, worktree, onCommitMerge, onPulled, onOpenChange]
+  );
 
   const checkForLocalChanges = useCallback(async () => {
     if (!worktree) return;
@@ -103,9 +159,7 @@ export function GitPullDialog({
         setPhase('local-changes');
       } else if (result.result?.pulled !== undefined) {
         // No local changes, pull went through (or already up to date)
-        setPullResult(result.result);
+        handleSuccessfulPull(result.result);
-        setPhase('success');
-        onPulled?.();
       } else {
         // Unexpected response: success but no recognizable fields
         setPullResult(result.result ?? null);
@@ -116,18 +170,33 @@ export function GitPullDialog({
       setErrorMessage(err instanceof Error ? err.message : 'Failed to check for changes');
       setPhase('error');
     }
-  }, [worktree, remote, onPulled]);
+  }, [worktree, remote, handleSuccessfulPull]);
 
-  // Reset state when dialog opens
+  // Keep a ref to the latest checkForLocalChanges to break the circular dependency
+  // between the "reset/start" effect and the callback chain. Without this, any
+  // change in onPulled (passed from the parent) would recreate handleSuccessfulPull
+  // → checkForLocalChanges → re-trigger the effect while the dialog is already open,
+  // causing the pull flow to restart unintentionally.
+  const checkForLocalChangesRef = useRef(checkForLocalChanges);
+  useEffect(() => {
+    checkForLocalChangesRef.current = checkForLocalChanges;
+  });
+
+  // Reset state when dialog opens and start the initial pull check.
+  // Depends only on `open` and `worktree` — NOT on `checkForLocalChanges` —
+  // so that parent callback re-creations don't restart the pull flow mid-flight.
   useEffect(() => {
     if (open && worktree) {
       setPhase('checking');
       setPullResult(null);
       setErrorMessage(null);
-      // Start the initial check
+      setRememberChoice(false);
-      checkForLocalChanges();
+      setShowMergeFiles(false);
+      // Start the initial check using the ref so we always call the latest version
+      // without making it a dependency of this effect.
+      checkForLocalChangesRef.current();
     }
-  }, [open, worktree, checkForLocalChanges]);
+  }, [open, worktree]);
 
   const handlePullWithStash = useCallback(async () => {
     if (!worktree) return;
@@ -155,8 +224,7 @@ export function GitPullDialog({
       if (result.result?.hasConflicts) {
         setPhase('conflict');
       } else if (result.result?.pulled) {
-        setPhase('success');
+        handleSuccessfulPull(result.result);
-        onPulled?.();
       } else {
         // Unrecognized response: no pulled flag and no conflicts
         console.warn('handlePullWithStash: unrecognized response', result.result);
@@ -167,7 +235,7 @@ export function GitPullDialog({
       setErrorMessage(err instanceof Error ? err.message : 'Failed to pull');
       setPhase('error');
     }
-  }, [worktree, remote, onPulled]);
+  }, [worktree, remote, handleSuccessfulPull]);
 
   const handleResolveWithAI = useCallback(() => {
     if (!worktree || !pullResult || !onCreateConflictResolutionFeature) return;
@@ -186,6 +254,35 @@ export function GitPullDialog({
     onOpenChange(false);
   }, [worktree, pullResult, remote, onCreateConflictResolutionFeature, onOpenChange]);
 
+  const handleCommitMerge = useCallback(() => {
+    if (!worktree || !onCommitMerge) {
+      // No handler available — show feedback and bail without persisting preference
+      toast.error('Commit merge is not available', {
+        description: 'The commit merge action is not configured for this context.',
+        duration: 4000,
+      });
+      return;
+    }
+    if (rememberChoice) {
+      setMergePostAction('commit');
+    }
+    onPulled?.();
+    onCommitMerge(worktree);
+    onOpenChange(false);
+  }, [rememberChoice, setMergePostAction, worktree, onCommitMerge, onPulled, onOpenChange]);
+
+  const handleMergeManually = useCallback(() => {
+    if (rememberChoice) {
+      setMergePostAction('manual');
+    }
+    toast.info('Merge left for manual review', {
+      description: 'Review the merged files and commit when ready.',
+      duration: 5000,
+    });
+    onPulled?.();
+    onOpenChange(false);
+  }, [rememberChoice, setMergePostAction, onPulled, onOpenChange]);
+
   const handleClose = useCallback(() => {
     onOpenChange(false);
   }, [onOpenChange]);
@@ -336,6 +433,137 @@ export function GitPullDialog({
           </>
         )}
 
+        {/* Merge Complete Phase — post-merge prompt */}
+        {phase === 'merge-complete' && (
+          <>
+            <DialogHeader>
+              <DialogTitle className="flex items-center gap-2">
+                <GitMerge className="w-5 h-5 text-purple-500" />
+                Merge Complete
+              </DialogTitle>
+              <DialogDescription asChild>
+                <div className="space-y-3">
+                  <span className="block">
+                    Pull resulted in a merge on{' '}
+                    <code className="font-mono bg-muted px-1 rounded">{worktree.branch}</code>
+                    {pullResult?.mergeAffectedFiles && pullResult.mergeAffectedFiles.length > 0 && (
+                      <span>
+                        {' '}
+                        affecting {pullResult.mergeAffectedFiles.length} file
+                        {pullResult.mergeAffectedFiles.length !== 1 ? 's' : ''}
+                      </span>
+                    )}
+                    . How would you like to proceed?
+                  </span>
+
+                  {pullResult?.mergeAffectedFiles && pullResult.mergeAffectedFiles.length > 0 && (
+                    <div>
+                      <button
+                        onClick={() => setShowMergeFiles(!showMergeFiles)}
+                        className="text-xs text-muted-foreground hover:text-foreground transition-colors inline-flex items-center gap-1"
+                      >
+                        <FileText className="w-3 h-3" />
+                        {showMergeFiles ? 'Hide' : 'Show'} affected files (
+                        {pullResult.mergeAffectedFiles.length})
+                      </button>
+                      {showMergeFiles && (
+                        <div className="mt-1.5 border border-border rounded-lg overflow-hidden max-h-[150px] overflow-y-auto scrollbar-visible">
+                          {pullResult.mergeAffectedFiles.map((file) => (
+                            <div
+                              key={file}
+                              className="flex items-center gap-2 px-3 py-1.5 text-xs font-mono border-b border-border last:border-b-0 hover:bg-accent/30"
+                            >
+                              <GitMerge className="w-3 h-3 text-purple-500 flex-shrink-0" />
+                              <span className="truncate">{file}</span>
+                            </div>
+                          ))}
+                        </div>
+                      )}
+                    </div>
+                  )}
+
+                  {pullResult?.stashed &&
+                    pullResult?.stashRestored &&
+                    !pullResult?.stashRecoveryFailed && (
+                      <div className="flex items-start gap-2 p-3 rounded-md bg-green-500/10 border border-green-500/20">
+                        <Archive className="w-4 h-4 text-green-500 mt-0.5 flex-shrink-0" />
+                        <span className="text-green-600 dark:text-green-400 text-sm">
+                          Your stashed changes have been restored successfully.
+                        </span>
+                      </div>
+                    )}
+
+                  <div className="mt-2 p-3 rounded-md bg-muted/50 border border-border">
+                    <p className="text-sm text-muted-foreground font-medium mb-2">
+                      Choose how to proceed:
+                    </p>
+                    <ul className="text-sm text-muted-foreground list-disc list-inside space-y-1">
+                      <li>
+                        <strong>Commit Merge</strong> &mdash; Open the commit dialog with a merge
+                        commit message
+                      </li>
+                      <li>
+                        <strong>Review Manually</strong> &mdash; Leave the working tree as-is for
+                        manual review
+                      </li>
+                    </ul>
+                  </div>
+                </div>
+              </DialogDescription>
+            </DialogHeader>
+
+            {/* Remember choice option */}
+            <div className="flex items-center gap-2 px-1">
+              <label className="flex items-center gap-2 text-xs text-muted-foreground cursor-pointer">
+                <Checkbox
+                  checked={rememberChoice}
+                  onCheckedChange={(checked) => setRememberChoice(checked === true)}
+                  className="rounded border-border"
+                />
+                <Settings className="w-3 h-3" />
+                Remember my choice for future merges
+              </label>
+              {(rememberChoice || mergePostAction) && (
+                <span className="text-xs text-muted-foreground ml-auto flex items-center gap-2">
+                  <span className="opacity-70">
+                    Current:{' '}
+                    {mergePostAction === 'commit'
+                      ? 'auto-commit'
+                      : mergePostAction === 'manual'
+                        ? 'manual review'
+                        : 'ask every time'}
+                  </span>
+                  <button
+                    onClick={() => {
+                      setMergePostAction(null);
+                      setRememberChoice(false);
+                    }}
+                    className="text-xs text-muted-foreground hover:text-foreground transition-colors"
+                  >
+                    Reset preference
+                  </button>
+                </span>
+              )}
+            </div>
+
+            <DialogFooter className={cn('flex-col sm:flex-row gap-2')}>
+              <Button variant="outline" onClick={handleMergeManually} className="w-full sm:w-auto">
+                <FileText className="w-4 h-4 mr-2" />
+                Review Manually
+              </Button>
+              {worktree && onCommitMerge && (
+                <Button
+                  onClick={handleCommitMerge}
+                  className="w-full sm:w-auto bg-purple-600 hover:bg-purple-700 text-white"
+                >
+                  <GitCommitHorizontal className="w-4 h-4 mr-2" />
+                  Commit Merge
+                </Button>
+              )}
+            </DialogFooter>
+          </>
+        )}
+
         {/* Conflict Phase */}
         {phase === 'conflict' && (
           <>

apps/ui/src/components/views/board-view/dialogs/post-merge-prompt-dialog.tsx

@@ -0,0 +1,190 @@
+/**
+ * Post-Merge Prompt Dialog
+ *
+ * Shown after a pull or stash apply results in a clean merge (no conflicts).
+ * Presents the user with two options:
+ * 1. Commit the merge — automatically stage all merge-result files and open commit dialog
+ * 2. Merge manually — leave the working tree as-is for manual review
+ *
+ * The user's choice can be persisted as a preference to avoid repeated prompts.
+ */
+
+import { useState, useCallback, useEffect } from 'react';
+import {
+  Dialog,
+  DialogContent,
+  DialogDescription,
+  DialogFooter,
+  DialogHeader,
+  DialogTitle,
+} from '@/components/ui/dialog';
+import { Button } from '@/components/ui/button';
+import { Checkbox } from '@/components/ui/checkbox';
+import { GitMerge, GitCommitHorizontal, FileText, Settings } from 'lucide-react';
+import { cn } from '@/lib/utils';
+
+export type MergePostAction = 'commit' | 'manual' | null;
+
+interface PostMergePromptDialogProps {
+  open: boolean;
+  onOpenChange: (open: boolean) => void;
+  /** Branch name where the merge happened */
+  branchName: string;
+  /** Number of files affected by the merge */
+  mergeFileCount: number;
+  /** List of files affected by the merge */
+  mergeAffectedFiles?: string[];
+  /** Called when the user chooses to commit the merge */
+  onCommitMerge: () => void;
+  /** Called when the user chooses to handle the merge manually */
+  onMergeManually: () => void;
+  /** Current saved preference (null = ask every time) */
+  savedPreference?: MergePostAction;
+  /** Called when the user changes the preference */
+  onSavePreference?: (preference: MergePostAction) => void;
+}
+
+export function PostMergePromptDialog({
+  open,
+  onOpenChange,
+  branchName,
+  mergeFileCount,
+  mergeAffectedFiles,
+  onCommitMerge,
+  onMergeManually,
+  savedPreference,
+  onSavePreference,
+}: PostMergePromptDialogProps) {
+  const [rememberChoice, setRememberChoice] = useState(false);
+  const [showFiles, setShowFiles] = useState(false);
+
+  // Reset transient state each time the dialog is opened
+  useEffect(() => {
+    if (open) {
+      setRememberChoice(false);
+      setShowFiles(false);
+    }
+  }, [open]);
+
+  const handleCommitMerge = useCallback(() => {
+    if (rememberChoice && onSavePreference) {
+      onSavePreference('commit');
+    }
+    onCommitMerge();
+    onOpenChange(false);
+  }, [rememberChoice, onSavePreference, onCommitMerge, onOpenChange]);
+
+  const handleMergeManually = useCallback(() => {
+    if (rememberChoice && onSavePreference) {
+      onSavePreference('manual');
+    }
+    onMergeManually();
+    onOpenChange(false);
+  }, [rememberChoice, onSavePreference, onMergeManually, onOpenChange]);
+
+  return (
+    <Dialog open={open} onOpenChange={onOpenChange}>
+      <DialogContent className="sm:max-w-[520px] w-full max-w-full sm:rounded-xl rounded-none dialog-fullscreen-mobile">
+        <DialogHeader>
+          <DialogTitle className="flex items-center gap-2">
+            <GitMerge className="w-5 h-5 text-purple-500" />
+            Merge Complete
+          </DialogTitle>
+          <DialogDescription asChild>
+            <div className="space-y-3">
+              <span className="block">
+                A merge was successfully completed on{' '}
+                <code className="font-mono bg-muted px-1 rounded">{branchName}</code>
+                {mergeFileCount > 0 && (
+                  <span>
+                    {' '}
+                    affecting {mergeFileCount} file{mergeFileCount !== 1 ? 's' : ''}
+                  </span>
+                )}
+                . How would you like to proceed?
+              </span>
+
+              {mergeAffectedFiles && mergeAffectedFiles.length > 0 && (
+                <div>
+                  <button
+                    onClick={() => setShowFiles(!showFiles)}
+                    className="text-xs text-muted-foreground hover:text-foreground transition-colors inline-flex items-center gap-1"
+                  >
+                    <FileText className="w-3 h-3" />
+                    {showFiles ? 'Hide' : 'Show'} affected files ({mergeAffectedFiles.length})
+                  </button>
+                  {showFiles && (
+                    <div className="mt-1.5 border border-border rounded-lg overflow-hidden max-h-[150px] overflow-y-auto scrollbar-visible">
+                      {mergeAffectedFiles.map((file) => (
+                        <div
+                          key={file}
+                          className="flex items-center gap-2 px-3 py-1.5 text-xs font-mono border-b border-border last:border-b-0 hover:bg-accent/30"
+                        >
+                          <GitMerge className="w-3 h-3 text-purple-500 flex-shrink-0" />
+                          <span className="truncate">{file}</span>
+                        </div>
+                      ))}
+                    </div>
+                  )}
+                </div>
+              )}
+
+              <div className="mt-2 p-3 rounded-md bg-muted/50 border border-border">
+                <p className="text-sm text-muted-foreground font-medium mb-2">
+                  Choose how to proceed:
+                </p>
+                <ul className="text-sm text-muted-foreground list-disc list-inside space-y-1">
+                  <li>
+                    <strong>Commit Merge</strong> &mdash; Stage all merge files and open the commit
+                    dialog with a pre-populated merge commit message
+                  </li>
+                  <li>
+                    <strong>Review Manually</strong> &mdash; Leave the working tree as-is so you can
+                    review changes and commit at your own pace
+                  </li>
+                </ul>
+              </div>
+            </div>
+          </DialogDescription>
+        </DialogHeader>
+
+        {/* Remember choice option */}
+        {onSavePreference && (
+          <div className="flex items-center gap-2 px-1">
+            <label className="flex items-center gap-2 text-xs text-muted-foreground cursor-pointer">
+              <Checkbox
+                checked={rememberChoice}
+                onCheckedChange={(checked) => setRememberChoice(checked)}
+                className="rounded border-border"
+              />
+              <Settings className="w-3 h-3" />
+              Remember my choice for future merges
+            </label>
+            {savedPreference && (
+              <button
+                onClick={() => onSavePreference(null)}
+                className="text-xs text-muted-foreground hover:text-foreground transition-colors ml-auto"
+              >
+                Reset preference
+              </button>
+            )}
+          </div>
+        )}
+
+        <DialogFooter className={cn('flex-col sm:flex-row gap-2')}>
+          <Button variant="outline" onClick={handleMergeManually} className="w-full sm:w-auto">
+            <FileText className="w-4 h-4 mr-2" />
+            Review Manually
+          </Button>
+          <Button
+            onClick={handleCommitMerge}
+            className="w-full sm:w-auto bg-purple-600 hover:bg-purple-700 text-white"
+          >
+            <GitCommitHorizontal className="w-4 h-4 mr-2" />
+            Commit Merge
+          </Button>
+        </DialogFooter>
+      </DialogContent>
+    </Dialog>
+  );
+}

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

@@ -251,7 +251,7 @@ export function ViewCommitsDialog({ open, onOpenChange, worktree }: ViewCommitsD
 
   return (
     <Dialog open={open} onOpenChange={onOpenChange}>
-      <DialogContent className="w-full h-full max-w-full max-h-full sm:w-[90vw] sm:max-w-[640px] sm:max-h-[100dvh] sm:h-auto sm:rounded-xl rounded-none flex flex-col dialog-fullscreen-mobile">
+      <DialogContent className="w-full h-full max-w-full max-h-full sm:w-[90vw] sm:max-w-[640px] sm:max-h-[85dvh] sm:h-auto sm:rounded-xl rounded-none flex flex-col dialog-fullscreen-mobile">
         <DialogHeader>
           <DialogTitle className="flex items-center gap-2">
             <GitCommit className="w-5 h-5" />
@@ -263,7 +263,7 @@ export function ViewCommitsDialog({ open, onOpenChange, worktree }: ViewCommitsD
           </DialogDescription>
         </DialogHeader>
 
-        <div className="flex-1 sm:min-h-[400px] sm:max-h-[60vh] overflow-y-auto scrollbar-visible -mx-6 -mb-6">
+        <div className="flex-1 min-h-0 sm:min-h-[400px] sm:max-h-[60vh] overflow-y-auto scrollbar-visible -mx-6 -mb-6">
           <div className="h-full px-6 pb-6">
             {isLoading && (
               <div className="flex items-center justify-center py-12">

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

@@ -367,7 +367,7 @@ export function ViewStashesDialog({
 
   return (
     <Dialog open={open} onOpenChange={onOpenChange}>
-      <DialogContent className="w-full h-full max-w-full max-h-full sm:w-[90vw] sm:max-w-[640px] sm:max-h-[100dvh] sm:h-auto sm:rounded-xl rounded-none flex flex-col dialog-fullscreen-mobile">
+      <DialogContent className="w-full h-full max-w-full max-h-full sm:w-[90vw] sm:max-w-[640px] sm:max-h-[85dvh] sm:h-auto sm:rounded-xl rounded-none flex flex-col dialog-fullscreen-mobile">
         <DialogHeader>
           <DialogTitle className="flex items-center gap-2">
             <Archive className="w-5 h-5" />

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

@@ -33,7 +33,7 @@ export function ViewWorktreeChangesDialog({
 
   return (
     <Dialog open={open} onOpenChange={onOpenChange}>
-      <DialogContent className="w-full h-full max-w-full max-h-full sm:w-[90vw] sm:max-w-[900px] sm:max-h-[100dvh] sm:h-auto sm:rounded-xl rounded-none flex flex-col dialog-fullscreen-mobile">
+      <DialogContent className="w-full h-full max-w-full max-h-full sm:w-[90vw] sm:max-w-[900px] sm:max-h-[85dvh] sm:h-auto sm:rounded-xl rounded-none flex flex-col dialog-fullscreen-mobile">
         <DialogHeader>
           <DialogTitle className="flex items-center gap-2">
             <FileText className="w-5 h-5" />
@@ -54,7 +54,7 @@ export function ViewWorktreeChangesDialog({
           </DialogDescription>
         </DialogHeader>
 
-        <div className="flex-1 sm:min-h-[600px] sm:max-h-[60vh]  overflow-y-auto scrollbar-visible -mx-6 -mb-6">
+        <div className="flex-1 min-h-0 overflow-y-auto scrollbar-visible -mx-6 -mb-6">
           <div className="h-full px-6 pb-6">
             <GitDiffPanel
               projectPath={projectPath}

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

@@ -94,8 +94,6 @@ export function useBoardActions({
     skipVerificationInAutoMode,
     isPrimaryWorktreeBranch,
     getPrimaryWorktreeBranch,
-    getAutoModeState,
-    getMaxConcurrencyForWorktree,
   } = useAppStore();
   const autoMode = useAutoMode();
 
@@ -561,38 +559,9 @@ export function useBoardActions({
 
   const handleStartImplementation = useCallback(
     async (feature: Feature) => {
-      // Check capacity for the feature's specific worktree, not the current view
+      // Note: No concurrency limit check here. Manual feature starts should never
-      // Normalize the branch name: if the feature's branch is the primary worktree branch,
+      // be blocked by the auto mode concurrency limit. The concurrency limit only
-      // treat it as null (main worktree) to match how running tasks are stored
+      // governs how many features the auto-loop picks up automatically.
-      const rawBranchName = feature.branchName ?? null;
-      const featureBranchName =
-        currentProject?.path &&
-        rawBranchName &&
-        isPrimaryWorktreeBranch(currentProject.path, rawBranchName)
-          ? null
-          : rawBranchName;
-      const featureWorktreeState = currentProject
-        ? getAutoModeState(currentProject.id, featureBranchName)
-        : null;
-      // Use getMaxConcurrencyForWorktree which correctly falls back to global maxConcurrency
-      // instead of autoMode.maxConcurrency which only falls back to DEFAULT_MAX_CONCURRENCY (1)
-      const featureMaxConcurrency = currentProject
-        ? getMaxConcurrencyForWorktree(currentProject.id, featureBranchName)
-        : autoMode.maxConcurrency;
-      const featureRunningCount = featureWorktreeState?.runningTasks?.length ?? 0;
-      const canStartInWorktree = featureRunningCount < featureMaxConcurrency;
-
-      if (!canStartInWorktree) {
-        const worktreeDesc = featureBranchName
-          ? `worktree "${featureBranchName}"`
-          : 'main worktree';
-        toast.error('Concurrency limit reached', {
-          description: `${worktreeDesc} can only have ${featureMaxConcurrency} task${
-            featureMaxConcurrency > 1 ? 's' : ''
-          } running at a time. Wait for a task to complete or increase the limit.`,
-        });
-        return false;
-      }
 
       // Check for blocking dependencies and show warning if enabled
       if (enableDependencyBlocking) {
@@ -681,18 +650,7 @@ export function useBoardActions({
         return false;
       }
     },
-    [
+    [enableDependencyBlocking, features, updateFeature, persistFeatureUpdate, handleRunFeature]
-      autoMode,
-      enableDependencyBlocking,
-      features,
-      updateFeature,
-      persistFeatureUpdate,
-      handleRunFeature,
-      currentProject,
-      getAutoModeState,
-      getMaxConcurrencyForWorktree,
-      isPrimaryWorktreeBranch,
-    ]
   );
 
   const handleVerifyFeature = useCallback(

apps/ui/src/components/views/board-view/hooks/use-board-drag-drop.ts

@@ -163,13 +163,22 @@ export function useBoardDragDrop({
 
       let targetStatus: ColumnId | null = null;
 
+      // Normalize the over ID: strip 'column-header-' prefix if the card was dropped
+      // directly onto the column header droppable zone (e.g. 'column-header-backlog' → 'backlog')
+      const effectiveOverId = overId.startsWith('column-header-')
+        ? overId.replace('column-header-', '')
+        : overId;
+
       // Check if we dropped on a column
-      const column = COLUMNS.find((c) => c.id === overId);
+      const column = COLUMNS.find((c) => c.id === effectiveOverId);
       if (column) {
         targetStatus = column.id;
+      } else if (effectiveOverId.startsWith('pipeline_')) {
+        // Pipeline step column (not in static COLUMNS list)
+        targetStatus = effectiveOverId as ColumnId;
       } else {
         // Dropped on another feature - find its column
-        const overFeature = features.find((f) => f.id === overId);
+        const overFeature = features.find((f) => f.id === effectiveOverId);
         if (overFeature) {
           targetStatus = overFeature.status;
         }

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

@@ -136,7 +136,7 @@ export function DevServerLogsPanel({
         compact
       >
         {/* Compact Header */}
-        <DialogHeader className="shrink-0 px-4 py-3 border-b border-border/50 pr-12">
+        <DialogHeader className="shrink-0 px-4 py-3 border-b border-border/50 pr-12 dialog-compact-header-mobile">
           <div className="flex items-center justify-between">
             <DialogTitle className="flex items-center gap-2 text-base">
               <Terminal className="w-4 h-4 text-primary" />

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

@@ -354,12 +354,19 @@ export function WorktreeActionsDropdown({
           <>
             <DropdownMenuLabel className="text-xs flex items-center gap-2">
               <span className="w-2 h-2 rounded-full bg-green-500 animate-pulse" />
-              Dev Server Running (:{devServerInfo?.port})
+              {devServerInfo?.urlDetected === false
+                ? 'Dev Server Starting...'
+                : `Dev Server Running (:${devServerInfo?.port})`}
             </DropdownMenuLabel>
             <DropdownMenuItem
               onClick={() => onOpenDevServerUrl(worktree)}
               className="text-xs"
-              aria-label={`Open dev server on port ${devServerInfo?.port} in browser`}
+              disabled={devServerInfo?.urlDetected === false}
+              aria-label={
+                devServerInfo?.urlDetected === false
+                  ? 'Open dev server in browser'
+                  : `Open dev server on port ${devServerInfo?.port} in browser`
+              }
             >
               <Globe className="w-3.5 h-3.5 mr-2" aria-hidden="true" />
               Open in Browser

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

@@ -308,7 +308,11 @@ export function WorktreeDropdown({
         {selectedStatus.devServerRunning && (
           <span
             className="inline-flex items-center justify-center h-4 w-4 text-green-500 shrink-0"
-            title={`Dev server running on port ${selectedStatus.devServerInfo?.port}`}
+            title={
+              selectedStatus.devServerInfo?.urlDetected === false
+                ? 'Dev server starting...'
+                : `Dev server running on port ${selectedStatus.devServerInfo?.port}`
+            }
           >
             <Globe className="w-3 h-3" />
           </span>

apps/ui/src/components/views/board-view/worktree-panel/hooks/use-dev-server-logs.ts

@@ -206,6 +206,16 @@ export function useDevServerLogs({ worktreePath, autoSubscribe = true }: UseDevS
           }));
           break;
         }
+        case 'dev-server:url-detected': {
+          const { payload } = event;
+          logger.info('Dev server URL detected:', payload);
+          setState((prev) => ({
+            ...prev,
+            url: payload.url,
+            port: payload.port,
+          }));
+          break;
+        }
       }
     });
 

apps/ui/src/components/views/board-view/worktree-panel/hooks/use-dev-servers.ts

@@ -25,7 +25,10 @@ export function useDevServers({ projectPath }: UseDevServersOptions) {
       if (result.success && result.result?.servers) {
         const serversMap = new Map<string, DevServerInfo>();
         for (const server of result.result.servers) {
-          serversMap.set(server.worktreePath, server);
+          serversMap.set(normalizePath(server.worktreePath), {
+            ...server,
+            urlDetected: server.urlDetected ?? true,
+          });
         }
         setRunningDevServers(serversMap);
       }
@@ -38,6 +41,39 @@ export function useDevServers({ projectPath }: UseDevServersOptions) {
     fetchDevServers();
   }, [fetchDevServers]);
 
+  // Subscribe to url-detected events to update port/url when the actual dev server port is detected
+  useEffect(() => {
+    const api = getElectronAPI();
+    if (!api?.worktree?.onDevServerLogEvent) return;
+
+    const unsubscribe = api.worktree.onDevServerLogEvent((event) => {
+      if (event.type === 'dev-server:url-detected') {
+        const { worktreePath, url, port } = event.payload;
+        const key = normalizePath(worktreePath);
+        let didUpdate = false;
+        setRunningDevServers((prev) => {
+          const existing = prev.get(key);
+          if (!existing) return prev;
+          const next = new Map(prev);
+          next.set(key, {
+            ...existing,
+            url,
+            port,
+            urlDetected: true,
+          });
+          didUpdate = true;
+          return next;
+        });
+        if (didUpdate) {
+          logger.info(`Dev server URL detected for ${worktreePath}: ${url} (port ${port})`);
+          toast.success(`Dev server running on port ${port}`);
+        }
+      }
+    });
+
+    return unsubscribe;
+  }, []);
+
   const getWorktreeKey = useCallback(
     (worktree: WorktreeInfo) => {
       const path = worktree.isMain ? projectPath : worktree.path;
@@ -68,10 +104,11 @@ export function useDevServers({ projectPath }: UseDevServersOptions) {
               worktreePath: result.result!.worktreePath,
               port: result.result!.port,
               url: result.result!.url,
+              urlDetected: false,
             });
             return next;
           });
-          toast.success(`Dev server started on port ${result.result.port}`);
+          toast.success('Dev server started, detecting port...');
         } else {
           toast.error(result.error || 'Failed to start dev server');
         }

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

@@ -34,6 +34,8 @@ export interface DevServerInfo {
   worktreePath: string;
   port: number;
   url: string;
+  /** Whether the actual URL/port has been detected from server output */
+  urlDetected?: boolean;
 }
 
 export interface TestSessionInfo {

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

@@ -646,57 +646,101 @@ export function WorktreePanel({
     setPushToRemoteDialogOpen(true);
   }, []);
 
+  // Keep a ref to pullDialogWorktree so handlePullCompleted can access the current
+  // value without including it in the dependency array. If pullDialogWorktree were
+  // a dep of handlePullCompleted, changing it would recreate the callback, which
+  // would propagate into GitPullDialog's onPulled prop and ultimately re-trigger
+  // the pull-check effect inside the dialog (causing the flow to run twice).
+  const pullDialogWorktreeRef = useRef(pullDialogWorktree);
+  useEffect(() => {
+    pullDialogWorktreeRef.current = pullDialogWorktree;
+  }, [pullDialogWorktree]);
+
   // Handle pull completed - refresh branches and worktrees
   const handlePullCompleted = useCallback(() => {
     // Refresh branch data (ahead/behind counts, tracking) and worktree list
     // after GitPullDialog completes the pull operation
-    if (pullDialogWorktree) {
+    if (pullDialogWorktreeRef.current) {
-      fetchBranches(pullDialogWorktree.path);
+      fetchBranches(pullDialogWorktreeRef.current.path);
     }
     fetchWorktrees({ silent: true });
-  }, [fetchWorktrees, fetchBranches, pullDialogWorktree]);
+  }, [fetchWorktrees, fetchBranches]);
+
+  // Wrapper for onCommit that works with the pull dialog's simpler WorktreeInfo.
+  // Uses the full pullDialogWorktree when available (via ref to avoid making it
+  // a dep that would cascade into handleSuccessfulPull → checkForLocalChanges recreations).
+  const handleCommitMerge = useCallback(
+    (_simpleWorktree: { path: string; branch: string; isMain: boolean }) => {
+      // Prefer the full worktree object we already have (from ref)
+      if (pullDialogWorktreeRef.current) {
+        onCommit(pullDialogWorktreeRef.current);
+      }
+    },
+    [onCommit]
+  );
 
   // Handle pull with remote selection when multiple remotes exist
   // Now opens the pull dialog which handles stash management and conflict resolution
-  const handlePullWithRemoteSelection = useCallback(async (worktree: WorktreeInfo) => {
+  // If the branch has a tracked remote, pull from it directly (skip the remote selection dialog)
-    try {
+  const handlePullWithRemoteSelection = useCallback(
-      const api = getHttpApiClient();
-      const result = await api.worktree.listRemotes(worktree.path);
-
-      if (result.success && result.result && result.result.remotes.length > 1) {
-        // Multiple remotes - show selection dialog first
-        setSelectRemoteWorktree(worktree);
-        setSelectRemoteOperation('pull');
-        setSelectRemoteDialogOpen(true);
-      } else if (result.success && result.result && result.result.remotes.length === 1) {
-        // Exactly one remote - open pull dialog directly with that remote
-        const remoteName = result.result.remotes[0].name;
-        setPullDialogRemote(remoteName);
-        setPullDialogWorktree(worktree);
-        setPullDialogOpen(true);
-      } else {
-        // No remotes - open pull dialog with default
-        setPullDialogRemote(undefined);
-        setPullDialogWorktree(worktree);
-        setPullDialogOpen(true);
-      }
-    } catch {
-      // If listing remotes fails, open pull dialog with default
-      setPullDialogRemote(undefined);
-      setPullDialogWorktree(worktree);
-      setPullDialogOpen(true);
-    }
-  }, []);
-
-  // Handle push with remote selection when multiple remotes exist
-  const handlePushWithRemoteSelection = useCallback(
     async (worktree: WorktreeInfo) => {
+      // If the branch already tracks a remote, pull from it directly — no dialog needed
+      const tracked = getTrackingRemote(worktree.path);
+      if (tracked) {
+        setPullDialogRemote(tracked);
+        setPullDialogWorktree(worktree);
+        setPullDialogOpen(true);
+        return;
+      }
+
       try {
         const api = getHttpApiClient();
         const result = await api.worktree.listRemotes(worktree.path);
 
         if (result.success && result.result && result.result.remotes.length > 1) {
-          // Multiple remotes - show selection dialog
+          // Multiple remotes and no tracking remote - show selection dialog
+          setSelectRemoteWorktree(worktree);
+          setSelectRemoteOperation('pull');
+          setSelectRemoteDialogOpen(true);
+        } else if (result.success && result.result && result.result.remotes.length === 1) {
+          // Exactly one remote - open pull dialog directly with that remote
+          const remoteName = result.result.remotes[0].name;
+          setPullDialogRemote(remoteName);
+          setPullDialogWorktree(worktree);
+          setPullDialogOpen(true);
+        } else {
+          // No remotes - open pull dialog with default
+          setPullDialogRemote(undefined);
+          setPullDialogWorktree(worktree);
+          setPullDialogOpen(true);
+        }
+      } catch {
+        // If listing remotes fails, open pull dialog with default
+        setPullDialogRemote(undefined);
+        setPullDialogWorktree(worktree);
+        setPullDialogOpen(true);
+      }
+    },
+    [getTrackingRemote]
+  );
+
+  // Handle push with remote selection when multiple remotes exist
+  // If the branch has a tracked remote, push to it directly (skip the remote selection dialog)
+  const handlePushWithRemoteSelection = useCallback(
+    async (worktree: WorktreeInfo) => {
+      // If the branch already tracks a remote, push to it directly — no dialog needed
+      const tracked = getTrackingRemote(worktree.path);
+      if (tracked) {
+        handlePush(worktree, tracked);
+        return;
+      }
+
+      try {
+        const api = getHttpApiClient();
+        const result = await api.worktree.listRemotes(worktree.path);
+
+        if (result.success && result.result && result.result.remotes.length > 1) {
+          // Multiple remotes and no tracking remote - show selection dialog
           setSelectRemoteWorktree(worktree);
           setSelectRemoteOperation('push');
           setSelectRemoteDialogOpen(true);
@@ -713,7 +757,7 @@ export function WorktreePanel({
         handlePush(worktree);
       }
     },
-    [handlePush]
+    [handlePush, getTrackingRemote]
   );
 
   // Handle confirming remote selection for pull/push
@@ -992,6 +1036,7 @@ export function WorktreePanel({
           remote={pullDialogRemote}
           onPulled={handlePullCompleted}
           onCreateConflictResolutionFeature={onCreateMergeConflictResolutionFeature}
+          onCommitMerge={handleCommitMerge}
         />
 
         {/* Dev Server Logs Panel */}
@@ -1445,6 +1490,7 @@ export function WorktreePanel({
         onOpenChange={setViewStashesDialogOpen}
         worktree={viewStashesWorktree}
         onStashApplied={handleStashApplied}
+        onStashApplyConflict={onStashApplyConflict}
       />
 
       {/* Cherry Pick Dialog */}
@@ -1463,6 +1509,7 @@ export function WorktreePanel({
         worktree={pullDialogWorktree}
         remote={pullDialogRemote}
         onPulled={handlePullCompleted}
+        onCommitMerge={handleCommitMerge}
         onCreateConflictResolutionFeature={onCreateMergeConflictResolutionFeature}
       />
     </div>

apps/ui/src/components/views/project-settings-view/worktree-preferences-section.tsx

@@ -25,6 +25,9 @@ import { getHttpApiClient } from '@/lib/http-api-client';
 import type { Project } from '@/lib/electron';
 import { ProjectFileSelectorDialog } from '@/components/dialogs/project-file-selector-dialog';
 
+// Stable empty array reference to prevent unnecessary re-renders when no copy files are set
+const EMPTY_FILES: string[] = [];
+
 interface WorktreePreferencesSectionProps {
   project: Project;
 }
@@ -38,20 +41,30 @@ interface InitScriptResponse {
 }
 
 export function WorktreePreferencesSection({ project }: WorktreePreferencesSectionProps) {
+  // Use direct store subscriptions (not getter functions) so the component
+  // properly re-renders when these values change in the store.
   const globalUseWorktrees = useAppStore((s) => s.useWorktrees);
-  const getProjectUseWorktrees = useAppStore((s) => s.getProjectUseWorktrees);
+  const projectUseWorktrees = useAppStore((s) => s.useWorktreesByProject[project.path]);
   const setProjectUseWorktrees = useAppStore((s) => s.setProjectUseWorktrees);
-  const getShowInitScriptIndicator = useAppStore((s) => s.getShowInitScriptIndicator);
+  const showIndicator = useAppStore(
+    (s) => s.showInitScriptIndicatorByProject[project.path] ?? true
+  );
   const setShowInitScriptIndicator = useAppStore((s) => s.setShowInitScriptIndicator);
-  const getDefaultDeleteBranch = useAppStore((s) => s.getDefaultDeleteBranch);
+  const defaultDeleteBranch = useAppStore(
+    (s) => s.defaultDeleteBranchByProject[project.path] ?? false
+  );
   const setDefaultDeleteBranch = useAppStore((s) => s.setDefaultDeleteBranch);
-  const getAutoDismissInitScriptIndicator = useAppStore((s) => s.getAutoDismissInitScriptIndicator);
+  const autoDismiss = useAppStore(
+    (s) => s.autoDismissInitScriptIndicatorByProject[project.path] ?? true
+  );
   const setAutoDismissInitScriptIndicator = useAppStore((s) => s.setAutoDismissInitScriptIndicator);
-  const copyFiles = useAppStore((s) => s.worktreeCopyFilesByProject[project.path] ?? []);
+  // Use a stable empty array reference to prevent new array on every render when
+  // worktreeCopyFilesByProject[project.path] is undefined (not yet loaded).
+  const copyFilesFromStore = useAppStore((s) => s.worktreeCopyFilesByProject[project.path]);
+  const copyFiles = copyFilesFromStore ?? EMPTY_FILES;
   const setWorktreeCopyFiles = useAppStore((s) => s.setWorktreeCopyFiles);
 
   // Get effective worktrees setting (project override or global fallback)
-  const projectUseWorktrees = getProjectUseWorktrees(project.path);
   const effectiveUseWorktrees = projectUseWorktrees ?? globalUseWorktrees;
 
   const [scriptContent, setScriptContent] = useState('');
@@ -65,11 +78,6 @@ export function WorktreePreferencesSection({ project }: WorktreePreferencesSecti
   const [newCopyFilePath, setNewCopyFilePath] = useState('');
   const [fileSelectorOpen, setFileSelectorOpen] = useState(false);
 
-  // Get the current settings for this project
-  const showIndicator = getShowInitScriptIndicator(project.path);
-  const defaultDeleteBranch = getDefaultDeleteBranch(project.path);
-  const autoDismiss = getAutoDismissInitScriptIndicator(project.path);
-
   // Check if there are unsaved changes
   const hasChanges = scriptContent !== originalContent;
 

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

@@ -1,12 +1,16 @@
 import { useState } from 'react';
-import { Workflow, RotateCcw, Replace, Sparkles } from 'lucide-react';
+import { Workflow, RotateCcw, Replace, Sparkles, Brain } from 'lucide-react';
 import { cn } from '@/lib/utils';
 import { useAppStore } from '@/store/app-store';
 import { Button } from '@/components/ui/button';
 import { PhaseModelSelector } from './phase-model-selector';
 import { BulkReplaceDialog } from './bulk-replace-dialog';
-import type { PhaseModelKey, PhaseModelEntry } from '@automaker/types';
+import type { PhaseModelKey, PhaseModelEntry, ThinkingLevel } from '@automaker/types';
-import { DEFAULT_PHASE_MODELS, DEFAULT_GLOBAL_SETTINGS } from '@automaker/types';
+import {
+  DEFAULT_PHASE_MODELS,
+  DEFAULT_GLOBAL_SETTINGS,
+  REASONING_EFFORT_LEVELS,
+} from '@automaker/types';
 
 interface PhaseConfig {
   key: PhaseModelKey;
@@ -161,6 +165,121 @@ function FeatureDefaultModelSection() {
   );
 }
 
+// Thinking level options with descriptions for the settings UI
+const THINKING_LEVEL_OPTIONS: { id: ThinkingLevel; label: string; description: string }[] = [
+  { id: 'none', label: 'None', description: 'No extended thinking' },
+  { id: 'low', label: 'Low', description: 'Light reasoning (1k tokens)' },
+  { id: 'medium', label: 'Medium', description: 'Moderate reasoning (10k tokens)' },
+  { id: 'high', label: 'High', description: 'Deep reasoning (16k tokens)' },
+  { id: 'ultrathink', label: 'Ultra', description: 'Maximum reasoning (32k tokens)' },
+  { id: 'adaptive', label: 'Adaptive', description: 'Model decides reasoning depth' },
+];
+
+/**
+ * Default thinking level / reasoning effort section.
+ * These defaults are applied when selecting a model via the primary button
+ * in the two-stage model selector (i.e. clicking the model name directly).
+ */
+function DefaultThinkingLevelSection() {
+  const {
+    defaultThinkingLevel,
+    setDefaultThinkingLevel,
+    defaultReasoningEffort,
+    setDefaultReasoningEffort,
+  } = useAppStore();
+
+  return (
+    <div className="space-y-4">
+      <div>
+        <h3 className="text-sm font-medium text-foreground">Quick-Select Defaults</h3>
+        <p className="text-xs text-muted-foreground">
+          Thinking/reasoning level applied when quick-selecting a model from the dropdown. You can
+          always fine-tune per model via the expand arrow.
+        </p>
+      </div>
+      <div className="space-y-3">
+        {/* Default Thinking Level (Claude models) */}
+        <div
+          className={cn(
+            'flex items-center justify-between p-4 rounded-xl',
+            'bg-accent/20 border border-border/30',
+            'hover:bg-accent/30 transition-colors'
+          )}
+        >
+          <div className="flex items-center gap-3 flex-1 pr-4">
+            <div className="w-8 h-8 rounded-lg bg-purple-500/10 flex items-center justify-center">
+              <Brain className="w-4 h-4 text-purple-500" />
+            </div>
+            <div>
+              <h4 className="text-sm font-medium text-foreground">Default Thinking Level</h4>
+              <p className="text-xs text-muted-foreground">
+                Applied to Claude models when quick-selected
+              </p>
+            </div>
+          </div>
+          <div className="flex items-center gap-1.5 flex-wrap justify-end">
+            {THINKING_LEVEL_OPTIONS.map((option) => (
+              <button
+                key={option.id}
+                onClick={() => setDefaultThinkingLevel(option.id)}
+                className={cn(
+                  'px-2.5 py-1.5 rounded-lg text-xs font-medium transition-all',
+                  'border',
+                  defaultThinkingLevel === option.id
+                    ? 'bg-primary text-primary-foreground border-primary shadow-sm'
+                    : 'bg-background border-border/50 text-muted-foreground hover:bg-accent hover:text-foreground'
+                )}
+                title={option.description}
+              >
+                {option.label}
+              </button>
+            ))}
+          </div>
+        </div>
+
+        {/* Default Reasoning Effort (Codex models) */}
+        <div
+          className={cn(
+            'flex items-center justify-between p-4 rounded-xl',
+            'bg-accent/20 border border-border/30',
+            'hover:bg-accent/30 transition-colors'
+          )}
+        >
+          <div className="flex items-center gap-3 flex-1 pr-4">
+            <div className="w-8 h-8 rounded-lg bg-blue-500/10 flex items-center justify-center">
+              <Brain className="w-4 h-4 text-blue-500" />
+            </div>
+            <div>
+              <h4 className="text-sm font-medium text-foreground">Default Reasoning Effort</h4>
+              <p className="text-xs text-muted-foreground">
+                Applied to Codex/OpenAI models when quick-selected
+              </p>
+            </div>
+          </div>
+          <div className="flex items-center gap-1.5 flex-wrap justify-end">
+            {REASONING_EFFORT_LEVELS.map((option) => (
+              <button
+                key={option.id}
+                onClick={() => setDefaultReasoningEffort(option.id)}
+                className={cn(
+                  'px-2.5 py-1.5 rounded-lg text-xs font-medium transition-all',
+                  'border',
+                  defaultReasoningEffort === option.id
+                    ? 'bg-primary text-primary-foreground border-primary shadow-sm'
+                    : 'bg-background border-border/50 text-muted-foreground hover:bg-accent hover:text-foreground'
+                )}
+                title={option.description}
+              >
+                {option.label}
+              </button>
+            ))}
+          </div>
+        </div>
+      </div>
+    </div>
+  );
+}
+
 export function ModelDefaultsSection() {
   const { resetPhaseModels, claudeCompatibleProviders } = useAppStore();
   const [showBulkReplace, setShowBulkReplace] = useState(false);
@@ -222,6 +341,9 @@ export function ModelDefaultsSection() {
         {/* Feature Defaults */}
         <FeatureDefaultModelSection />
 
+        {/* Default Thinking Level / Reasoning Effort */}
+        <DefaultThinkingLevelSection />
+
         {/* Quick Tasks */}
         <PhaseGroup
           title="Quick Tasks"

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

@@ -13,6 +13,9 @@ import {
   X,
   SquarePlus,
   Settings,
+  GitBranch,
+  ChevronDown,
+  FolderGit,
 } from 'lucide-react';
 import { Spinner } from '@/components/ui/spinner';
 import { getServerUrlSync } from '@/lib/http-api-client';
@@ -28,6 +31,17 @@ import { Label } from '@/components/ui/label';
 import { Slider } from '@/components/ui/slider';
 import { Switch } from '@/components/ui/switch';
 import { Popover, PopoverContent, PopoverTrigger } from '@/components/ui/popover';
+import {
+  DropdownMenu,
+  DropdownMenuContent,
+  DropdownMenuItem,
+  DropdownMenuLabel,
+  DropdownMenuSeparator,
+  DropdownMenuSub,
+  DropdownMenuSubContent,
+  DropdownMenuSubTrigger,
+  DropdownMenuTrigger,
+} from '@/components/ui/dropdown-menu';
 import {
   Select,
   SelectContent,
@@ -255,6 +269,8 @@ export function TerminalView({ initialCwd, initialBranch, initialMode, nonce }:
     setTerminalScrollbackLines,
     setTerminalScreenReaderMode,
     updateTerminalPanelSizes,
+    currentWorktreeByProject,
+    worktreesByProject,
   } = useAppStore();
 
   const navigate = useNavigate();
@@ -946,13 +962,50 @@ export function TerminalView({ initialCwd, initialBranch, initialMode, nonce }:
     }
   };
 
+  // Helper: find the branchName of the given session ID within a layout tree
+  const findSessionBranchName = (
+    layout: TerminalPanelContent | null,
+    sessionId: string
+  ): string | undefined => {
+    if (!layout) return undefined;
+    if (layout.type === 'terminal') {
+      return layout.sessionId === sessionId ? layout.branchName : undefined;
+    }
+    if (layout.type === 'split') {
+      for (const panel of layout.panels) {
+        const found = findSessionBranchName(panel, sessionId);
+        if (found !== undefined) return found;
+      }
+    }
+    return undefined;
+  };
+
+  // Helper: resolve the worktree cwd and branchName for the currently active terminal session.
+  // Returns { cwd, branchName } if the active terminal was opened in a worktree, or {} otherwise.
+  const getActiveSessionWorktreeInfo = (): { cwd?: string; branchName?: string } => {
+    const activeSessionId = terminalState.activeSessionId;
+    if (!activeSessionId || !activeTab?.layout || !currentProject) return {};
+
+    const branchName = findSessionBranchName(activeTab.layout, activeSessionId);
+    if (!branchName) return {};
+
+    // Look up the worktree path for this branch in the project's worktree list
+    const projectWorktrees = worktreesByProject[currentProject.path] ?? [];
+    const worktree = projectWorktrees.find((wt) => wt.branch === branchName);
+    if (!worktree) return { branchName };
+
+    return { cwd: worktree.path, branchName };
+  };
+
   // Create a new terminal session
   // targetSessionId: the terminal to split (if splitting an existing terminal)
   // customCwd: optional working directory to use instead of the current project path
+  // branchName: optional branch name to display in the terminal panel header
   const createTerminal = async (
     direction?: 'horizontal' | 'vertical',
     targetSessionId?: string,
-    customCwd?: string
+    customCwd?: string,
+    branchName?: string
   ) => {
     if (!canCreateTerminal('[Terminal] Debounced terminal creation')) {
       return;
@@ -971,7 +1024,7 @@ export function TerminalView({ initialCwd, initialBranch, initialMode, nonce }:
       const data = await response.json();
 
       if (data.success) {
-        addTerminalToLayout(data.data.id, direction, targetSessionId);
+        addTerminalToLayout(data.data.id, direction, targetSessionId, branchName);
         // Mark this session as new for running initial command
         if (defaultRunScript) {
           setNewSessionIds((prev) => new Set(prev).add(data.data.id));
@@ -1004,11 +1057,18 @@ export function TerminalView({ initialCwd, initialBranch, initialMode, nonce }:
   };
 
   // Create terminal in new tab
-  const createTerminalInNewTab = async () => {
+  // customCwd: optional working directory (e.g., a specific worktree path)
+  // branchName: optional branch name to display in the terminal panel header
+  const createTerminalInNewTab = async (customCwd?: string, branchName?: string) => {
     if (!canCreateTerminal('[Terminal] Debounced terminal tab creation')) {
       return;
     }
 
+    // Use provided cwd/branch, or inherit from active session's worktree
+    const { cwd: worktreeCwd, branchName: worktreeBranch } = customCwd
+      ? { cwd: customCwd, branchName: branchName }
+      : getActiveSessionWorktreeInfo();
+
     const tabId = addTerminalTab();
     try {
       const headers: Record<string, string> = {};
@@ -1018,14 +1078,14 @@ export function TerminalView({ initialCwd, initialBranch, initialMode, nonce }:
 
       const response = await apiFetch('/api/terminal/sessions', 'POST', {
         headers,
-        body: { cwd: currentProject?.path || undefined, cols: 80, rows: 24 },
+        body: { cwd: worktreeCwd || currentProject?.path || undefined, cols: 80, rows: 24 },
       });
       const data = await response.json();
 
       if (data.success) {
-        // Add to the newly created tab
+        // Add to the newly created tab (passing branchName so the panel header shows the branch badge)
         const { addTerminalToTab } = useAppStore.getState();
-        addTerminalToTab(data.data.id, tabId);
+        addTerminalToTab(data.data.id, tabId, undefined, worktreeBranch);
         // Mark this session as new for running initial command
         if (defaultRunScript) {
           setNewSessionIds((prev) => new Set(prev).add(data.data.id));
@@ -1344,8 +1404,14 @@ export function TerminalView({ initialCwd, initialBranch, initialMode, nonce }:
             isActive={terminalState.activeSessionId === content.sessionId}
             onFocus={() => setActiveTerminalSession(content.sessionId)}
             onClose={() => killTerminal(content.sessionId)}
-            onSplitHorizontal={() => createTerminal('horizontal', content.sessionId)}
+            onSplitHorizontal={() => {
-            onSplitVertical={() => createTerminal('vertical', content.sessionId)}
+              const { cwd, branchName } = getActiveSessionWorktreeInfo();
+              createTerminal('horizontal', content.sessionId, cwd, branchName);
+            }}
+            onSplitVertical={() => {
+              const { cwd, branchName } = getActiveSessionWorktreeInfo();
+              createTerminal('vertical', content.sessionId, cwd, branchName);
+            }}
             onNewTab={createTerminalInNewTab}
             onNavigateUp={() => navigateToTerminal('up')}
             onNavigateDown={() => navigateToTerminal('down')}
@@ -1502,6 +1568,15 @@ export function TerminalView({ initialCwd, initialBranch, initialMode, nonce }:
 
   // No terminals yet - show welcome screen
   if (terminalState.tabs.length === 0) {
+    // Get the current worktree for this project (if any)
+    const currentWorktreeInfo = currentProject
+      ? (currentWorktreeByProject[currentProject.path] ?? null)
+      : null;
+    // Only show worktree button when the current worktree has a specific path set
+    // (non-null path means a worktree is selected, as opposed to the main project)
+    const currentWorktreePath = currentWorktreeInfo?.path ?? null;
+    const currentWorktreeBranch = currentWorktreeInfo?.branch ?? null;
+
     return (
       <div className="flex-1 flex flex-col items-center justify-center text-center p-6">
         <div className="p-4 rounded-full bg-brand-500/10 mb-4">
@@ -1518,10 +1593,40 @@ export function TerminalView({ initialCwd, initialBranch, initialMode, nonce }:
           )}
         </p>
 
-        <Button onClick={() => createTerminal()}>
+        <div className="flex flex-col items-center gap-3 w-full max-w-xs">
-          <Plus className="h-4 w-4 mr-2" />
+          {currentWorktreePath && (
-          New Terminal
+            <Button
-        </Button>
+              className="w-full flex-col h-auto py-2"
+              onClick={() =>
+                createTerminal(
+                  undefined,
+                  undefined,
+                  currentWorktreePath,
+                  currentWorktreeBranch ?? undefined
+                )
+              }
+            >
+              <span className="flex items-center">
+                <GitBranch className="h-4 w-4 mr-2 shrink-0" />
+                Open Terminal in Worktree
+              </span>
+              {currentWorktreeBranch && (
+                <span className="text-xs opacity-70 truncate max-w-full px-2">
+                  {currentWorktreeBranch}
+                </span>
+              )}
+            </Button>
+          )}
+
+          <Button
+            className="w-full"
+            variant={currentWorktreePath ? 'outline' : 'default'}
+            onClick={() => createTerminal()}
+          >
+            <Plus className="h-4 w-4 mr-2" />
+            New Terminal
+          </Button>
+        </div>
 
         {status?.platform && (
           <p className="text-xs text-muted-foreground mt-6">
@@ -1564,14 +1669,94 @@ export function TerminalView({ initialCwd, initialBranch, initialMode, nonce }:
 
             {(activeDragId || activeDragTabId) && <NewTabDropZone isDropTarget={true} />}
 
-            {/* New tab button */}
+            {/* New tab split button */}
-            <button
+            <div className="flex items-center">
-              className="flex items-center justify-center p-1.5 rounded hover:bg-accent text-muted-foreground hover:text-foreground"
+              <button
-              onClick={createTerminalInNewTab}
+                className="flex items-center justify-center p-1.5 rounded-l hover:bg-accent text-muted-foreground hover:text-foreground"
-              title="New Tab"
+                onClick={() => createTerminalInNewTab()}
-            >
+                title="New Tab"
-              <Plus className="h-4 w-4" />
+              >
-            </button>
+                <Plus className="h-4 w-4" />
+              </button>
+              <DropdownMenu>
+                <DropdownMenuTrigger asChild>
+                  <button
+                    className="flex items-center justify-center px-0.5 py-1.5 rounded-r hover:bg-accent text-muted-foreground hover:text-foreground border-l border-border"
+                    title="New Terminal Options"
+                  >
+                    <ChevronDown className="h-3 w-3" />
+                  </button>
+                </DropdownMenuTrigger>
+                <DropdownMenuContent align="start" side="bottom" className="w-56">
+                  <DropdownMenuItem onClick={() => createTerminalInNewTab()} className="gap-2">
+                    <Plus className="h-4 w-4" />
+                    New Tab
+                  </DropdownMenuItem>
+                  <DropdownMenuSeparator />
+                  <DropdownMenuItem
+                    onClick={() => {
+                      const { cwd, branchName } = getActiveSessionWorktreeInfo();
+                      createTerminal('horizontal', undefined, cwd, branchName);
+                    }}
+                    className="gap-2"
+                  >
+                    <SplitSquareHorizontal className="h-4 w-4" />
+                    Split Right
+                  </DropdownMenuItem>
+                  <DropdownMenuItem
+                    onClick={() => {
+                      const { cwd, branchName } = getActiveSessionWorktreeInfo();
+                      createTerminal('vertical', undefined, cwd, branchName);
+                    }}
+                    className="gap-2"
+                  >
+                    <SplitSquareVertical className="h-4 w-4" />
+                    Split Down
+                  </DropdownMenuItem>
+                  {/* Worktree options - show when project has worktrees */}
+                  {(() => {
+                    const projectWorktrees = currentProject
+                      ? (worktreesByProject[currentProject.path] ?? [])
+                      : [];
+                    if (projectWorktrees.length === 0) return null;
+                    const mainWorktree = projectWorktrees.find((wt) => wt.isMain);
+                    const featureWorktrees = projectWorktrees.filter((wt) => !wt.isMain);
+                    return (
+                      <>
+                        <DropdownMenuSeparator />
+                        <DropdownMenuLabel className="text-xs text-muted-foreground">
+                          Open in Worktree
+                        </DropdownMenuLabel>
+                        {mainWorktree && (
+                          <DropdownMenuItem
+                            onClick={() =>
+                              createTerminalInNewTab(mainWorktree.path, mainWorktree.branch)
+                            }
+                            className="gap-2"
+                          >
+                            <FolderGit className="h-4 w-4" />
+                            <span className="truncate">{mainWorktree.branch}</span>
+                            <span className="ml-auto text-[10px] text-muted-foreground shrink-0">
+                              main
+                            </span>
+                          </DropdownMenuItem>
+                        )}
+                        {featureWorktrees.map((wt) => (
+                          <DropdownMenuItem
+                            key={wt.path}
+                            onClick={() => createTerminalInNewTab(wt.path, wt.branch)}
+                            className="gap-2"
+                          >
+                            <GitBranch className="h-4 w-4" />
+                            <span className="truncate">{wt.branch}</span>
+                          </DropdownMenuItem>
+                        ))}
+                      </>
+                    );
+                  })()}
+                </DropdownMenuContent>
+              </DropdownMenu>
+            </div>
           </div>
 
           {/* Toolbar buttons */}
@@ -1580,7 +1765,10 @@ export function TerminalView({ initialCwd, initialBranch, initialMode, nonce }:
               variant="ghost"
               size="sm"
               className="h-7 px-2 text-muted-foreground hover:text-foreground"
-              onClick={() => createTerminal('horizontal')}
+              onClick={() => {
+                const { cwd, branchName } = getActiveSessionWorktreeInfo();
+                createTerminal('horizontal', undefined, cwd, branchName);
+              }}
               title="Split Right"
             >
               <SplitSquareHorizontal className="h-4 w-4" />
@@ -1589,7 +1777,10 @@ export function TerminalView({ initialCwd, initialBranch, initialMode, nonce }:
               variant="ghost"
               size="sm"
               className="h-7 px-2 text-muted-foreground hover:text-foreground"
-              onClick={() => createTerminal('vertical')}
+              onClick={() => {
+                const { cwd, branchName } = getActiveSessionWorktreeInfo();
+                createTerminal('vertical', undefined, cwd, branchName);
+              }}
               title="Split Down"
             >
               <SplitSquareVertical className="h-4 w-4" />
@@ -1771,12 +1962,14 @@ export function TerminalView({ initialCwd, initialBranch, initialMode, nonce }:
                 isActive={true}
                 onFocus={() => setActiveTerminalSession(terminalState.maximizedSessionId!)}
                 onClose={() => killTerminal(terminalState.maximizedSessionId!)}
-                onSplitHorizontal={() =>
+                onSplitHorizontal={() => {
-                  createTerminal('horizontal', terminalState.maximizedSessionId!)
+                  const { cwd, branchName } = getActiveSessionWorktreeInfo();
-                }
+                  createTerminal('horizontal', terminalState.maximizedSessionId!, cwd, branchName);
-                onSplitVertical={() =>
+                }}
-                  createTerminal('vertical', terminalState.maximizedSessionId!)
+                onSplitVertical={() => {
-                }
+                  const { cwd, branchName } = getActiveSessionWorktreeInfo();
+                  createTerminal('vertical', terminalState.maximizedSessionId!, cwd, branchName);
+                }}
                 onNewTab={createTerminalInNewTab}
                 onSessionInvalid={() => {
                   const sessionId = terminalState.maximizedSessionId!;

apps/ui/src/components/views/terminal-view/mobile-terminal-shortcuts.tsx

@@ -1,6 +1,18 @@
 import { useCallback, useRef, useEffect, useState } from 'react';
-import { ArrowUp, ArrowDown, ArrowLeft, ArrowRight, ChevronUp, ChevronDown } from 'lucide-react';
+import {
+  ArrowUp,
+  ArrowDown,
+  ArrowLeft,
+  ArrowRight,
+  ChevronUp,
+  ChevronDown,
+  Copy,
+  ClipboardPaste,
+  CheckSquare,
+  TextSelect,
+} from 'lucide-react';
 import { cn } from '@/lib/utils';
+import { StickyModifierKeys, type StickyModifier } from './sticky-modifier-keys';
 
 /**
  * ANSI escape sequences for special keys.
@@ -37,6 +49,20 @@ interface MobileTerminalShortcutsProps {
   onSendInput: (data: string) => void;
   /** Whether the terminal is connected and ready */
   isConnected: boolean;
+  /** Currently active sticky modifier (Ctrl or Alt) */
+  activeModifier: StickyModifier;
+  /** Callback when sticky modifier is toggled */
+  onModifierChange: (modifier: StickyModifier) => void;
+  /** Callback to copy selected text to clipboard */
+  onCopy?: () => void;
+  /** Callback to paste from clipboard into terminal */
+  onPaste?: () => void;
+  /** Callback to select all terminal content */
+  onSelectAll?: () => void;
+  /** Callback to toggle text selection mode (renders selectable text overlay) */
+  onToggleSelectMode?: () => void;
+  /** Whether text selection mode is currently active */
+  isSelectMode?: boolean;
 }
 
 /**
@@ -50,6 +76,13 @@ interface MobileTerminalShortcutsProps {
 export function MobileTerminalShortcuts({
   onSendInput,
   isConnected,
+  activeModifier,
+  onModifierChange,
+  onCopy,
+  onPaste,
+  onSelectAll,
+  onToggleSelectMode,
+  isSelectMode,
 }: MobileTerminalShortcutsProps) {
   const [isCollapsed, setIsCollapsed] = useState(false);
 
@@ -135,6 +168,54 @@ export function MobileTerminalShortcuts({
       {/* Separator */}
       <div className="w-px h-6 bg-border shrink-0" />
 
+      {/* Sticky modifier keys (Ctrl, Alt) - at the beginning of the bar */}
+      <StickyModifierKeys
+        activeModifier={activeModifier}
+        onModifierChange={onModifierChange}
+        isConnected={isConnected}
+      />
+
+      {/* Separator */}
+      <div className="w-px h-6 bg-border shrink-0" />
+
+      {/* Clipboard actions */}
+      {onToggleSelectMode && (
+        <IconShortcutButton
+          icon={TextSelect}
+          title={isSelectMode ? 'Exit select mode' : 'Select text'}
+          onPress={onToggleSelectMode}
+          disabled={!isConnected}
+          active={isSelectMode}
+        />
+      )}
+      {onSelectAll && (
+        <IconShortcutButton
+          icon={CheckSquare}
+          title="Select all"
+          onPress={onSelectAll}
+          disabled={!isConnected}
+        />
+      )}
+      {onCopy && (
+        <IconShortcutButton
+          icon={Copy}
+          title="Copy selection"
+          onPress={onCopy}
+          disabled={!isConnected}
+        />
+      )}
+      {onPaste && (
+        <IconShortcutButton
+          icon={ClipboardPaste}
+          title="Paste from clipboard"
+          onPress={onPaste}
+          disabled={!isConnected}
+        />
+      )}
+
+      {/* Separator */}
+      <div className="w-px h-6 bg-border shrink-0" />
+
       {/* Special keys */}
       <ShortcutButton
         label="Esc"
@@ -300,3 +381,42 @@ function ArrowButton({
     </button>
   );
 }
+
+/**
+ * Icon-based shortcut button for clipboard actions.
+ * Uses a Lucide icon instead of text label for a cleaner mobile UI.
+ */
+function IconShortcutButton({
+  icon: Icon,
+  title,
+  onPress,
+  disabled = false,
+  active = false,
+}: {
+  icon: React.ComponentType<{ className?: string }>;
+  title: string;
+  onPress: () => void;
+  disabled?: boolean;
+  active?: boolean;
+}) {
+  return (
+    <button
+      className={cn(
+        'p-2 rounded-md shrink-0 select-none transition-colors min-w-[36px] min-h-[36px] flex items-center justify-center',
+        'active:scale-95 touch-manipulation',
+        active
+          ? 'bg-brand-500/20 text-brand-500 ring-1 ring-brand-500/40'
+          : 'bg-muted/80 text-foreground hover:bg-accent',
+        disabled && 'opacity-40 pointer-events-none'
+      )}
+      onPointerDown={(e) => {
+        e.preventDefault(); // Prevent focus stealing from terminal
+        onPress();
+      }}
+      title={title}
+      disabled={disabled}
+    >
+      <Icon className="h-4 w-4" />
+    </button>
+  );
+}

apps/ui/src/components/views/terminal-view/terminal-panel.tsx

@@ -51,14 +51,11 @@ import { DEFAULT_FONT_VALUE } from '@/config/ui-font-options';
 import { toast } from 'sonner';
 import { getElectronAPI } from '@/lib/electron';
 import { getApiKey, getSessionToken, getServerUrlSync } from '@/lib/http-api-client';
+import { writeToClipboard, readFromClipboard } from '@/lib/clipboard-utils';
 import { useIsMobile } from '@/hooks/use-media-query';
 import { useVirtualKeyboardResize } from '@/hooks/use-virtual-keyboard-resize';
 import { MobileTerminalShortcuts } from './mobile-terminal-shortcuts';
-import {
+import { applyStickyModifier, type StickyModifier } from './sticky-modifier-keys';
-  StickyModifierKeys,
-  applyStickyModifier,
-  type StickyModifier,
-} from './sticky-modifier-keys';
 import { TerminalScriptsDropdown } from './terminal-scripts-dropdown';
 
 const logger = createLogger('Terminal');
@@ -81,6 +78,9 @@ const LARGE_PASTE_WARNING_THRESHOLD = 1024 * 1024; // 1MB - show warning for pas
 const PASTE_CHUNK_SIZE = 8 * 1024; // 8KB chunks for large pastes
 const PASTE_CHUNK_DELAY_MS = 10; // Small delay between chunks to prevent overwhelming WebSocket
 
+// Mobile overlay buffer cap - limit lines read from terminal buffer to avoid DOM blow-up on mobile
+const MAX_OVERLAY_LINES = 1000; // Maximum number of lines to read for the mobile select-mode overlay
+
 interface TerminalPanelProps {
   sessionId: string;
   authToken: string | null;
@@ -157,6 +157,9 @@ export function TerminalPanel({
   const [isImageDragOver, setIsImageDragOver] = useState(false);
   const [isProcessingImage, setIsProcessingImage] = useState(false);
   const hasRunInitialCommandRef = useRef(false);
+  // Long-press timer for mobile context menu
+  const longPressTimerRef = useRef<NodeJS.Timeout | null>(null);
+  const longPressTouchStartRef = useRef<{ x: number; y: number } | null>(null);
   // Tracks whether the connected shell is a Windows shell (PowerShell, cmd, etc.).
   // Maintained as a ref (not state) so sendCommand can read the current value without
   // causing unnecessary re-renders or stale closure issues. Set inside ws.onmessage
@@ -169,6 +172,10 @@ export function TerminalPanel({
   const showSearchRef = useRef(false);
   const [isAtBottom, setIsAtBottom] = useState(true);
 
+  // Mobile text selection mode - renders terminal buffer as selectable DOM text
+  const [isSelectMode, setIsSelectMode] = useState(false);
+  const [selectModeText, setSelectModeText] = useState('');
+
   // Sticky modifier key state (Ctrl or Alt) for the terminal toolbar
   const [stickyModifier, setStickyModifier] = useState<StickyModifier>(null);
   const stickyModifierRef = useRef<StickyModifier>(null);
@@ -330,9 +337,16 @@ export function TerminalPanel({
     try {
       // Strip any ANSI escape codes that might be in the selection
       const cleanText = stripAnsi(selection);
-      await navigator.clipboard.writeText(cleanText);
+      const success = await writeToClipboard(cleanText);
-      toast.success('Copied to clipboard');
+      if (success) {
-      return true;
+        toast.success('Copied to clipboard');
+        return true;
+      } else {
+        toast.error('Copy failed', {
+          description: 'Could not access clipboard',
+        });
+        return false;
+      }
     } catch (err) {
       logger.error('Copy failed:', err);
       const errorMessage = err instanceof Error ? err.message : 'Unknown error';
@@ -399,7 +413,7 @@ export function TerminalPanel({
     if (!terminal || !wsRef.current) return;
 
     try {
-      const text = await navigator.clipboard.readText();
+      const text = await readFromClipboard();
       if (!text) {
         toast.error('Nothing to paste', {
           description: 'Clipboard is empty',
@@ -428,7 +442,9 @@ export function TerminalPanel({
       toast.error('Paste failed', {
         description: errorMessage.includes('permission')
           ? 'Clipboard permission denied'
-          : 'Could not read from clipboard',
+          : errorMessage.includes('not supported')
+            ? errorMessage
+            : 'Could not read from clipboard',
       });
     }
   }, [sendTextInChunks]);
@@ -439,6 +455,45 @@ export function TerminalPanel({
     xtermRef.current?.selectAll();
   }, []);
 
+  // Extract terminal buffer text for mobile selection mode overlay
+  const getTerminalBufferText = useCallback((): string => {
+    const terminal = xtermRef.current;
+    if (!terminal) return '';
+
+    const buffer = terminal.buffer.active;
+    const lines: string[] = [];
+
+    // Cap the number of lines read to MAX_OVERLAY_LINES to avoid blowing up the DOM on mobile
+    const startIndex = Math.max(0, buffer.length - MAX_OVERLAY_LINES);
+    for (let i = startIndex; i < buffer.length; i++) {
+      const line = buffer.getLine(i);
+      if (line) {
+        lines.push(line.translateToString(true));
+      }
+    }
+
+    // Trim trailing empty lines but keep internal structure
+    while (lines.length > 0 && lines[lines.length - 1].trim() === '') {
+      lines.pop();
+    }
+
+    return lines.join('\n');
+  }, []);
+
+  // Toggle mobile text selection mode
+  const toggleSelectMode = useCallback(() => {
+    if (isSelectMode) {
+      setIsSelectMode(false);
+      setSelectModeText('');
+    } else {
+      const text = getTerminalBufferText();
+      // Strip ANSI escape codes for clean display
+      const cleanText = stripAnsi(text);
+      setSelectModeText(cleanText);
+      setIsSelectMode(true);
+    }
+  }, [isSelectMode, getTerminalBufferText]);
+
   // Clear terminal
   const clearTerminal = useCallback(() => {
     xtermRef.current?.clear();
@@ -944,17 +999,17 @@ export function TerminalPanel({
         const otherModKey = isMacRef.current ? event.ctrlKey : event.metaKey;
 
         // Ctrl+Shift+C / Cmd+Shift+C - Always copy (Linux terminal convention)
+        // Don't preventDefault() — allow the native browser copy to work alongside our custom copy
         if (modKey && !otherModKey && event.shiftKey && !event.altKey && code === 'KeyC') {
-          event.preventDefault();
           copySelectionRef.current();
           return false;
         }
 
         // Ctrl+C / Cmd+C - Copy if text is selected, otherwise send SIGINT
+        // Don't preventDefault() when copying — allow the native browser copy to work alongside our custom copy
         if (modKey && !otherModKey && !event.shiftKey && !event.altKey && code === 'KeyC') {
           const hasSelection = terminal.hasSelection();
           if (hasSelection) {
-            event.preventDefault();
             copySelectionRef.current();
             terminal.clearSelection();
             return false;
@@ -964,9 +1019,11 @@ export function TerminalPanel({
         }
 
         // Ctrl+V / Cmd+V or Ctrl+Shift+V / Cmd+Shift+V - Paste
+        // Don't preventDefault() — allow the native browser paste to work.
+        // Return false to prevent xterm from sending \x16 (literal next),
+        // but the browser's native paste event will still fire and xterm will
+        // receive the pasted text through its onData handler.
         if (modKey && !otherModKey && !event.altKey && code === 'KeyV') {
-          event.preventDefault();
-          pasteFromClipboardRef.current();
           return false;
         }
 
@@ -1014,6 +1071,12 @@ export function TerminalPanel({
         resizeDebounceRef.current = null;
       }
 
+      // Clear long-press timer
+      if (longPressTimerRef.current) {
+        clearTimeout(longPressTimerRef.current);
+        longPressTimerRef.current = null;
+      }
+
       // Clear search decorations before disposing to prevent visual artifacts
       if (searchAddonRef.current) {
         searchAddonRef.current.clearDecorations();
@@ -1571,6 +1634,17 @@ export function TerminalPanel({
     buttons[focusedMenuIndex]?.focus();
   }, [focusedMenuIndex, contextMenu]);
 
+  // Reset select mode when viewport transitions from mobile to non-mobile.
+  // The select-mode overlay is only rendered when (isSelectMode && isMobile), so if the
+  // viewport becomes non-mobile while isSelectMode is true the overlay disappears but the
+  // state is left dirty with no UI to clear it. Resetting here keeps state consistent.
+  useEffect(() => {
+    if (!isMobile && isSelectMode) {
+      setIsSelectMode(false);
+      setSelectModeText('');
+    }
+  }, [isMobile]); // eslint-disable-line react-hooks/exhaustive-deps
+
   // Handle right-click context menu with boundary checking
   const handleContextMenu = useCallback((e: React.MouseEvent) => {
     e.preventDefault();
@@ -1602,6 +1676,77 @@ export function TerminalPanel({
     setContextMenu({ x, y });
   }, []);
 
+  // Long-press handlers for mobile context menu
+  // On mobile, there's no right-click, so we trigger the context menu on long-press (500ms hold)
+  const LONG_PRESS_DURATION = 500; // ms
+  const LONG_PRESS_MOVE_THRESHOLD = 10; // px - cancel if finger moves more than this
+
+  const handleTouchStart = useCallback(
+    (e: React.TouchEvent) => {
+      if (!isMobile) return;
+      const touch = e.touches[0];
+      if (!touch) return;
+
+      // Clear any existing timer before creating a new one to avoid orphaned timeouts
+      if (longPressTimerRef.current) {
+        clearTimeout(longPressTimerRef.current);
+        longPressTimerRef.current = null;
+      }
+
+      // Capture initial touch coordinates into an immutable local snapshot
+      const startPos = { x: touch.clientX, y: touch.clientY };
+      longPressTouchStartRef.current = startPos;
+
+      longPressTimerRef.current = setTimeout(() => {
+        // Use the locally captured startPos rather than re-reading the ref
+        // Menu dimensions (approximate)
+        const menuWidth = 160;
+        const menuHeight = 152;
+        const padding = 8;
+
+        let x = startPos.x;
+        let y = startPos.y;
+
+        // Boundary checks
+        if (x + menuWidth + padding > window.innerWidth) {
+          x = window.innerWidth - menuWidth - padding;
+        }
+        if (y + menuHeight + padding > window.innerHeight) {
+          y = window.innerHeight - menuHeight - padding;
+        }
+        x = Math.max(padding, x);
+        y = Math.max(padding, y);
+
+        setContextMenu({ x, y });
+        longPressTouchStartRef.current = null;
+      }, LONG_PRESS_DURATION);
+    },
+    [isMobile]
+  );
+
+  const handleTouchMove = useCallback((e: React.TouchEvent) => {
+    if (!longPressTimerRef.current || !longPressTouchStartRef.current) return;
+    const touch = e.touches[0];
+    if (!touch) return;
+
+    const dx = touch.clientX - longPressTouchStartRef.current.x;
+    const dy = touch.clientY - longPressTouchStartRef.current.y;
+    if (Math.sqrt(dx * dx + dy * dy) > LONG_PRESS_MOVE_THRESHOLD) {
+      // Finger moved too far, cancel long-press
+      clearTimeout(longPressTimerRef.current);
+      longPressTimerRef.current = null;
+      longPressTouchStartRef.current = null;
+    }
+  }, []);
+
+  const handleTouchEnd = useCallback(() => {
+    if (longPressTimerRef.current) {
+      clearTimeout(longPressTimerRef.current);
+      longPressTimerRef.current = null;
+    }
+    longPressTouchStartRef.current = null;
+  }, []);
+
   // Convert file to base64
   const fileToBase64 = useCallback((file: File): Promise<string> => {
     return new Promise((resolve, reject) => {
@@ -2092,15 +2237,6 @@ export function TerminalPanel({
 
           <div className="w-px h-3 mx-0.5 bg-border" />
 
-          {/* Sticky modifier keys (Ctrl, Alt) */}
-          <StickyModifierKeys
-            activeModifier={stickyModifier}
-            onModifierChange={handleStickyModifierChange}
-            isConnected={connectionStatus === 'connected'}
-          />
-
-          <div className="w-px h-3 mx-0.5 bg-border" />
-
           {/* Split/close buttons */}
           <Button
             variant="ghost"
@@ -2221,24 +2357,116 @@ export function TerminalPanel({
         </div>
       )}
 
-      {/* Mobile shortcuts bar - special keys and arrow keys for touch devices */}
+      {/* Mobile shortcuts bar - special keys, clipboard, and arrow keys for touch devices */}
       {isMobile && (
         <MobileTerminalShortcuts
           onSendInput={sendTerminalInput}
           isConnected={connectionStatus === 'connected'}
+          activeModifier={stickyModifier}
+          onModifierChange={handleStickyModifierChange}
+          onSelectAll={selectAll}
+          onCopy={() => {
+            // On mobile, if nothing is selected, auto-select all before copying.
+            // This provides a convenient "tap to copy all" experience since
+            // touch-based text selection in xterm.js canvas is not possible.
+            const terminal = xtermRef.current;
+            if (terminal && !terminal.hasSelection()) {
+              terminal.selectAll();
+            }
+            copySelectionRef.current();
+          }}
+          onPaste={() => pasteFromClipboardRef.current()}
+          onToggleSelectMode={toggleSelectMode}
+          isSelectMode={isSelectMode}
         />
       )}
 
-      {/* Terminal container - uses terminal theme */}
+      {/* Terminal area wrapper - relative container for the terminal and selection overlay */}
-      <div
+      <div className="flex-1 overflow-hidden relative">
-        ref={terminalRef}
+        {/* Terminal container - xterm.js mounts here */}
-        className="flex-1 overflow-hidden relative"
+        <div
-        style={{ backgroundColor: currentTerminalTheme.background }}
+          ref={terminalRef}
-        onContextMenu={handleContextMenu}
+          className="absolute inset-0"
-        onDragOver={handleImageDragOver}
+          style={{ backgroundColor: currentTerminalTheme.background }}
-        onDragLeave={handleImageDragLeave}
+          onContextMenu={handleContextMenu}
-        onDrop={handleImageDrop}
+          onTouchStart={handleTouchStart}
-      />
+          onTouchMove={handleTouchMove}
+          onTouchEnd={handleTouchEnd}
+          onTouchCancel={handleTouchEnd}
+          onDragOver={handleImageDragOver}
+          onDragLeave={handleImageDragLeave}
+          onDrop={handleImageDrop}
+        />
+
+        {/* Mobile text selection overlay - renders terminal buffer as native selectable text.
+            Overlays the canvas so users can use native touch selection on real DOM text.
+            xterm.js renders to a <canvas>, which prevents native text selection on mobile.
+            This overlay shows the same content as real DOM text that supports touch selection. */}
+        {isSelectMode && isMobile && (
+          <div className="absolute inset-0 z-30 flex flex-col">
+            {/* Header bar with copy/done actions */}
+            <div className="flex items-center justify-between px-3 py-2 bg-brand-500/95 backdrop-blur-sm text-white shrink-0">
+              <span className="text-xs font-medium">Touch &amp; hold to select text</span>
+              <div className="flex items-center gap-2">
+                <button
+                  className="px-3 py-1.5 text-xs font-medium rounded-md bg-white/20 hover:bg-white/30 active:scale-95 transition-all touch-manipulation"
+                  onClick={async () => {
+                    const selection = window.getSelection();
+                    const selectedText = selection?.toString();
+                    if (selectedText) {
+                      const success = await writeToClipboard(selectedText);
+                      if (success) {
+                        toast.success('Copied to clipboard');
+                      } else {
+                        toast.error('Copy failed');
+                      }
+                    } else {
+                      const success = await writeToClipboard(selectModeText);
+                      if (success) {
+                        toast.success('Copied all text to clipboard');
+                      } else {
+                        toast.error('Copy failed');
+                      }
+                    }
+                  }}
+                >
+                  Copy
+                </button>
+                <button
+                  className="px-3 py-1.5 text-xs font-medium rounded-md bg-white/20 hover:bg-white/30 active:scale-95 transition-all touch-manipulation"
+                  onClick={() => {
+                    setIsSelectMode(false);
+                    setSelectModeText('');
+                  }}
+                >
+                  Done
+                </button>
+              </div>
+            </div>
+            {/* Scrollable text content matching terminal appearance */}
+            <div
+              className="flex-1 overflow-auto"
+              style={
+                {
+                  backgroundColor: currentTerminalTheme.background,
+                  color: currentTerminalTheme.foreground,
+                  fontFamily: getTerminalFontFamily(fontFamily),
+                  fontSize: `${fontSize}px`,
+                  lineHeight: `${lineHeight || 1.0}`,
+                  padding: '12px 16px',
+                  whiteSpace: 'pre-wrap',
+                  wordBreak: 'break-all',
+                  userSelect: 'text',
+                  WebkitUserSelect: 'text',
+                  touchAction: 'auto',
+                } as React.CSSProperties
+              }
+            >
+              {selectModeText || 'No terminal content to select.'}
+            </div>
+          </div>
+        )}
+      </div>
 
       {/* Jump to bottom button - shown when scrolled up */}
       {!isAtBottom && (

apps/ui/src/hooks/queries/use-git.ts

@@ -32,6 +32,7 @@ export function useGitDiffs(projectPath: string | undefined, enabled = true) {
       return {
         files: result.files ?? [],
         diff: result.diff ?? '',
+        ...(result.mergeState ? { mergeState: result.mergeState } : {}),
       };
     },
     enabled: !!projectPath && enabled,

apps/ui/src/hooks/queries/use-worktrees.ts

@@ -160,6 +160,7 @@ export function useWorktreeDiffs(projectPath: string | undefined, featureId: str
       return {
         files: result.files ?? [],
         diff: result.diff ?? '',
+        ...(result.mergeState ? { mergeState: result.mergeState } : {}),
       };
     },
     enabled: !!projectPath && !!featureId,

apps/ui/src/hooks/use-auto-mode.ts

@@ -157,8 +157,40 @@ export function useAutoMode(worktree?: WorktreeInfo) {
   // Check if we can start a new task based on concurrency limit
   const canStartNewTask = runningAutoTasks.length < maxConcurrency;
 
-  // Ref to prevent refreshStatus from overwriting optimistic state during start/stop
+  // Ref to prevent refreshStatus and WebSocket handlers from overwriting optimistic state
+  // during start/stop transitions.
   const isTransitioningRef = useRef(false);
+  // Tracks specifically a restart-for-concurrency transition. When true, the
+  // auto_mode_started WebSocket handler will clear isTransitioningRef, ensuring
+  // delayed auto_mode_stopped events that arrive after the HTTP calls complete
+  // (but before the WebSocket events) are still suppressed.
+  const isRestartTransitionRef = useRef(false);
+  // Safety timeout ID to clear the transition flag if the auto_mode_started event never arrives
+  const restartSafetyTimeoutRef = useRef<ReturnType<typeof setTimeout> | null>(null);
+
+  // Use refs for mutable state in refreshStatus to avoid unstable callback identity.
+  // This prevents the useEffect that calls refreshStatus on mount from re-firing
+  // every time isAutoModeRunning or runningAutoTasks changes, which was a source of
+  // flickering as refreshStatus would race with WebSocket events and optimistic updates.
+  const isAutoModeRunningRef = useRef(isAutoModeRunning);
+  const runningAutoTasksRef = useRef(runningAutoTasks);
+  useEffect(() => {
+    isAutoModeRunningRef.current = isAutoModeRunning;
+  }, [isAutoModeRunning]);
+  useEffect(() => {
+    runningAutoTasksRef.current = runningAutoTasks;
+  }, [runningAutoTasks]);
+
+  // Clean up safety timeout on unmount to prevent timer leaks and misleading log warnings
+  useEffect(() => {
+    return () => {
+      if (restartSafetyTimeoutRef.current) {
+        clearTimeout(restartSafetyTimeoutRef.current);
+        restartSafetyTimeoutRef.current = null;
+      }
+      isRestartTransitionRef.current = false;
+    };
+  }, []);
 
   const refreshStatus = useCallback(async () => {
     if (!currentProject) return;
@@ -175,20 +207,25 @@ export function useAutoMode(worktree?: WorktreeInfo) {
       if (result.success && result.isAutoLoopRunning !== undefined) {
         const backendIsRunning = result.isAutoLoopRunning;
         const backendRunningFeatures = result.runningFeatures ?? [];
+        // Read latest state from refs to avoid stale closure values
+        const currentIsRunning = isAutoModeRunningRef.current;
+        const currentRunningTasks = runningAutoTasksRef.current;
         const needsSync =
-          backendIsRunning !== isAutoModeRunning ||
+          backendIsRunning !== currentIsRunning ||
           // Also sync when backend has runningFeatures we're missing (handles missed WebSocket events)
           (backendIsRunning &&
             Array.isArray(backendRunningFeatures) &&
             backendRunningFeatures.length > 0 &&
-            !arraysEqual(backendRunningFeatures, runningAutoTasks)) ||
+            !arraysEqual(backendRunningFeatures, currentRunningTasks)) ||
           // Also sync when UI has stale running tasks but backend has none
           // (handles server restart where features were reconciled to backlog/ready)
-          (!backendIsRunning && runningAutoTasks.length > 0 && backendRunningFeatures.length === 0);
+          (!backendIsRunning &&
+            currentRunningTasks.length > 0 &&
+            backendRunningFeatures.length === 0);
 
         if (needsSync) {
           const worktreeDesc = branchName ? `worktree ${branchName}` : 'main worktree';
-          if (backendIsRunning !== isAutoModeRunning) {
+          if (backendIsRunning !== currentIsRunning) {
             logger.info(
               `[AutoMode] Syncing UI state with backend for ${worktreeDesc} in ${currentProject.path}: ${backendIsRunning ? 'ON' : 'OFF'}`
             );
@@ -206,7 +243,7 @@ export function useAutoMode(worktree?: WorktreeInfo) {
     } catch (error) {
       logger.error('Error syncing auto mode state with backend:', error);
     }
-  }, [branchName, currentProject, isAutoModeRunning, runningAutoTasks, setAutoModeRunning]);
+  }, [branchName, currentProject, setAutoModeRunning]);
 
   // On mount, query backend for current auto loop status and sync UI state.
   // This handles cases where the backend is still running after a page refresh.
@@ -281,8 +318,23 @@ export function useAutoMode(worktree?: WorktreeInfo) {
                 'maxConcurrency' in event && typeof event.maxConcurrency === 'number'
                   ? event.maxConcurrency
                   : getMaxConcurrencyForWorktree(eventProjectId, eventBranchName);
+              // Always apply start events even during transitions - this confirms the optimistic state
               setAutoModeRunning(eventProjectId, eventBranchName, true, eventMaxConcurrency);
             }
+            // If we were in a restart transition (concurrency change), the arrival of
+            // auto_mode_started confirms the restart is complete. Clear the transition
+            // flags so future auto_mode_stopped events are processed normally.
+            // Only clear transition refs when the event is for this hook's worktree,
+            // to avoid events for worktree B incorrectly affecting worktree A's state.
+            if (isRestartTransitionRef.current && eventBranchName === branchName) {
+              logger.debug(`[AutoMode] Restart transition complete for ${worktreeDesc}`);
+              isTransitioningRef.current = false;
+              isRestartTransitionRef.current = false;
+              if (restartSafetyTimeoutRef.current) {
+                clearTimeout(restartSafetyTimeoutRef.current);
+                restartSafetyTimeoutRef.current = null;
+              }
+            }
           }
           break;
 
@@ -307,12 +359,23 @@ export function useAutoMode(worktree?: WorktreeInfo) {
           break;
 
         case 'auto_mode_stopped':
-          // Backend stopped auto loop - update UI state
+          // Backend stopped auto loop - update UI state.
+          // Skip during transitions (e.g., restartWithConcurrency) to avoid flickering the toggle
+          // off between stop and start. The transition handler will set the correct final state.
+          // Only suppress (and only apply transition guard) when the event is for this hook's
+          // worktree, to avoid worktree B's stop events being incorrectly suppressed by
+          // worktree A's transition state.
           {
             const worktreeDesc = eventBranchName ? `worktree ${eventBranchName}` : 'main worktree';
-            logger.info(`[AutoMode] Backend stopped auto loop for ${worktreeDesc}`);
+            if (eventBranchName === branchName && isTransitioningRef.current) {
-            if (eventProjectId) {
+              logger.info(
-              setAutoModeRunning(eventProjectId, eventBranchName, false);
+                `[AutoMode] Backend stopped auto loop for ${worktreeDesc} (ignored during transition)`
+              );
+            } else {
+              logger.info(`[AutoMode] Backend stopped auto loop for ${worktreeDesc}`);
+              if (eventProjectId) {
+                setAutoModeRunning(eventProjectId, eventBranchName, false);
+              }
             }
           }
           break;
@@ -574,6 +637,7 @@ export function useAutoMode(worktree?: WorktreeInfo) {
     return unsubscribe;
   }, [
     projectId,
+    branchName,
     addRunningTask,
     removeRunningTask,
     addAutoModeActivity,
@@ -582,7 +646,6 @@ export function useAutoMode(worktree?: WorktreeInfo) {
     setAutoModeRunning,
     currentProject?.path,
     getMaxConcurrencyForWorktree,
-    setMaxConcurrencyForWorktree,
     isPrimaryWorktreeBranch,
   ]);
 
@@ -624,8 +687,10 @@ export function useAutoMode(worktree?: WorktreeInfo) {
       }
 
       logger.debug(`[AutoMode] Started successfully for ${worktreeDesc}`);
-      // Sync with backend after success (gets runningFeatures if events were delayed)
+      // Sync with backend after a short delay to get runningFeatures if events were delayed.
-      queueMicrotask(() => void refreshStatus());
+      // The delay ensures the backend has fully processed the start before we poll status,
+      // avoiding a race where status returns stale data and briefly flickers the toggle.
+      setTimeout(() => void refreshStatus(), 500);
     } catch (error) {
       // Revert UI state on error
       setAutoModeSessionForWorktree(currentProject.path, branchName, false);
@@ -635,7 +700,7 @@ export function useAutoMode(worktree?: WorktreeInfo) {
     } finally {
       isTransitioningRef.current = false;
     }
-  }, [currentProject, branchName, setAutoModeRunning, getMaxConcurrencyForWorktree]);
+  }, [currentProject, branchName, setAutoModeRunning, getMaxConcurrencyForWorktree, refreshStatus]);
 
   // Stop auto mode - calls backend to stop the auto loop for this worktree
   const stop = useCallback(async () => {
@@ -672,8 +737,8 @@ export function useAutoMode(worktree?: WorktreeInfo) {
       // NOTE: Running tasks will continue until natural completion.
       // The backend stops picking up new features but doesn't abort running ones.
       logger.info(`Stopped ${worktreeDesc} - running tasks will continue`);
-      // Sync with backend after success
+      // Sync with backend after a short delay to confirm stopped state
-      queueMicrotask(() => void refreshStatus());
+      setTimeout(() => void refreshStatus(), 500);
     } catch (error) {
       // Revert UI state on error
       setAutoModeSessionForWorktree(currentProject.path, branchName, true);
@@ -683,7 +748,95 @@ export function useAutoMode(worktree?: WorktreeInfo) {
     } finally {
       isTransitioningRef.current = false;
     }
-  }, [currentProject, branchName, setAutoModeRunning]);
+  }, [currentProject, branchName, setAutoModeRunning, refreshStatus]);
+
+  // Restart auto mode with new concurrency without flickering the toggle.
+  // Unlike stop() + start(), this keeps isRunning=true throughout the transition
+  // so the toggle switch never visually turns off.
+  //
+  // IMPORTANT: isTransitioningRef is NOT cleared in the finally block here.
+  // Instead, it stays true until the auto_mode_started WebSocket event arrives,
+  // which confirms the backend restart is complete. This prevents a race condition
+  // where a delayed auto_mode_stopped WebSocket event (sent by the backend during
+  // stop()) arrives after the HTTP calls complete but before the WebSocket events,
+  // which would briefly set isRunning=false and cause a visible toggle flicker.
+  // A safety timeout ensures the flag is cleared even if the event never arrives.
+  const restartWithConcurrency = useCallback(async () => {
+    if (!currentProject) {
+      logger.error('No project selected');
+      return;
+    }
+
+    // Clear any previous safety timeout
+    if (restartSafetyTimeoutRef.current) {
+      clearTimeout(restartSafetyTimeoutRef.current);
+      restartSafetyTimeoutRef.current = null;
+    }
+
+    isTransitioningRef.current = true;
+    isRestartTransitionRef.current = true;
+    try {
+      const api = getElectronAPI();
+      if (!api?.autoMode?.stop || !api?.autoMode?.start) {
+        throw new Error('Auto mode API not available');
+      }
+
+      const worktreeDesc = branchName ? `worktree ${branchName}` : 'main worktree';
+      logger.info(
+        `[AutoMode] Restarting with new concurrency for ${worktreeDesc} in ${currentProject.path}`
+      );
+
+      // Stop backend without updating UI state (keep isRunning=true)
+      const stopResult = await api.autoMode.stop(currentProject.path, branchName);
+
+      if (!stopResult.success) {
+        logger.error('Failed to stop auto mode during restart:', stopResult.error);
+        // Don't throw - try to start anyway since the goal is to update concurrency
+      }
+
+      // Start backend with the new concurrency (UI state stays isRunning=true)
+      const currentMaxConcurrency = getMaxConcurrencyForWorktree(currentProject.id, branchName);
+      const startResult = await api.autoMode.start(
+        currentProject.path,
+        branchName,
+        currentMaxConcurrency
+      );
+
+      if (!startResult.success) {
+        // If start fails, we need to revert UI state since we're actually stopped now
+        isTransitioningRef.current = false;
+        isRestartTransitionRef.current = false;
+        setAutoModeSessionForWorktree(currentProject.path, branchName, false);
+        setAutoModeRunning(currentProject.id, branchName, false);
+        logger.error('Failed to restart auto mode with new concurrency:', startResult.error);
+        throw new Error(startResult.error || 'Failed to restart auto mode');
+      }
+
+      logger.debug(`[AutoMode] Restarted successfully for ${worktreeDesc}`);
+
+      // Don't clear isTransitioningRef here - let the auto_mode_started WebSocket
+      // event handler clear it. Set a safety timeout in case the event never arrives.
+      restartSafetyTimeoutRef.current = setTimeout(() => {
+        if (isRestartTransitionRef.current) {
+          logger.warn('[AutoMode] Restart transition safety timeout - clearing transition flag');
+          isTransitioningRef.current = false;
+          isRestartTransitionRef.current = false;
+          restartSafetyTimeoutRef.current = null;
+        }
+      }, 5000);
+    } catch (error) {
+      // On error, clear the transition flags immediately
+      isTransitioningRef.current = false;
+      isRestartTransitionRef.current = false;
+      // Revert UI state since the backend may be stopped after a partial restart
+      if (currentProject) {
+        setAutoModeSessionForWorktree(currentProject.path, branchName, false);
+        setAutoModeRunning(currentProject.id, branchName, false);
+      }
+      logger.error('Error restarting auto mode:', error);
+      throw error;
+    }
+  }, [currentProject, branchName, setAutoModeRunning, getMaxConcurrencyForWorktree]);
 
   // Stop a specific feature
   const stopFeature = useCallback(
@@ -731,6 +884,7 @@ export function useAutoMode(worktree?: WorktreeInfo) {
     start,
     stop,
     stopFeature,
+    restartWithConcurrency,
     refreshStatus,
   };
 }

apps/ui/src/hooks/use-settings-migration.ts

@@ -166,6 +166,7 @@ export function parseLocalStorageSettings(): Partial<GlobalSettings> | null {
       defaultSkipTests: state.defaultSkipTests as boolean,
       enableDependencyBlocking: state.enableDependencyBlocking as boolean,
       skipVerificationInAutoMode: state.skipVerificationInAutoMode as boolean,
+      mergePostAction: (state.mergePostAction as 'commit' | 'manual' | null) ?? null,
       useWorktrees: state.useWorktrees as boolean,
       defaultPlanningMode: state.defaultPlanningMode as GlobalSettings['defaultPlanningMode'],
       defaultRequirePlanApproval: state.defaultRequirePlanApproval as boolean,
@@ -704,6 +705,7 @@ export function hydrateStoreFromSettings(settings: GlobalSettings): void {
     defaultSkipTests: settings.defaultSkipTests ?? true,
     enableDependencyBlocking: settings.enableDependencyBlocking ?? true,
     skipVerificationInAutoMode: settings.skipVerificationInAutoMode ?? false,
+    mergePostAction: settings.mergePostAction ?? null,
     useWorktrees: settings.useWorktrees ?? true,
     defaultPlanningMode: settings.defaultPlanningMode ?? 'skip',
     defaultRequirePlanApproval: settings.defaultRequirePlanApproval ?? false,
@@ -718,6 +720,8 @@ export function hydrateStoreFromSettings(settings: GlobalSettings): void {
     enhancementModel: settings.enhancementModel ?? 'claude-sonnet',
     validationModel: settings.validationModel ?? 'claude-opus',
     phaseModels: settings.phaseModels ?? current.phaseModels,
+    defaultThinkingLevel: settings.defaultThinkingLevel ?? 'none',
+    defaultReasoningEffort: settings.defaultReasoningEffort ?? 'none',
     enabledCursorModels: allCursorModels, // Always use ALL cursor models
     cursorDefaultModel: sanitizedCursorDefaultModel,
     enabledOpencodeModels: sanitizedEnabledOpencodeModels,
@@ -749,6 +753,7 @@ export function hydrateStoreFromSettings(settings: GlobalSettings): void {
     projectHistory: settings.projectHistory ?? [],
     projectHistoryIndex: settings.projectHistoryIndex ?? -1,
     lastSelectedSessionByProject: settings.lastSelectedSessionByProject ?? {},
+    currentWorktreeByProject: settings.currentWorktreeByProject ?? {},
     // UI State
     worktreePanelCollapsed: settings.worktreePanelCollapsed ?? false,
     lastProjectDir: settings.lastProjectDir ?? '',
@@ -802,6 +807,7 @@ function buildSettingsUpdateFromStore(): Record<string, unknown> {
     defaultSkipTests: state.defaultSkipTests,
     enableDependencyBlocking: state.enableDependencyBlocking,
     skipVerificationInAutoMode: state.skipVerificationInAutoMode,
+    mergePostAction: state.mergePostAction,
     useWorktrees: state.useWorktrees,
     defaultPlanningMode: state.defaultPlanningMode,
     defaultRequirePlanApproval: state.defaultRequirePlanApproval,
@@ -812,6 +818,8 @@ function buildSettingsUpdateFromStore(): Record<string, unknown> {
     enhancementModel: state.enhancementModel,
     validationModel: state.validationModel,
     phaseModels: state.phaseModels,
+    defaultThinkingLevel: state.defaultThinkingLevel,
+    defaultReasoningEffort: state.defaultReasoningEffort,
     enabledDynamicModelIds: state.enabledDynamicModelIds,
     disabledProviders: state.disabledProviders,
     autoLoadClaudeMd: state.autoLoadClaudeMd,
@@ -836,6 +844,7 @@ function buildSettingsUpdateFromStore(): Record<string, unknown> {
     projectHistory: state.projectHistory,
     projectHistoryIndex: state.projectHistoryIndex,
     lastSelectedSessionByProject: state.lastSelectedSessionByProject,
+    currentWorktreeByProject: state.currentWorktreeByProject,
     worktreePanelCollapsed: state.worktreePanelCollapsed,
     lastProjectDir: state.lastProjectDir,
     recentFolders: state.recentFolders,

apps/ui/src/hooks/use-settings-sync.ts

@@ -58,6 +58,7 @@ const SETTINGS_FIELDS_TO_SYNC = [
   'defaultSkipTests',
   'enableDependencyBlocking',
   'skipVerificationInAutoMode',
+  'mergePostAction',
   'useWorktrees',
   'defaultPlanningMode',
   'defaultRequirePlanApproval',
@@ -717,6 +718,7 @@ export async function refreshSettingsFromServer(): Promise<boolean> {
       defaultSkipTests: serverSettings.defaultSkipTests,
       enableDependencyBlocking: serverSettings.enableDependencyBlocking,
       skipVerificationInAutoMode: serverSettings.skipVerificationInAutoMode,
+      mergePostAction: serverSettings.mergePostAction ?? null,
       useWorktrees: serverSettings.useWorktrees,
       defaultPlanningMode: serverSettings.defaultPlanningMode,
       defaultRequirePlanApproval: serverSettings.defaultRequirePlanApproval,

apps/ui/src/lib/clipboard-utils.ts

@@ -0,0 +1,145 @@
+/**
+ * Clipboard utility functions with fallbacks for non-HTTPS (insecure) contexts.
+ *
+ * The modern Clipboard API (`navigator.clipboard`) requires a Secure Context (HTTPS).
+ * When running on HTTP, these APIs are unavailable or throw errors.
+ * This module provides `writeToClipboard` and `readFromClipboard` that automatically
+ * fall back to the legacy `document.execCommand` approach using a hidden textarea.
+ */
+
+/**
+ * Check whether the modern Clipboard API is available.
+ * It requires a secure context (HTTPS or localhost) and the API to exist.
+ */
+function isClipboardApiAvailable(): boolean {
+  return (
+    typeof navigator !== 'undefined' &&
+    !!navigator.clipboard &&
+    typeof navigator.clipboard.writeText === 'function' &&
+    typeof navigator.clipboard.readText === 'function' &&
+    typeof window !== 'undefined' &&
+    window.isSecureContext !== false
+  );
+}
+
+/**
+ * Write text to the clipboard using the modern Clipboard API with a
+ * fallback to `document.execCommand('copy')` for insecure contexts.
+ *
+ * @param text - The text to write to the clipboard.
+ * @returns `true` if the text was successfully copied; `false` otherwise.
+ */
+export async function writeToClipboard(text: string): Promise<boolean> {
+  // Try the modern Clipboard API first
+  if (isClipboardApiAvailable()) {
+    try {
+      await navigator.clipboard.writeText(text);
+      return true;
+    } catch {
+      // Fall through to legacy approach
+    }
+  }
+
+  // Legacy fallback using a hidden textarea + execCommand
+  return writeToClipboardLegacy(text);
+}
+
+/**
+ * Read text from the clipboard using the modern Clipboard API with a
+ * fallback to `document.execCommand('paste')` for insecure contexts.
+ *
+ * Note: The legacy fallback for *reading* is limited. `document.execCommand('paste')`
+ * only works in some browsers (mainly older ones). On modern browsers in insecure
+ * contexts, reading from the clipboard may not be possible at all. In those cases,
+ * this function throws an error so the caller can show an appropriate message.
+ *
+ * @returns The text from the clipboard.
+ * @throws If clipboard reading is not supported or permission is denied.
+ */
+export async function readFromClipboard(): Promise<string> {
+  // Try the modern Clipboard API first
+  if (isClipboardApiAvailable()) {
+    try {
+      return await navigator.clipboard.readText();
+    } catch (err) {
+      // Check if this is a permission-related error
+      if (err instanceof Error) {
+        // Re-throw permission errors so they propagate to the caller
+        if (err.name === 'NotAllowedError' || err.name === 'NotReadableError') {
+          throw err;
+        }
+      }
+      // For other errors, fall through to legacy approach
+    }
+  }
+
+  // Legacy fallback using a hidden textarea + execCommand
+  return readFromClipboardLegacy();
+}
+
+/**
+ * Legacy clipboard write using a hidden textarea and `document.execCommand('copy')`.
+ * This works in both secure and insecure contexts in most browsers.
+ */
+function writeToClipboardLegacy(text: string): boolean {
+  const textarea = document.createElement('textarea');
+  textarea.value = text;
+
+  // Prevent scrolling and make invisible
+  textarea.style.position = 'fixed';
+  textarea.style.left = '-9999px';
+  textarea.style.top = '-9999px';
+  textarea.style.opacity = '0';
+
+  document.body.appendChild(textarea);
+
+  try {
+    textarea.select();
+    textarea.setSelectionRange(0, text.length);
+    const success = document.execCommand('copy');
+    return success;
+  } catch {
+    return false;
+  } finally {
+    document.body.removeChild(textarea);
+  }
+}
+
+/**
+ * Legacy clipboard read using a hidden textarea and `document.execCommand('paste')`.
+ * This has very limited browser support. Most modern browsers block this for security.
+ * When it fails, we throw an error to let the caller handle it gracefully.
+ */
+function readFromClipboardLegacy(): string {
+  const textarea = document.createElement('textarea');
+
+  // Prevent scrolling and make invisible
+  textarea.style.position = 'fixed';
+  textarea.style.left = '-9999px';
+  textarea.style.top = '-9999px';
+  textarea.style.opacity = '0';
+
+  document.body.appendChild(textarea);
+  textarea.focus();
+
+  try {
+    const success = document.execCommand('paste');
+    if (success && textarea.value) {
+      return textarea.value;
+    }
+    throw new Error(
+      'Clipboard paste is not supported in this browser on non-HTTPS sites. ' +
+        'Please use HTTPS or paste manually with keyboard shortcuts.'
+    );
+  } catch (err) {
+    if (err instanceof Error && err.message.includes('Clipboard paste is not supported')) {
+      throw err;
+    }
+    throw new Error(
+      'Clipboard paste is not supported in this browser on non-HTTPS sites. ' +
+        'Please use HTTPS or paste manually with keyboard shortcuts.'
+    );
+  } finally {
+    document.body.removeChild(textarea);
+  }
+}

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

@@ -568,6 +568,7 @@ type EventType =
   | 'dev-server:started'
   | 'dev-server:output'
   | 'dev-server:stopped'
+  | 'dev-server:url-detected'
   | 'test-runner:started'
   | 'test-runner:output'
   | 'test-runner:completed'
@@ -576,13 +577,17 @@ type EventType =
 /**
  * Dev server log event payloads for WebSocket streaming
  */
-export interface DevServerStartedEvent {
+
+/** Shared base for dev server events that carry URL/port information */
+interface DevServerUrlEvent {
   worktreePath: string;
-  port: number;
   url: string;
+  port: number;
   timestamp: string;
 }
 
+export type DevServerStartedEvent = DevServerUrlEvent;
+
 export interface DevServerOutputEvent {
   worktreePath: string;
   content: string;
@@ -597,10 +602,13 @@ export interface DevServerStoppedEvent {
   timestamp: string;
 }
 
+export type DevServerUrlDetectedEvent = DevServerUrlEvent;
+
 export type DevServerLogEvent =
   | { type: 'dev-server:started'; payload: DevServerStartedEvent }
   | { type: 'dev-server:output'; payload: DevServerOutputEvent }
-  | { type: 'dev-server:stopped'; payload: DevServerStoppedEvent };
+  | { type: 'dev-server:stopped'; payload: DevServerStoppedEvent }
+  | { type: 'dev-server:url-detected'; payload: DevServerUrlDetectedEvent };
 
 /**
  * Test runner event payloads for WebSocket streaming
@@ -2204,10 +2212,14 @@ export class HttpApiClient implements ElectronAPI {
       const unsub3 = this.subscribeToEvent('dev-server:stopped', (payload) =>
         callback({ type: 'dev-server:stopped', payload: payload as DevServerStoppedEvent })
       );
+      const unsub4 = this.subscribeToEvent('dev-server:url-detected', (payload) =>
+        callback({ type: 'dev-server:url-detected', payload: payload as DevServerUrlDetectedEvent })
+      );
       return () => {
         unsub1();
         unsub2();
         unsub3();
+        unsub4();
       };
     },
     getPRInfo: (worktreePath: string, branchName: string) =>

apps/ui/src/routes/__root.tsx

@@ -305,6 +305,7 @@ function RootLayoutContent() {
         sidebarStyle: state.sidebarStyle,
         worktreePanelCollapsed: state.worktreePanelCollapsed,
         collapsedNavSections: state.collapsedNavSections,
+        currentWorktreeByProject: state.currentWorktreeByProject,
       });
     });
     return unsubscribe;

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

@@ -298,6 +298,7 @@ const initialState: AppState = {
   enableDependencyBlocking: true,
   skipVerificationInAutoMode: false,
   enableAiCommitMessages: true,
+  mergePostAction: null,
   planUseSelectedWorktreeBranch: true,
   addFeatureUseSelectedWorktreeBranch: false,
   useWorktrees: true,
@@ -362,6 +363,8 @@ const initialState: AppState = {
   defaultPlanningMode: 'skip' as PlanningMode,
   defaultRequirePlanApproval: false,
   defaultFeatureModel: DEFAULT_GLOBAL_SETTINGS.defaultFeatureModel,
+  defaultThinkingLevel: DEFAULT_GLOBAL_SETTINGS.defaultThinkingLevel ?? 'none',
+  defaultReasoningEffort: DEFAULT_GLOBAL_SETTINGS.defaultReasoningEffort ?? 'none',
   pendingPlanApproval: null,
   claudeRefreshInterval: 60,
   claudeUsage: null,
@@ -1117,6 +1120,16 @@ export const useAppStore = create<AppState & AppActions>()((set, get) => ({
       logger.error('Failed to sync enableAiCommitMessages:', error);
     }
   },
+  setMergePostAction: async (action) => {
+    set({ mergePostAction: action });
+    // Sync to server
+    try {
+      const httpApi = getHttpApiClient();
+      await httpApi.put('/api/settings', { mergePostAction: action });
+    } catch (error) {
+      logger.error('Failed to sync mergePostAction:', error);
+    }
+  },
   setPlanUseSelectedWorktreeBranch: async (enabled) => {
     set({ planUseSelectedWorktreeBranch: enabled });
     // Sync to server
@@ -2313,6 +2326,28 @@ export const useAppStore = create<AppState & AppActions>()((set, get) => ({
   setDefaultRequirePlanApproval: (require) => set({ defaultRequirePlanApproval: require }),
   setDefaultFeatureModel: (entry) => set({ defaultFeatureModel: entry }),
 
+  setDefaultThinkingLevel: async (level) => {
+    set({ defaultThinkingLevel: level });
+    // Sync to server
+    try {
+      const httpApi = getHttpApiClient();
+      await httpApi.put('/api/settings', { defaultThinkingLevel: level });
+    } catch (error) {
+      logger.error('Failed to sync defaultThinkingLevel:', error);
+    }
+  },
+
+  setDefaultReasoningEffort: async (effort) => {
+    set({ defaultReasoningEffort: effort });
+    // Sync to server
+    try {
+      const httpApi = getHttpApiClient();
+      await httpApi.put('/api/settings', { defaultReasoningEffort: effort });
+    } catch (error) {
+      logger.error('Failed to sync defaultReasoningEffort:', error);
+    }
+  },
+
   // Plan Approval actions
   setPendingPlanApproval: (approval) => set({ pendingPlanApproval: approval }),
 

apps/ui/src/store/types/state-types.ts

@@ -21,6 +21,8 @@ import type {
   ClaudeApiProfile,
   ClaudeCompatibleProvider,
   SidebarStyle,
+  ThinkingLevel,
+  ReasoningEffort,
 } from '@automaker/types';
 
 import type {
@@ -127,6 +129,7 @@ export interface AppState {
   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)
   enableAiCommitMessages: boolean; // When true, auto-generate commit messages using AI when opening commit dialog
+  mergePostAction: 'commit' | 'manual' | null; // User's preferred action after a clean merge (null = ask every time)
   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
 
@@ -175,6 +178,10 @@ export interface AppState {
   phaseModels: PhaseModelConfig;
   favoriteModels: string[];
 
+  // Default thinking/reasoning levels for two-stage model selector primary button
+  defaultThinkingLevel: ThinkingLevel;
+  defaultReasoningEffort: ReasoningEffort;
+
   // Cursor CLI Settings (global)
   enabledCursorModels: CursorModelId[]; // Which Cursor models are available in feature modal
   cursorDefaultModel: CursorModelId; // Default Cursor model selection
@@ -488,6 +495,7 @@ export interface AppActions {
   setEnableDependencyBlocking: (enabled: boolean) => void;
   setSkipVerificationInAutoMode: (enabled: boolean) => Promise<void>;
   setEnableAiCommitMessages: (enabled: boolean) => Promise<void>;
+  setMergePostAction: (action: 'commit' | 'manual' | null) => Promise<void>;
   setPlanUseSelectedWorktreeBranch: (enabled: boolean) => Promise<void>;
   setAddFeatureUseSelectedWorktreeBranch: (enabled: boolean) => Promise<void>;
 
@@ -548,6 +556,8 @@ export interface AppActions {
   setPhaseModels: (models: Partial<PhaseModelConfig>) => Promise<void>;
   resetPhaseModels: () => Promise<void>;
   toggleFavoriteModel: (modelId: string) => void;
+  setDefaultThinkingLevel: (level: ThinkingLevel) => void;
+  setDefaultReasoningEffort: (effort: ReasoningEffort) => void;
 
   // Cursor CLI Settings actions
   setEnabledCursorModels: (models: CursorModelId[]) => void;

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

@@ -35,6 +35,8 @@ interface UICacheState {
   cachedWorktreePanelCollapsed: boolean;
   /** Collapsed nav sections */
   cachedCollapsedNavSections: Record<string, boolean>;
+  /** Selected worktree per project (path + branch) for instant restore on PWA reload */
+  cachedCurrentWorktreeByProject: Record<string, { path: string | null; branch: string }>;
 }
 
 interface UICacheActions {
@@ -52,19 +54,29 @@ export const useUICacheStore = create<UICacheState & UICacheActions>()(
       cachedSidebarStyle: 'unified',
       cachedWorktreePanelCollapsed: false,
       cachedCollapsedNavSections: {},
+      cachedCurrentWorktreeByProject: {},
 
       updateFromAppStore: (state) => set(state),
     }),
     {
       name: STORE_NAME,
-      version: 1,
+      version: 2,
       partialize: (state) => ({
         cachedProjectId: state.cachedProjectId,
         cachedSidebarOpen: state.cachedSidebarOpen,
         cachedSidebarStyle: state.cachedSidebarStyle,
         cachedWorktreePanelCollapsed: state.cachedWorktreePanelCollapsed,
         cachedCollapsedNavSections: state.cachedCollapsedNavSections,
+        cachedCurrentWorktreeByProject: state.cachedCurrentWorktreeByProject,
       }),
+      migrate: (persistedState: unknown, version: number) => {
+        const state = persistedState as Record<string, unknown>;
+        if (version < 2) {
+          // Migration from v1: add cachedCurrentWorktreeByProject
+          state.cachedCurrentWorktreeByProject = {};
+        }
+        return state as unknown as UICacheState & UICacheActions;
+      },
     }
   )
 );
@@ -82,6 +94,7 @@ export function syncUICache(appState: {
   sidebarStyle?: 'unified' | 'discord';
   worktreePanelCollapsed?: boolean;
   collapsedNavSections?: Record<string, boolean>;
+  currentWorktreeByProject?: Record<string, { path: string | null; branch: string }>;
 }): void {
   const update: Partial<UICacheState> = {};
 
@@ -100,6 +113,9 @@ export function syncUICache(appState: {
   if ('collapsedNavSections' in appState) {
     update.cachedCollapsedNavSections = appState.collapsedNavSections;
   }
+  if ('currentWorktreeByProject' in appState) {
+    update.cachedCurrentWorktreeByProject = appState.currentWorktreeByProject;
+  }
 
   if (Object.keys(update).length > 0) {
     useUICacheStore.getState().updateFromAppStore(update);
@@ -142,6 +158,15 @@ export function restoreFromUICache(
     collapsedNavSections: cache.cachedCollapsedNavSections,
   };
 
+  // Restore last selected worktree per project so the board doesn't
+  // reset to main branch after PWA memory eviction or tab discard.
+  if (
+    cache.cachedCurrentWorktreeByProject &&
+    Object.keys(cache.cachedCurrentWorktreeByProject).length > 0
+  ) {
+    stateUpdate.currentWorktreeByProject = cache.cachedCurrentWorktreeByProject;
+  }
+
   // Restore the project context when the project object is available.
   // When projects are not yet loaded (empty array), currentProject remains
   // null and will be properly set later by hydrateStoreFromSettings().

apps/ui/src/styles/global.css

@@ -572,6 +572,34 @@
     }
   }
 
+  /* Safe-area-aware close button positioning for full-screen mobile dialogs.
+     On mobile, shift the close button down by the safe-area-inset-top so it
+     remains reachable and not hidden behind the notch or Dynamic Island.
+     On sm+ (desktop), use standard top positioning. */
+  .dialog-fullscreen-mobile [data-slot='dialog-close'] {
+    top: calc(env(safe-area-inset-top, 0px) + 0.75rem);
+  }
+
+  @media (min-width: 640px) {
+    .dialog-fullscreen-mobile [data-slot='dialog-close'] {
+      top: 0.75rem;
+    }
+  }
+
+  /* Safe-area-aware top padding for compact dialog headers (p-0 dialogs with own header).
+     Ensures the header content starts below the Dynamic Island / notch on iOS.
+     Used in dev-server-logs and test-logs panels that use p-0 on DialogContent.
+     On sm+ (desktop), the dialog is centered so no safe-area adjustment needed. */
+  .dialog-compact-header-mobile {
+    padding-top: calc(env(safe-area-inset-top, 0px) + 0.75rem);
+  }
+
+  @media (min-width: 640px) {
+    .dialog-compact-header-mobile {
+      padding-top: 0.75rem;
+    }
+  }
+
   .glass-subtle {
     @apply backdrop-blur-sm border-white/5;
   }

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

@@ -8,7 +8,7 @@ import type {
   ZaiUsageResponse,
   GeminiUsageResponse,
 } from '@/store/app-store';
-import type { ParsedTask, FeatureStatusWithPipeline } from '@automaker/types';
+import type { ParsedTask, FeatureStatusWithPipeline, MergeStateInfo } from '@automaker/types';
 
 export interface ImageAttachment {
   id?: string; // Optional - may not be present in messages loaded from server
@@ -759,6 +759,10 @@ export interface FileStatus {
   indexStatus?: string;
   /** Raw working tree status character from git porcelain format */
   workTreeStatus?: string;
+  /** Whether this file is involved in a merge operation */
+  isMergeAffected?: boolean;
+  /** Type of merge involvement (e.g. 'both-modified', 'added-by-us', etc.) */
+  mergeType?: string;
 }
 
 export interface FileDiffsResult {
@@ -767,6 +771,8 @@ export interface FileDiffsResult {
   files?: FileStatus[];
   hasChanges?: boolean;
   error?: string;
+  /** Merge state info, present when a merge/rebase/cherry-pick is in progress */
+  mergeState?: MergeStateInfo;
 }
 
 export interface FileDiffResult {
@@ -1286,6 +1292,7 @@ export interface WorktreeAPI {
         worktreePath: string;
         port: number;
         url: string;
+        urlDetected: boolean;
       }>;
     };
     error?: string;
@@ -1304,7 +1311,7 @@ export interface WorktreeAPI {
     error?: string;
   }>;
 
-  // Subscribe to dev server log events (started, output, stopped)
+  // Subscribe to dev server log events (started, output, stopped, url-detected)
   onDevServerLogEvent: (
     callback: (
       event:
@@ -1326,6 +1333,15 @@ export interface WorktreeAPI {
               timestamp: string;
             };
           }
+        | {
+            type: 'dev-server:url-detected';
+            payload: {
+              worktreePath: string;
+              url: string;
+              port: number;
+              timestamp: string;
+            };
+          }
     ) => void
   ) => () => void;
 

apps/ui/tests/features/running-task-card-display.spec.ts

@@ -0,0 +1,211 @@
+/**
+ * Running Task Card Display E2E Test
+ *
+ * Tests that task cards with a running state display the correct UI controls.
+ *
+ * This test verifies that:
+ * 1. A feature in the in_progress column with status 'in_progress' shows Logs/Stop controls (not Make)
+ * 2. A feature with status 'backlog' that is tracked as running (stale status race condition)
+ *    shows Logs/Stop controls instead of the Make button when placed in in_progress column
+ * 3. The Make button only appears for genuinely idle backlog/interrupted/ready features
+ * 4. Features in backlog that are NOT running show the correct Edit/Make buttons
+ */
+
+import { test, expect } from '@playwright/test';
+import * as fs from 'fs';
+import * as path from 'path';
+import {
+  createTempDirPath,
+  cleanupTempDir,
+  setupRealProject,
+  waitForNetworkIdle,
+  getKanbanColumn,
+  authenticateForTests,
+  handleLoginScreenIfPresent,
+} from '../utils';
+
+const TEST_TEMP_DIR = createTempDirPath('running-task-display-test');
+
+// Generate deterministic projectId once at test module load
+const TEST_PROJECT_ID = `project-running-task-${Date.now()}`;
+
+test.describe('Running Task Card Display', () => {
+  let projectPath: string;
+  const projectName = `test-project-${Date.now()}`;
+  const backlogFeatureId = 'test-feature-backlog';
+  const inProgressFeatureId = 'test-feature-in-progress';
+
+  test.beforeAll(async () => {
+    if (!fs.existsSync(TEST_TEMP_DIR)) {
+      fs.mkdirSync(TEST_TEMP_DIR, { recursive: true });
+    }
+
+    projectPath = path.join(TEST_TEMP_DIR, projectName);
+    fs.mkdirSync(projectPath, { recursive: true });
+
+    fs.writeFileSync(
+      path.join(projectPath, 'package.json'),
+      JSON.stringify({ name: projectName, version: '1.0.0' }, null, 2)
+    );
+
+    const automakerDir = path.join(projectPath, '.automaker');
+    fs.mkdirSync(automakerDir, { recursive: true });
+    fs.mkdirSync(path.join(automakerDir, 'features'), { recursive: true });
+    fs.mkdirSync(path.join(automakerDir, 'context'), { recursive: true });
+
+    fs.writeFileSync(
+      path.join(automakerDir, 'categories.json'),
+      JSON.stringify({ categories: [] }, null, 2)
+    );
+
+    fs.writeFileSync(
+      path.join(automakerDir, 'app_spec.txt'),
+      `# ${projectName}\n\nA test project for e2e testing.`
+    );
+  });
+
+  test.afterAll(async () => {
+    cleanupTempDir(TEST_TEMP_DIR);
+  });
+
+  test('should show Logs/Stop buttons for in_progress features, not Make button', async ({
+    page,
+  }) => {
+    // Set up the project in localStorage with a deterministic projectId
+    await setupRealProject(page, projectPath, projectName, {
+      setAsCurrent: true,
+      projectId: TEST_PROJECT_ID,
+    });
+
+    // Intercept settings API to ensure our test project remains current
+    await page.route('**/api/settings/global', async (route) => {
+      const method = route.request().method();
+      if (method === 'PUT') {
+        return route.continue();
+      }
+      const response = await route.fetch();
+      const json = await response.json();
+      if (json.settings) {
+        const existingProjects = json.settings.projects || [];
+        let testProject = existingProjects.find((p: { path: string }) => p.path === projectPath);
+        if (!testProject) {
+          testProject = {
+            id: TEST_PROJECT_ID,
+            name: projectName,
+            path: projectPath,
+            lastOpened: new Date().toISOString(),
+          };
+          json.settings.projects = [testProject, ...existingProjects];
+        }
+        json.settings.currentProjectId = testProject.id;
+        json.settings.setupComplete = true;
+        json.settings.isFirstRun = false;
+      }
+      await route.fulfill({ response, json });
+    });
+
+    await authenticateForTests(page);
+
+    // Navigate to board
+    await page.goto('/board');
+    await page.waitForLoadState('load');
+    await handleLoginScreenIfPresent(page);
+    await waitForNetworkIdle(page);
+    await expect(page.locator('[data-testid="board-view"]')).toBeVisible({ timeout: 10000 });
+
+    // Create a feature that is already in_progress status (simulates a running task)
+    const inProgressFeature = {
+      id: inProgressFeatureId,
+      description: 'Test feature that is currently running',
+      category: 'test',
+      status: 'in_progress',
+      skipTests: false,
+      model: 'sonnet',
+      thinkingLevel: 'none',
+      createdAt: new Date().toISOString(),
+      startedAt: new Date().toISOString(),
+      branchName: '',
+      priority: 2,
+    };
+
+    // Create a feature in backlog status (idle, should show Make button)
+    const backlogFeature = {
+      id: backlogFeatureId,
+      description: 'Test feature in backlog waiting to start',
+      category: 'test',
+      status: 'backlog',
+      skipTests: false,
+      model: 'sonnet',
+      thinkingLevel: 'none',
+      createdAt: new Date().toISOString(),
+      branchName: '',
+      priority: 2,
+    };
+
+    const API_BASE_URL = process.env.SERVER_URL || 'http://localhost:3008';
+
+    // Create both features via HTTP API
+    const createInProgress = await page.request.post(`${API_BASE_URL}/api/features/create`, {
+      data: { projectPath, feature: inProgressFeature },
+      headers: { 'Content-Type': 'application/json' },
+    });
+    if (!createInProgress.ok()) {
+      throw new Error(`Failed to create in_progress feature: ${await createInProgress.text()}`);
+    }
+
+    const createBacklog = await page.request.post(`${API_BASE_URL}/api/features/create`, {
+      data: { projectPath, feature: backlogFeature },
+      headers: { 'Content-Type': 'application/json' },
+    });
+    if (!createBacklog.ok()) {
+      throw new Error(`Failed to create backlog feature: ${await createBacklog.text()}`);
+    }
+
+    // Reload to pick up the new features
+    await page.reload();
+    await page.waitForLoadState('load');
+    await handleLoginScreenIfPresent(page);
+    await waitForNetworkIdle(page);
+    await expect(page.locator('[data-testid="board-view"]')).toBeVisible({ timeout: 10000 });
+
+    // Wait for both feature cards to appear
+    const inProgressCard = page.locator(`[data-testid="kanban-card-${inProgressFeatureId}"]`);
+    const backlogCard = page.locator(`[data-testid="kanban-card-${backlogFeatureId}"]`);
+    await expect(inProgressCard).toBeVisible({ timeout: 20000 });
+    await expect(backlogCard).toBeVisible({ timeout: 20000 });
+
+    // Verify the in_progress feature is in the in_progress column
+    const inProgressColumn = await getKanbanColumn(page, 'in_progress');
+    await expect(inProgressColumn).toBeVisible({ timeout: 5000 });
+    const cardInInProgress = inProgressColumn.locator(
+      `[data-testid="kanban-card-${inProgressFeatureId}"]`
+    );
+    await expect(cardInInProgress).toBeVisible({ timeout: 5000 });
+
+    // Verify the backlog feature is in the backlog column
+    const backlogColumn = await getKanbanColumn(page, 'backlog');
+    await expect(backlogColumn).toBeVisible({ timeout: 5000 });
+    const cardInBacklog = backlogColumn.locator(`[data-testid="kanban-card-${backlogFeatureId}"]`);
+    await expect(cardInBacklog).toBeVisible({ timeout: 5000 });
+
+    // CRITICAL: Verify the in_progress feature does NOT show a Make button
+    // The Make button should only appear on backlog/interrupted/ready features that are NOT running
+    const makeButtonOnInProgress = page.locator(`[data-testid="make-${inProgressFeatureId}"]`);
+    await expect(makeButtonOnInProgress).not.toBeVisible({ timeout: 3000 });
+
+    // Verify the in_progress feature shows appropriate controls
+    // (view-output/force-stop buttons should be present for in_progress without error)
+    const viewOutputButton = page.locator(`[data-testid="view-output-${inProgressFeatureId}"]`);
+    await expect(viewOutputButton).toBeVisible({ timeout: 5000 });
+    const forceStopButton = page.locator(`[data-testid="force-stop-${inProgressFeatureId}"]`);
+    await expect(forceStopButton).toBeVisible({ timeout: 5000 });
+
+    // Verify the backlog feature DOES show a Make button
+    const makeButtonOnBacklog = page.locator(`[data-testid="make-${backlogFeatureId}"]`);
+    await expect(makeButtonOnBacklog).toBeVisible({ timeout: 5000 });
+
+    // Verify the backlog feature also shows an Edit button
+    const editButton = page.locator(`[data-testid="edit-backlog-${backlogFeatureId}"]`);
+    await expect(editButton).toBeVisible({ timeout: 5000 });
+  });
+});

libs/git-utils/src/diff.ts

@@ -7,8 +7,8 @@ import { secureFs } from '@automaker/platform';
 import path from 'path';
 import { exec } from 'child_process';
 import { promisify } from 'util';
-import { BINARY_EXTENSIONS, type FileStatus } from './types.js';
+import { BINARY_EXTENSIONS, type FileStatus, type MergeStateInfo } from './types.js';
-import { isGitRepo, parseGitStatus } from './status.js';
+import { isGitRepo, parseGitStatus, detectMergeState, detectMergeCommit } from './status.js';
 
 const execAsync = promisify(exec);
 const logger = createLogger('GitUtils');
@@ -243,11 +243,15 @@ export async function generateDiffsForNonGitDirectory(
 
 /**
  * Get git repository diffs for a given path
- * Handles both git repos and non-git directories
+ * Handles both git repos and non-git directories.
+ * Also detects merge state and annotates files accordingly.
  */
-export async function getGitRepositoryDiffs(
+export async function getGitRepositoryDiffs(repoPath: string): Promise<{
-  repoPath: string
+  diff: string;
-): Promise<{ diff: string; files: FileStatus[]; hasChanges: boolean }> {
+  files: FileStatus[];
+  hasChanges: boolean;
+  mergeState?: MergeStateInfo;
+}> {
   // Check if it's a git repository
   const isRepo = await isGitRepo(repoPath);
 
@@ -273,11 +277,133 @@ export async function getGitRepositoryDiffs(
   const files = parseGitStatus(status);
 
   // Generate synthetic diffs for untracked (new) files
-  const combinedDiff = await appendUntrackedFileDiffs(repoPath, diff, files);
+  let combinedDiff = await appendUntrackedFileDiffs(repoPath, diff, files);
+
+  // Detect merge state (in-progress merge/rebase/cherry-pick)
+  const mergeState = await detectMergeState(repoPath);
+
+  // If no in-progress merge, check if HEAD is a completed merge commit
+  // and include merge commit changes in the diff and file list
+  if (!mergeState.isMerging) {
+    const mergeCommitInfo = await detectMergeCommit(repoPath);
+
+    if (mergeCommitInfo.isMergeCommit && mergeCommitInfo.mergeAffectedFiles.length > 0) {
+      // Get the diff of the merge commit relative to first parent
+      try {
+        const { stdout: mergeDiff } = await execAsync('git diff HEAD~1 HEAD', {
+          cwd: repoPath,
+          maxBuffer: 10 * 1024 * 1024,
+        });
+
+        // Add merge-affected files to the file list (avoid duplicates with working tree changes)
+        const fileByPath = new Map(files.map((f) => [f.path, f]));
+        const existingPaths = new Set(fileByPath.keys());
+        for (const filePath of mergeCommitInfo.mergeAffectedFiles) {
+          if (!existingPaths.has(filePath)) {
+            const newFile = {
+              status: 'M',
+              path: filePath,
+              statusText: 'Merged',
+              indexStatus: ' ',
+              workTreeStatus: ' ',
+              isMergeAffected: true,
+              mergeType: 'merged',
+            };
+            files.push(newFile);
+            fileByPath.set(filePath, newFile);
+            existingPaths.add(filePath);
+          } else {
+            // Mark existing file as also merge-affected
+            const existing = fileByPath.get(filePath);
+            if (existing) {
+              existing.isMergeAffected = true;
+              existing.mergeType = 'merged';
+            }
+          }
+        }
+
+        // Prepend merge diff to the combined diff so merge changes appear
+        // For files that only exist in the merge (not in working tree), we need their diffs
+        if (mergeDiff.trim()) {
+          // Parse the existing working tree diff to find which files it covers
+          const workingTreeDiffPaths = new Set<string>();
+          const diffLines = combinedDiff.split('\n');
+          for (const line of diffLines) {
+            if (line.startsWith('diff --git')) {
+              const match = line.match(/diff --git a\/(.*?) b\/(.*)/);
+              if (match) {
+                workingTreeDiffPaths.add(match[2]);
+              }
+            }
+          }
+
+          // Only include merge diff entries for files NOT already in working tree diff
+          const mergeDiffFiles = mergeDiff.split(/(?=diff --git)/);
+          const newMergeDiffs: string[] = [];
+          for (const fileDiff of mergeDiffFiles) {
+            if (!fileDiff.trim()) continue;
+            const match = fileDiff.match(/diff --git a\/(.*?) b\/(.*)/);
+            if (match && !workingTreeDiffPaths.has(match[2])) {
+              newMergeDiffs.push(fileDiff);
+            }
+          }
+
+          if (newMergeDiffs.length > 0) {
+            combinedDiff = newMergeDiffs.join('') + combinedDiff;
+          }
+        }
+      } catch (mergeError) {
+        // Best-effort: log and continue without merge diff
+        logger.error('Failed to get merge commit diff:', mergeError);
+
+        // Ensure files[] is consistent with mergeState.mergeAffectedFiles even when the
+        // diff command failed. Without this, mergeAffectedFiles would list paths that have
+        // no corresponding entry in the files array.
+        const existingPathsAfterError = new Set(files.map((f) => f.path));
+        for (const filePath of mergeCommitInfo.mergeAffectedFiles) {
+          if (!existingPathsAfterError.has(filePath)) {
+            files.push({
+              status: 'M',
+              path: filePath,
+              statusText: 'Merged',
+              indexStatus: ' ',
+              workTreeStatus: ' ',
+              isMergeAffected: true,
+              mergeType: 'merged',
+            });
+            existingPathsAfterError.add(filePath);
+          } else {
+            // Mark existing file as also merge-affected
+            const existing = files.find((f) => f.path === filePath);
+            if (existing) {
+              existing.isMergeAffected = true;
+              existing.mergeType = 'merged';
+            }
+          }
+        }
+      }
+
+      // Return with merge commit info in the mergeState
+      return {
+        diff: combinedDiff,
+        files,
+        hasChanges: files.length > 0,
+        mergeState: {
+          isMerging: false,
+          mergeOperationType: 'merge',
+          isCleanMerge: true,
+          mergeAffectedFiles: mergeCommitInfo.mergeAffectedFiles,
+          conflictFiles: [],
+          isMergeCommit: true,
+        },
+      };
+    }
+  }
 
   return {
     diff: combinedDiff,
     files,
     hasChanges: files.length > 0,
+    ...(mergeState.isMerging ? { mergeState } : {}),
   };
 }

libs/git-utils/src/index.ts

@@ -7,10 +7,15 @@
 export { execGitCommand } from './exec.js';
 
 // Export types and constants
-export { BINARY_EXTENSIONS, GIT_STATUS_MAP, type FileStatus } from './types.js';
+export {
+  BINARY_EXTENSIONS,
+  GIT_STATUS_MAP,
+  type FileStatus,
+  type MergeStateInfo,
+} from './types.js';
 
 // Export status utilities
-export { isGitRepo, parseGitStatus } from './status.js';
+export { isGitRepo, parseGitStatus, detectMergeState, detectMergeCommit } from './status.js';
 
 // Export diff utilities
 export {

libs/git-utils/src/status.ts

@@ -4,7 +4,9 @@
 
 import { exec } from 'child_process';
 import { promisify } from 'util';
-import { GIT_STATUS_MAP, type FileStatus } from './types.js';
+import fs from 'fs/promises';
+import path from 'path';
+import { GIT_STATUS_MAP, type FileStatus, type MergeStateInfo } from './types.js';
 
 const execAsync = promisify(exec);
 
@@ -95,12 +97,161 @@ export function parseGitStatus(statusOutput: string): FileStatus[] {
         primaryStatus = workTreeStatus; // Working tree change
       }
 
+      // Detect merge-affected files: when both X and Y are 'U', or U appears in either position
+      // In merge state, git uses 'U' (unmerged) to indicate merge-affected entries
+      const isMergeAffected =
+        indexStatus === 'U' ||
+        workTreeStatus === 'U' ||
+        (indexStatus === 'A' && workTreeStatus === 'A') || // both-added
+        (indexStatus === 'D' && workTreeStatus === 'D'); // both-deleted (during merge)
+
+      let mergeType: string | undefined;
+      if (isMergeAffected) {
+        if (indexStatus === 'U' && workTreeStatus === 'U') mergeType = 'both-modified';
+        else if (indexStatus === 'A' && workTreeStatus === 'U') mergeType = 'added-by-us';
+        else if (indexStatus === 'U' && workTreeStatus === 'A') mergeType = 'added-by-them';
+        else if (indexStatus === 'D' && workTreeStatus === 'U') mergeType = 'deleted-by-us';
+        else if (indexStatus === 'U' && workTreeStatus === 'D') mergeType = 'deleted-by-them';
+        else if (indexStatus === 'A' && workTreeStatus === 'A') mergeType = 'both-added';
+        else if (indexStatus === 'D' && workTreeStatus === 'D') mergeType = 'both-deleted';
+        else mergeType = 'unmerged';
+      }
+
       return {
         status: primaryStatus,
         path: filePath,
         statusText: getStatusText(indexStatus, workTreeStatus),
         indexStatus,
         workTreeStatus,
+        ...(isMergeAffected && { isMergeAffected: true }),
+        ...(mergeType && { mergeType }),
       };
     });
 }
+
+/**
+ * Check if the current HEAD commit is a merge commit (has more than one parent).
+ * This is used to detect completed merge commits so we can show what the merge changed.
+ *
+ * @param repoPath - Path to the git repository or worktree
+ * @returns Object with isMergeCommit flag and the list of files affected by the merge
+ */
+export async function detectMergeCommit(
+  repoPath: string
+): Promise<{ isMergeCommit: boolean; mergeAffectedFiles: string[] }> {
+  try {
+    // Check how many parents HEAD has using rev-parse
+    // For a merge commit, HEAD^2 exists (second parent); for non-merge commits it doesn't
+    try {
+      await execAsync('git rev-parse --verify "HEAD^2"', { cwd: repoPath });
+    } catch {
+      // HEAD^2 doesn't exist — not a merge commit
+      return { isMergeCommit: false, mergeAffectedFiles: [] };
+    }
+
+    // HEAD is a merge commit - get the files it changed relative to first parent
+    let mergeAffectedFiles: string[] = [];
+    try {
+      const { stdout: diffOutput } = await execAsync('git diff --name-only "HEAD~1" "HEAD"', {
+        cwd: repoPath,
+      });
+      mergeAffectedFiles = diffOutput
+        .trim()
+        .split('\n')
+        .filter((f) => f.trim().length > 0);
+    } catch {
+      // Ignore errors getting affected files
+    }
+
+    return { isMergeCommit: true, mergeAffectedFiles };
+  } catch {
+    return { isMergeCommit: false, mergeAffectedFiles: [] };
+  }
+}
+
+/**
+ * Detect the current merge state of a git repository.
+ * Checks for .git/MERGE_HEAD, .git/REBASE_HEAD, .git/CHERRY_PICK_HEAD
+ * to determine if a merge/rebase/cherry-pick is in progress.
+ *
+ * @param repoPath - Path to the git repository or worktree
+ * @returns MergeStateInfo describing the current merge state
+ */
+export async function detectMergeState(repoPath: string): Promise<MergeStateInfo> {
+  const defaultState: MergeStateInfo = {
+    isMerging: false,
+    mergeOperationType: null,
+    isCleanMerge: false,
+    mergeAffectedFiles: [],
+    conflictFiles: [],
+  };
+
+  try {
+    // Find the actual .git directory (handles worktrees with .git file pointing to main repo)
+    const { stdout: gitDirRaw } = await execAsync('git rev-parse --git-dir', { cwd: repoPath });
+    const gitDir = path.resolve(repoPath, gitDirRaw.trim());
+
+    // Check for merge/rebase/cherry-pick indicators
+    let mergeOperationType: 'merge' | 'rebase' | 'cherry-pick' | null = null;
+
+    const checks = [
+      { file: 'MERGE_HEAD', type: 'merge' as const },
+      { file: 'REBASE_HEAD', type: 'rebase' as const },
+      { file: 'rebase-merge', type: 'rebase' as const },
+      { file: 'rebase-apply', type: 'rebase' as const },
+      { file: 'CHERRY_PICK_HEAD', type: 'cherry-pick' as const },
+    ];
+
+    for (const check of checks) {
+      try {
+        await fs.access(path.join(gitDir, check.file));
+        mergeOperationType = check.type;
+        break;
+      } catch {
+        // File doesn't exist, continue checking
+      }
+    }
+
+    if (!mergeOperationType) {
+      return defaultState;
+    }
+
+    // Get unmerged files (files with conflicts)
+    let conflictFiles: string[] = [];
+    try {
+      const { stdout: diffOutput } = await execAsync('git diff --name-only --diff-filter=U', {
+        cwd: repoPath,
+      });
+      conflictFiles = diffOutput
+        .trim()
+        .split('\n')
+        .filter((f) => f.trim().length > 0);
+    } catch {
+      // Ignore errors getting conflict files
+    }
+
+    // Get all files affected by the merge (staged files that came from the merge)
+    let mergeAffectedFiles: string[] = [];
+    try {
+      const { stdout: statusOutput } = await execAsync('git status --porcelain', {
+        cwd: repoPath,
+      });
+      const files = parseGitStatus(statusOutput);
+      mergeAffectedFiles = files
+        .filter((f) => f.isMergeAffected || (f.indexStatus !== ' ' && f.indexStatus !== '?'))
+        .map((f) => f.path);
+    } catch {
+      // Ignore errors
+    }
+
+    return {
+      isMerging: true,
+      mergeOperationType,
+      isCleanMerge: conflictFiles.length === 0,
+      mergeAffectedFiles,
+      conflictFiles,
+    };
+  } catch {
+    return defaultState;
+  }
+}

libs/git-utils/src/types.ts

@@ -2,6 +2,9 @@
  * Git utilities types and constants
  */
 
+// Re-export MergeStateInfo from the centralized @automaker/types package
+export type { MergeStateInfo } from '@automaker/types';
+
 // Binary file extensions to skip
 export const BINARY_EXTENSIONS = new Set([
   '.png',
@@ -74,4 +77,8 @@ export interface FileStatus {
   indexStatus?: string;
   /** Raw working tree status character from git porcelain format */
   workTreeStatus?: string;
+  /** Whether this file is involved in a merge operation (both-modified, added-by-us, etc.) */
+  isMergeAffected?: boolean;
+  /** Type of merge involvement: 'both-modified' | 'added-by-us' | 'added-by-them' | 'deleted-by-us' | 'deleted-by-them' | 'both-added' | 'both-deleted' */
+  mergeType?: string;
 }

libs/types/src/index.ts

@@ -200,6 +200,7 @@ export {
   getThinkingTokenBudget,
   isAdaptiveThinkingModel,
   getThinkingLevelsForModel,
+  getDefaultThinkingLevel,
   // Event hook constants
   EVENT_HOOK_TRIGGER_LABELS,
   // Claude-compatible provider templates (new)
@@ -359,6 +360,7 @@ export type {
   AddRemoteResult,
   AddRemoteResponse,
   AddRemoteErrorResponse,
+  MergeStateInfo,
 } from './worktree.js';
 export { PR_STATES, validatePRState } from './worktree.js';
 

libs/types/src/settings.ts

@@ -268,6 +268,16 @@ export function getThinkingLevelsForModel(model: string): ThinkingLevel[] {
   return ['none', 'low', 'medium', 'high', 'ultrathink'];
 }
 
+/**
+ * Get the default thinking level for a given model.
+ * Used when selecting a model via the primary button in the two-stage selector.
+ * Always returns 'none' — users can configure their preferred default
+ * via the defaultThinkingLevel setting in the model defaults page.
+ */
+export function getDefaultThinkingLevel(_model: string): ThinkingLevel {
+  return 'none';
+}
+
 /** ModelProvider - AI model provider for credentials and API key management */
 export type ModelProvider = 'claude' | 'cursor' | 'codex' | 'opencode' | 'gemini' | 'copilot';
 
@@ -1051,6 +1061,8 @@ export interface GlobalSettings {
   enableDependencyBlocking: boolean;
   /** Skip verification requirement in auto-mode (treat 'completed' same as 'verified') */
   skipVerificationInAutoMode: boolean;
+  /** User's preferred action after a clean merge (null = ask every time) */
+  mergePostAction: 'commit' | 'manual' | null;
   /** Default: use git worktrees for feature branches */
   useWorktrees: boolean;
   /** Default: planning approach (skip/lite/spec/full) */
@@ -1086,6 +1098,15 @@ export interface GlobalSettings {
   /** Phase-specific AI model configuration */
   phaseModels: PhaseModelConfig;
 
+  /** Default thinking level applied when selecting a model via the primary button
+   * in the two-stage model selector. Users can still adjust per-model via the expand arrow.
+   * Defaults to 'none' (no extended thinking). */
+  defaultThinkingLevel?: ThinkingLevel;
+
+  /** Default reasoning effort applied when selecting a Codex model via the primary button
+   * in the two-stage model selector. Defaults to 'none'. */
+  defaultReasoningEffort?: ReasoningEffort;
+
   // Legacy AI Model Selection (deprecated - use phaseModels instead)
   /** @deprecated Use phaseModels.enhancementModel instead */
   enhancementModel: ModelAlias;
@@ -1150,6 +1171,10 @@ export interface GlobalSettings {
   /** Maps project path -> last selected session ID in that project */
   lastSelectedSessionByProject: Record<string, string>;
 
+  // Worktree Selection Tracking
+  /** Maps project path -> last selected worktree (path + branch) for restoring on PWA reload */
+  currentWorktreeByProject?: Record<string, { path: string | null; branch: string }>;
+
   // Window State (Electron only)
   /** Persisted window bounds for restoring position/size across sessions */
   windowBounds?: WindowBounds;
@@ -1574,6 +1599,7 @@ export const DEFAULT_GLOBAL_SETTINGS: GlobalSettings = {
   defaultSkipTests: true,
   enableDependencyBlocking: true,
   skipVerificationInAutoMode: false,
+  mergePostAction: null,
   useWorktrees: true,
   defaultPlanningMode: 'skip',
   defaultRequirePlanApproval: false,
@@ -1585,6 +1611,8 @@ export const DEFAULT_GLOBAL_SETTINGS: GlobalSettings = {
   showQueryDevtools: true,
   enableAiCommitMessages: true,
   phaseModels: DEFAULT_PHASE_MODELS,
+  defaultThinkingLevel: 'none',
+  defaultReasoningEffort: 'none',
   enhancementModel: 'sonnet', // Legacy alias still supported
   validationModel: 'opus', // Legacy alias still supported
   enabledCursorModels: getAllCursorModelIds(), // Returns prefixed IDs
@@ -1607,6 +1635,7 @@ export const DEFAULT_GLOBAL_SETTINGS: GlobalSettings = {
   recentFolders: [],
   worktreePanelCollapsed: false,
   lastSelectedSessionByProject: {},
+  currentWorktreeByProject: {},
   autoLoadClaudeMd: true,
   skipSandboxWarning: false,
   codexAutoLoadAgents: DEFAULT_CODEX_AUTO_LOAD_AGENTS,

libs/types/src/worktree.ts

@@ -74,3 +74,21 @@ export interface AddRemoteErrorResponse {
   /** Optional error code for specific error types (e.g., 'REMOTE_EXISTS') */
   code?: string;
 }
+
+/**
+ * Merge state information for a git repository
+ */
+export interface MergeStateInfo {
+  /** Whether a merge is currently in progress */
+  isMerging: boolean;
+  /** Type of merge operation: 'merge' | 'rebase' | 'cherry-pick' | null */
+  mergeOperationType: 'merge' | 'rebase' | 'cherry-pick' | null;
+  /** Whether the merge completed cleanly (no conflicts) */
+  isCleanMerge: boolean;
+  /** Files affected by the merge */
+  mergeAffectedFiles: string[];
+  /** Files with unresolved conflicts */
+  conflictFiles: string[];
+  /** Whether the current HEAD is a completed merge commit (has multiple parents) */
+  isMergeCommit?: boolean;
+}

package-lock.json

@@ -3864,9 +3864,9 @@
       }
     },
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