Merge main into refactor/frontend

Merge latest features from main including:
- PR #161 (worktree-confusion): Clarified branch handling in dialogs
- PR #160 (speckits-rebase): Planning mode functionality

Resolved conflicts:
- add-feature-dialog.tsx: Combined TanStack Router navigation with branch selection state
- worktree-integration.spec.ts: Updated tests for new worktree behavior (created at execution time)
- package-lock.json: Regenerated after merge

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

apps/server/src/lib/error-handler.ts

@@ -21,6 +21,22 @@ export function isAbortError(error: unknown): boolean {
   );
 }
 
+/**
+ * Check if an error is a user-initiated cancellation
+ *
+ * @param errorMessage - The error message to check
+ * @returns True if the error is a user-initiated cancellation
+ */
+export function isCancellationError(errorMessage: string): boolean {
+  const lowerMessage = errorMessage.toLowerCase();
+  return (
+    lowerMessage.includes("cancelled") ||
+    lowerMessage.includes("canceled") ||
+    lowerMessage.includes("stopped") ||
+    lowerMessage.includes("aborted")
+  );
+}
+
 /**
  * Check if an error is an authentication/API key error
  *
@@ -39,7 +55,7 @@ export function isAuthenticationError(errorMessage: string): boolean {
 /**
  * Error type classification
  */
-export type ErrorType = "authentication" | "abort" | "execution" | "unknown";
+export type ErrorType = "authentication" | "cancellation" | "abort" | "execution" | "unknown";
 
 /**
  * Classified error information
@@ -49,6 +65,7 @@ export interface ErrorInfo {
   message: string;
   isAbort: boolean;
   isAuth: boolean;
+  isCancellation: boolean;
   originalError: unknown;
 }
 
@@ -62,12 +79,15 @@ export function classifyError(error: unknown): ErrorInfo {
   const message = error instanceof Error ? error.message : String(error || "Unknown error");
   const isAbort = isAbortError(error);
   const isAuth = isAuthenticationError(message);
+  const isCancellation = isCancellationError(message);
 
   let type: ErrorType;
   if (isAuth) {
     type = "authentication";
   } else if (isAbort) {
     type = "abort";
+  } else if (isCancellation) {
+    type = "cancellation";
   } else if (error instanceof Error) {
     type = "execution";
   } else {
@@ -79,6 +99,7 @@ export function classifyError(error: unknown): ErrorInfo {
     message,
     isAbort,
     isAuth,
+    isCancellation,
     originalError: error,
   };
 }

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

@@ -23,3 +23,4 @@ export function createSpecRegenerationRoutes(events: EventEmitter): Router {
 }
 
 
+

apps/server/src/routes/auto-mode/index.ts

@@ -6,8 +6,6 @@
 
 import { Router } from "express";
 import type { AutoModeService } from "../../services/auto-mode-service.js";
-import { createStartHandler } from "./routes/start.js";
-import { createStopHandler } from "./routes/stop.js";
 import { createStopFeatureHandler } from "./routes/stop-feature.js";
 import { createStatusHandler } from "./routes/status.js";
 import { createRunFeatureHandler } from "./routes/run-feature.js";
@@ -17,12 +15,11 @@ import { createContextExistsHandler } from "./routes/context-exists.js";
 import { createAnalyzeProjectHandler } from "./routes/analyze-project.js";
 import { createFollowUpFeatureHandler } from "./routes/follow-up-feature.js";
 import { createCommitFeatureHandler } from "./routes/commit-feature.js";
+import { createApprovePlanHandler } from "./routes/approve-plan.js";
 
 export function createAutoModeRoutes(autoModeService: AutoModeService): Router {
   const router = Router();
 
-  router.post("/start", createStartHandler(autoModeService));
-  router.post("/stop", createStopHandler(autoModeService));
   router.post("/stop-feature", createStopFeatureHandler(autoModeService));
   router.post("/status", createStatusHandler(autoModeService));
   router.post("/run-feature", createRunFeatureHandler(autoModeService));
@@ -35,6 +32,7 @@ export function createAutoModeRoutes(autoModeService: AutoModeService): Router {
     createFollowUpFeatureHandler(autoModeService)
   );
   router.post("/commit-feature", createCommitFeatureHandler(autoModeService));
+  router.post("/approve-plan", createApprovePlanHandler(autoModeService));
 
   return router;
 }

apps/server/src/routes/auto-mode/routes/approve-plan.ts

@@ -0,0 +1,78 @@
+/**
+ * POST /approve-plan endpoint - Approve or reject a generated plan/spec
+ */
+
+import type { Request, Response } from "express";
+import type { AutoModeService } from "../../../services/auto-mode-service.js";
+import { createLogger } from "../../../lib/logger.js";
+import { getErrorMessage, logError } from "../common.js";
+
+const logger = createLogger("AutoMode");
+
+export function createApprovePlanHandler(autoModeService: AutoModeService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { featureId, approved, editedPlan, feedback, projectPath } = req.body as {
+        featureId: string;
+        approved: boolean;
+        editedPlan?: string;
+        feedback?: string;
+        projectPath?: string;
+      };
+
+      if (!featureId) {
+        res.status(400).json({
+          success: false,
+          error: "featureId is required",
+        });
+        return;
+      }
+
+      if (typeof approved !== "boolean") {
+        res.status(400).json({
+          success: false,
+          error: "approved must be a boolean",
+        });
+        return;
+      }
+
+      // Note: We no longer check hasPendingApproval here because resolvePlanApproval
+      // can handle recovery when pending approval is not in Map but feature has planSpec.status='generated'
+      // This supports cases where the server restarted while waiting for approval
+
+      logger.info(
+        `[AutoMode] Plan ${approved ? "approved" : "rejected"} for feature ${featureId}${
+          editedPlan ? " (with edits)" : ""
+        }${feedback ? ` - Feedback: ${feedback}` : ""}`
+      );
+
+      // Resolve the pending approval (with recovery support)
+      const result = await autoModeService.resolvePlanApproval(
+        featureId,
+        approved,
+        editedPlan,
+        feedback,
+        projectPath
+      );
+
+      if (!result.success) {
+        res.status(500).json({
+          success: false,
+          error: result.error,
+        });
+        return;
+      }
+
+      res.json({
+        success: true,
+        approved,
+        message: approved
+          ? "Plan approved - implementation will continue"
+          : "Plan rejected - feature execution stopped",
+      });
+    } catch (error) {
+      logError(error, "Approve plan failed");
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

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

@@ -12,13 +12,14 @@ const logger = createLogger("AutoMode");
 export function createFollowUpFeatureHandler(autoModeService: AutoModeService) {
   return async (req: Request, res: Response): Promise<void> => {
     try {
-      const { projectPath, featureId, prompt, imagePaths, worktreePath } = req.body as {
-        projectPath: string;
-        featureId: string;
-        prompt: string;
-        imagePaths?: string[];
-        worktreePath?: string;
-      };
+      const { projectPath, featureId, prompt, imagePaths, useWorktrees } =
+        req.body as {
+          projectPath: string;
+          featureId: string;
+          prompt: string;
+          imagePaths?: string[];
+          useWorktrees?: boolean;
+        };
 
       if (!projectPath || !featureId || !prompt) {
         res.status(400).json({
@@ -28,14 +29,25 @@ export function createFollowUpFeatureHandler(autoModeService: AutoModeService) {
         return;
       }
 
-      // Start follow-up in background, using the feature's worktreePath for correct branch
+      // Start follow-up in background
+      // followUpFeature derives workDir from feature.branchName
       autoModeService
-        .followUpFeature(projectPath, featureId, prompt, imagePaths, worktreePath)
+        .followUpFeature(
+          projectPath,
+          featureId,
+          prompt,
+          imagePaths,
+          useWorktrees ?? true
+        )
         .catch((error) => {
           logger.error(
             `[AutoMode] Follow up feature ${featureId} error:`,
             error
           );
+        })
+        .finally(() => {
+          // Release the starting slot when follow-up completes (success or error)
+          // Note: The feature should be in runningFeatures by this point
         });
 
       res.json({ success: true });

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

@@ -19,12 +19,10 @@ export function createResumeFeatureHandler(autoModeService: AutoModeService) {
       };
 
       if (!projectPath || !featureId) {
-        res
-          .status(400)
-          .json({
-            success: false,
-            error: "projectPath and featureId are required",
-          });
+        res.status(400).json({
+          success: false,
+          error: "projectPath and featureId are required",
+        });
         return;
       }
 

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

@@ -12,30 +12,30 @@ const logger = createLogger("AutoMode");
 export function createRunFeatureHandler(autoModeService: AutoModeService) {
   return async (req: Request, res: Response): Promise<void> => {
     try {
-      const { projectPath, featureId, useWorktrees, worktreePath } = req.body as {
+      const { projectPath, featureId, useWorktrees } = req.body as {
         projectPath: string;
         featureId: string;
         useWorktrees?: boolean;
-        worktreePath?: string;
       };
 
       if (!projectPath || !featureId) {
-        res
-          .status(400)
-          .json({
-            success: false,
-            error: "projectPath and featureId are required",
-          });
+        res.status(400).json({
+          success: false,
+          error: "projectPath and featureId are required",
+        });
         return;
       }
 
       // Start execution in background
-      // If worktreePath is provided, use it directly; otherwise let the service decide
-      // Default to false - worktrees should only be used when explicitly enabled
+      // executeFeature derives workDir from feature.branchName
       autoModeService
-        .executeFeature(projectPath, featureId, useWorktrees ?? false, false, worktreePath)
+        .executeFeature(projectPath, featureId, useWorktrees ?? false, false)
         .catch((error) => {
           logger.error(`[AutoMode] Feature ${featureId} error:`, error);
+        })
+        .finally(() => {
+          // Release the starting slot when execution completes (success or error)
+          // Note: The feature should be in runningFeatures by this point
         });
 
       res.json({ success: true });

apps/server/src/routes/auto-mode/routes/start.ts

@@ -1,31 +0,0 @@
-/**
- * POST /start endpoint - Start auto mode loop
- */
-
-import type { Request, Response } from "express";
-import type { AutoModeService } from "../../../services/auto-mode-service.js";
-import { getErrorMessage, logError } from "../common.js";
-
-export function createStartHandler(autoModeService: AutoModeService) {
-  return async (req: Request, res: Response): Promise<void> => {
-    try {
-      const { projectPath, maxConcurrency } = req.body as {
-        projectPath: string;
-        maxConcurrency?: number;
-      };
-
-      if (!projectPath) {
-        res
-          .status(400)
-          .json({ success: false, error: "projectPath is required" });
-        return;
-      }
-
-      await autoModeService.startAutoLoop(projectPath, maxConcurrency || 3);
-      res.json({ success: true });
-    } catch (error) {
-      logError(error, "Start auto loop failed");
-      res.status(500).json({ success: false, error: getErrorMessage(error) });
-    }
-  };
-}

apps/server/src/routes/auto-mode/routes/stop.ts

@@ -1,19 +0,0 @@
-/**
- * POST /stop endpoint - Stop auto mode loop
- */
-
-import type { Request, Response } from "express";
-import type { AutoModeService } from "../../../services/auto-mode-service.js";
-import { getErrorMessage, logError } from "../common.js";
-
-export function createStopHandler(autoModeService: AutoModeService) {
-  return async (req: Request, res: Response): Promise<void> => {
-    try {
-      const runningCount = await autoModeService.stopAutoLoop();
-      res.json({ success: true, runningFeatures: runningCount });
-    } catch (error) {
-      logError(error, "Stop auto loop failed");
-      res.status(500).json({ success: false, error: getErrorMessage(error) });
-    }
-  };
-}

apps/server/src/routes/running-agents/routes/index.ts

@@ -16,7 +16,6 @@ export function createIndexHandler(autoModeService: AutoModeService) {
         success: true,
         runningAgents,
         totalCount: runningAgents.length,
-        autoLoopRunning: status.autoLoopRunning,
       });
     } catch (error) {
       logError(error, "Get running agents failed");

apps/server/src/routes/setup/routes/delete-api-key.ts

@@ -103,3 +103,4 @@ export function createDeleteApiKeyHandler() {
 }
 
 
+

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

@@ -8,6 +8,7 @@
 import type { Request, Response } from "express";
 import { exec } from "child_process";
 import { promisify } from "util";
+import { existsSync } from "fs";
 import { isGitRepo, getErrorMessage, logError, normalizePath } from "../common.js";
 
 const execAsync = promisify(exec);
@@ -58,10 +59,12 @@ export function createListHandler() {
       });
 
       const worktrees: WorktreeInfo[] = [];
+      const removedWorktrees: Array<{ path: string; branch: string }> = [];
       const lines = stdout.split("\n");
       let current: { path?: string; branch?: string } = {};
       let isFirst = true;
 
+      // First pass: detect removed worktrees
       for (const line of lines) {
         if (line.startsWith("worktree ")) {
           current.path = normalizePath(line.slice(9));
@@ -69,19 +72,40 @@ export function createListHandler() {
           current.branch = line.slice(7).replace("refs/heads/", "");
         } else if (line === "") {
           if (current.path && current.branch) {
-            worktrees.push({
-              path: current.path,
-              branch: current.branch,
-              isMain: isFirst,
-              isCurrent: current.branch === currentBranch,
-              hasWorktree: true,
-            });
-            isFirst = false;
+            const isMainWorktree = isFirst;
+            // Check if the worktree directory actually exists
+            // Skip checking/pruning the main worktree (projectPath itself)
+            if (!isMainWorktree && !existsSync(current.path)) {
+              // Worktree directory doesn't exist - it was manually deleted
+              removedWorktrees.push({
+                path: current.path,
+                branch: current.branch,
+              });
+            } else {
+              // Worktree exists (or is main worktree), add it to the list
+              worktrees.push({
+                path: current.path,
+                branch: current.branch,
+                isMain: isMainWorktree,
+                isCurrent: current.branch === currentBranch,
+                hasWorktree: true,
+              });
+              isFirst = false;
+            }
           }
           current = {};
         }
       }
 
+      // Prune removed worktrees from git (only if any were detected)
+      if (removedWorktrees.length > 0) {
+        try {
+          await execAsync("git worktree prune", { cwd: projectPath });
+        } catch {
+          // Prune failed, but we'll still report the removed worktrees
+        }
+      }
+
       // If includeDetails is requested, fetch change status for each worktree
       if (includeDetails) {
         for (const worktree of worktrees) {
@@ -103,7 +127,11 @@ export function createListHandler() {
         }
       }
 
-      res.json({ success: true, worktrees });
+      res.json({ 
+        success: true, 
+        worktrees,
+        removedWorktrees: removedWorktrees.length > 0 ? removedWorktrees : undefined,
+      });
     } catch (error) {
       logError(error, "List worktrees failed");
       res.status(500).json({ success: false, error: getErrorMessage(error) });

apps/server/src/services/feature-loader.ts

@@ -24,7 +24,26 @@ export interface Feature {
   spec?: string;
   model?: string;
   imagePaths?: Array<string | { path: string; [key: string]: unknown }>;
-  [key: string]: unknown;
+  // Branch info - worktree path is derived at runtime from branchName
+  branchName?: string; // Name of the feature branch (undefined = use current worktree)
+  skipTests?: boolean;
+  thinkingLevel?: string;
+  planningMode?: 'skip' | 'lite' | 'spec' | 'full';
+  requirePlanApproval?: boolean;
+  planSpec?: {
+    status: 'pending' | 'generating' | 'generated' | 'approved' | 'rejected';
+    content?: string;
+    version: number;
+    generatedAt?: string;
+    approvedAt?: string;
+    reviewedByUser: boolean;
+    tasksCompleted?: number;
+    tasksTotal?: number;
+  };
+  error?: string;
+  summary?: string;
+  startedAt?: string;
+  [key: string]: unknown;  // Keep catch-all for extensibility
 }
 
 export class FeatureLoader {