feat: Address review comments, add stage/unstage functionality, conflict resolution improvements, support for Sonnet 4.6

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

@@ -6,12 +6,14 @@ import { Router } from 'express';
 import { validatePathParams } from '../../middleware/validate-paths.js';
 import { createDiffsHandler } from './routes/diffs.js';
 import { createFileDiffHandler } from './routes/file-diff.js';
+import { createStageFilesHandler } from './routes/stage-files.js';
 
 export function createGitRoutes(): Router {
   const router = Router();
 
   router.post('/diffs', validatePathParams('projectPath'), createDiffsHandler());
   router.post('/file-diff', validatePathParams('projectPath', 'filePath'), createFileDiffHandler());
+  router.post('/stage-files', validatePathParams('projectPath'), createStageFilesHandler());
 
   return router;
 }

apps/server/src/routes/git/routes/stage-files.ts

@@ -0,0 +1,60 @@
+/**
+ * POST /stage-files endpoint - Stage or unstage files in the main project
+ */
+
+import type { Request, Response } from 'express';
+import { getErrorMessage, logError } from '../common.js';
+import { execGitCommand } from '../../../lib/git.js';
+
+export function createStageFilesHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, files, operation } = req.body as {
+        projectPath: string;
+        files: string[];
+        operation: 'stage' | 'unstage';
+      };
+
+      if (!projectPath) {
+        res.status(400).json({
+          success: false,
+          error: 'projectPath required',
+        });
+        return;
+      }
+
+      if (!files || files.length === 0) {
+        res.status(400).json({
+          success: false,
+          error: 'files array required and must not be empty',
+        });
+        return;
+      }
+
+      if (operation !== 'stage' && operation !== 'unstage') {
+        res.status(400).json({
+          success: false,
+          error: 'operation must be "stage" or "unstage"',
+        });
+        return;
+      }
+
+      if (operation === 'stage') {
+        await execGitCommand(['add', '--', ...files], projectPath);
+      } else {
+        await execGitCommand(['reset', 'HEAD', '--', ...files], projectPath);
+      }
+
+      res.json({
+        success: true,
+        result: {
+          operation,
+          filesCount: files.length,
+        },
+      });
+    } catch (error) {
+      logError(error, `${(req.body as { operation?: string })?.operation ?? 'stage'} files failed`);
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/setup/routes/verify-claude-auth.ts

@@ -158,7 +158,7 @@ export function createVerifyClaudeAuthHandler() {
         const stream = query({
           prompt: "Reply with only the word 'ok'",
           options: {
-            model: 'claude-sonnet-4-20250514',
+            model: 'claude-sonnet-4-6',
             maxTurns: 1,
             allowedTools: [],
             abortController,

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

@@ -63,6 +63,9 @@ import { createCherryPickHandler } from './routes/cherry-pick.js';
 import { createBranchCommitLogHandler } from './routes/branch-commit-log.js';
 import { createGeneratePRDescriptionHandler } from './routes/generate-pr-description.js';
 import { createRebaseHandler } from './routes/rebase.js';
+import { createAbortOperationHandler } from './routes/abort-operation.js';
+import { createContinueOperationHandler } from './routes/continue-operation.js';
+import { createStageFilesHandler } from './routes/stage-files.js';
 import type { SettingsService } from '../../services/settings-service.js';
 
 export function createWorktreeRoutes(
@@ -276,5 +279,29 @@ export function createWorktreeRoutes(
     createRebaseHandler(events)
   );
 
+  // Abort in-progress merge/rebase/cherry-pick
+  router.post(
+    '/abort-operation',
+    validatePathParams('worktreePath'),
+    requireGitRepoOnly,
+    createAbortOperationHandler(events)
+  );
+
+  // Continue in-progress merge/rebase/cherry-pick after resolving conflicts
+  router.post(
+    '/continue-operation',
+    validatePathParams('worktreePath'),
+    requireGitRepoOnly,
+    createContinueOperationHandler(events)
+  );
+
+  // Stage/unstage files route
+  router.post(
+    '/stage-files',
+    validatePathParams('worktreePath'),
+    requireGitRepoOnly,
+    createStageFilesHandler()
+  );
+
   return router;
 }

apps/server/src/routes/worktree/routes/abort-operation.ts

@@ -0,0 +1,117 @@
+/**
+ * POST /abort-operation endpoint - Abort an in-progress merge, rebase, or cherry-pick
+ *
+ * Detects which operation (merge, rebase, or cherry-pick) is in progress
+ * and aborts it, returning the repository to a clean state.
+ */
+
+import type { Request, Response } from 'express';
+import path from 'path';
+import * as fs from 'fs/promises';
+import { getErrorMessage, logError, execAsync } from '../common.js';
+import type { EventEmitter } from '../../../lib/events.js';
+
+/**
+ * Detect what type of conflict operation is currently in progress
+ */
+async function detectOperation(
+  worktreePath: string
+): Promise<'merge' | 'rebase' | 'cherry-pick' | null> {
+  try {
+    const { stdout: gitDirRaw } = await execAsync('git rev-parse --git-dir', {
+      cwd: worktreePath,
+    });
+    const gitDir = path.resolve(worktreePath, gitDirRaw.trim());
+
+    const [rebaseMergeExists, rebaseApplyExists, mergeHeadExists, cherryPickHeadExists] =
+      await Promise.all([
+        fs
+          .access(path.join(gitDir, 'rebase-merge'))
+          .then(() => true)
+          .catch(() => false),
+        fs
+          .access(path.join(gitDir, 'rebase-apply'))
+          .then(() => true)
+          .catch(() => false),
+        fs
+          .access(path.join(gitDir, 'MERGE_HEAD'))
+          .then(() => true)
+          .catch(() => false),
+        fs
+          .access(path.join(gitDir, 'CHERRY_PICK_HEAD'))
+          .then(() => true)
+          .catch(() => false),
+      ]);
+
+    if (rebaseMergeExists || rebaseApplyExists) return 'rebase';
+    if (mergeHeadExists) return 'merge';
+    if (cherryPickHeadExists) return 'cherry-pick';
+    return null;
+  } catch {
+    return null;
+  }
+}
+
+export function createAbortOperationHandler(events: EventEmitter) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { worktreePath } = req.body as {
+        worktreePath: string;
+      };
+
+      if (!worktreePath) {
+        res.status(400).json({
+          success: false,
+          error: 'worktreePath is required',
+        });
+        return;
+      }
+
+      const resolvedWorktreePath = path.resolve(worktreePath);
+
+      // Detect what operation is in progress
+      const operation = await detectOperation(resolvedWorktreePath);
+
+      if (!operation) {
+        res.status(400).json({
+          success: false,
+          error: 'No merge, rebase, or cherry-pick in progress',
+        });
+        return;
+      }
+
+      // Abort the operation
+      let abortCommand: string;
+      switch (operation) {
+        case 'merge':
+          abortCommand = 'git merge --abort';
+          break;
+        case 'rebase':
+          abortCommand = 'git rebase --abort';
+          break;
+        case 'cherry-pick':
+          abortCommand = 'git cherry-pick --abort';
+          break;
+      }
+
+      await execAsync(abortCommand, { cwd: resolvedWorktreePath });
+
+      // Emit event
+      events.emit('conflict:aborted', {
+        worktreePath: resolvedWorktreePath,
+        operation,
+      });
+
+      res.json({
+        success: true,
+        result: {
+          operation,
+          message: `${operation.charAt(0).toUpperCase() + operation.slice(1)} aborted successfully`,
+        },
+      });
+    } catch (error) {
+      logError(error, 'Abort operation failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/worktree/routes/continue-operation.ts

@@ -0,0 +1,151 @@
+/**
+ * POST /continue-operation endpoint - Continue an in-progress merge, rebase, or cherry-pick
+ *
+ * After conflicts have been resolved, this endpoint continues the operation.
+ * For merge: performs git commit (merge is auto-committed after conflict resolution)
+ * For rebase: runs git rebase --continue
+ * For cherry-pick: runs git cherry-pick --continue
+ */
+
+import type { Request, Response } from 'express';
+import path from 'path';
+import * as fs from 'fs/promises';
+import { getErrorMessage, logError, execAsync } from '../common.js';
+import type { EventEmitter } from '../../../lib/events.js';
+
+/**
+ * Detect what type of conflict operation is currently in progress
+ */
+async function detectOperation(
+  worktreePath: string
+): Promise<'merge' | 'rebase' | 'cherry-pick' | null> {
+  try {
+    const { stdout: gitDirRaw } = await execAsync('git rev-parse --git-dir', {
+      cwd: worktreePath,
+    });
+    const gitDir = path.resolve(worktreePath, gitDirRaw.trim());
+
+    const [rebaseMergeExists, rebaseApplyExists, mergeHeadExists, cherryPickHeadExists] =
+      await Promise.all([
+        fs
+          .access(path.join(gitDir, 'rebase-merge'))
+          .then(() => true)
+          .catch(() => false),
+        fs
+          .access(path.join(gitDir, 'rebase-apply'))
+          .then(() => true)
+          .catch(() => false),
+        fs
+          .access(path.join(gitDir, 'MERGE_HEAD'))
+          .then(() => true)
+          .catch(() => false),
+        fs
+          .access(path.join(gitDir, 'CHERRY_PICK_HEAD'))
+          .then(() => true)
+          .catch(() => false),
+      ]);
+
+    if (rebaseMergeExists || rebaseApplyExists) return 'rebase';
+    if (mergeHeadExists) return 'merge';
+    if (cherryPickHeadExists) return 'cherry-pick';
+    return null;
+  } catch {
+    return null;
+  }
+}
+
+/**
+ * Check if there are still unmerged paths (unresolved conflicts)
+ */
+async function hasUnmergedPaths(worktreePath: string): Promise<boolean> {
+  try {
+    const { stdout: statusOutput } = await execAsync('git status --porcelain', {
+      cwd: worktreePath,
+    });
+    return statusOutput.split('\n').some((line) => /^(UU|AA|DD|AU|UA|DU|UD)/.test(line));
+  } catch {
+    return false;
+  }
+}
+
+export function createContinueOperationHandler(events: EventEmitter) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { worktreePath } = req.body as {
+        worktreePath: string;
+      };
+
+      if (!worktreePath) {
+        res.status(400).json({
+          success: false,
+          error: 'worktreePath is required',
+        });
+        return;
+      }
+
+      const resolvedWorktreePath = path.resolve(worktreePath);
+
+      // Detect what operation is in progress
+      const operation = await detectOperation(resolvedWorktreePath);
+
+      if (!operation) {
+        res.status(400).json({
+          success: false,
+          error: 'No merge, rebase, or cherry-pick in progress',
+        });
+        return;
+      }
+
+      // Check for unresolved conflicts
+      if (await hasUnmergedPaths(resolvedWorktreePath)) {
+        res.status(409).json({
+          success: false,
+          error:
+            'There are still unresolved conflicts. Please resolve all conflicts before continuing.',
+          hasUnresolvedConflicts: true,
+        });
+        return;
+      }
+
+      // Stage all resolved files first
+      await execAsync('git add -A', { cwd: resolvedWorktreePath });
+
+      // Continue the operation
+      let continueCommand: string;
+      switch (operation) {
+        case 'merge':
+          // For merge, we need to commit after resolving conflicts
+          continueCommand = 'git commit --no-edit';
+          break;
+        case 'rebase':
+          continueCommand = 'git rebase --continue';
+          break;
+        case 'cherry-pick':
+          continueCommand = 'git cherry-pick --continue';
+          break;
+      }
+
+      await execAsync(continueCommand, {
+        cwd: resolvedWorktreePath,
+        env: { ...process.env, GIT_EDITOR: 'true' }, // Prevent editor from opening
+      });
+
+      // Emit event
+      events.emit('conflict:resolved', {
+        worktreePath: resolvedWorktreePath,
+        operation,
+      });
+
+      res.json({
+        success: true,
+        result: {
+          operation,
+          message: `${operation.charAt(0).toUpperCase() + operation.slice(1)} continued successfully`,
+        },
+      });
+    } catch (error) {
+      logError(error, 'Continue operation failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

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

@@ -58,6 +58,88 @@ interface WorktreeInfo {
   hasChanges?: boolean;
   changedFilesCount?: number;
   pr?: WorktreePRInfo; // PR info if a PR has been created for this branch
+  /** Whether a merge or rebase is in progress (has conflicts) */
+  hasConflicts?: boolean;
+  /** Type of conflict operation in progress */
+  conflictType?: 'merge' | 'rebase' | 'cherry-pick';
+  /** List of files with conflicts */
+  conflictFiles?: string[];
+}
+
+/**
+ * Detect if a merge, rebase, or cherry-pick is in progress for a worktree.
+ * Checks for the presence of state files/directories that git creates
+ * during these operations.
+ */
+async function detectConflictState(worktreePath: string): Promise<{
+  hasConflicts: boolean;
+  conflictType?: 'merge' | 'rebase' | 'cherry-pick';
+  conflictFiles?: string[];
+}> {
+  try {
+    // Find the canonical .git directory for this worktree
+    const { stdout: gitDirRaw } = await execAsync('git rev-parse --git-dir', {
+      cwd: worktreePath,
+    });
+    const gitDir = path.resolve(worktreePath, gitDirRaw.trim());
+
+    // Check for merge, rebase, and cherry-pick state files/directories
+    const [mergeHeadExists, rebaseMergeExists, rebaseApplyExists, cherryPickHeadExists] =
+      await Promise.all([
+        secureFs
+          .access(path.join(gitDir, 'MERGE_HEAD'))
+          .then(() => true)
+          .catch(() => false),
+        secureFs
+          .access(path.join(gitDir, 'rebase-merge'))
+          .then(() => true)
+          .catch(() => false),
+        secureFs
+          .access(path.join(gitDir, 'rebase-apply'))
+          .then(() => true)
+          .catch(() => false),
+        secureFs
+          .access(path.join(gitDir, 'CHERRY_PICK_HEAD'))
+          .then(() => true)
+          .catch(() => false),
+      ]);
+
+    let conflictType: 'merge' | 'rebase' | 'cherry-pick' | undefined;
+    if (rebaseMergeExists || rebaseApplyExists) {
+      conflictType = 'rebase';
+    } else if (mergeHeadExists) {
+      conflictType = 'merge';
+    } else if (cherryPickHeadExists) {
+      conflictType = 'cherry-pick';
+    }
+
+    if (!conflictType) {
+      return { hasConflicts: false };
+    }
+
+    // Get list of conflicted files using machine-readable git status
+    let conflictFiles: string[] = [];
+    try {
+      const { stdout: statusOutput } = await execAsync('git diff --name-only --diff-filter=U', {
+        cwd: worktreePath,
+      });
+      conflictFiles = statusOutput
+        .trim()
+        .split('\n')
+        .filter((f) => f.trim().length > 0);
+    } catch {
+      // Fall back to empty list if diff fails
+    }
+
+    return {
+      hasConflicts: true,
+      conflictType,
+      conflictFiles,
+    };
+  } catch {
+    // If anything fails, assume no conflicts
+    return { hasConflicts: false };
+  }
 }
 
 async function getCurrentBranch(cwd: string): Promise<string> {
@@ -373,7 +455,7 @@ export function createListHandler() {
       // Read all worktree metadata to get PR info
       const allMetadata = await readAllWorktreeMetadata(projectPath);
 
-      // If includeDetails is requested, fetch change status for each worktree
+      // If includeDetails is requested, fetch change status and conflict state for each worktree
       if (includeDetails) {
         for (const worktree of worktrees) {
           try {
@@ -390,6 +472,18 @@ export function createListHandler() {
             worktree.hasChanges = false;
             worktree.changedFilesCount = 0;
           }
+
+          // Detect merge/rebase/cherry-pick in progress
+          try {
+            const conflictState = await detectConflictState(worktree.path);
+            if (conflictState.hasConflicts) {
+              worktree.hasConflicts = true;
+              worktree.conflictType = conflictState.conflictType;
+              worktree.conflictFiles = conflictState.conflictFiles;
+            }
+          } catch {
+            // Ignore conflict detection errors
+          }
         }
       }
 

apps/server/src/routes/worktree/routes/stage-files.ts

@@ -0,0 +1,69 @@
+/**
+ * POST /stage-files endpoint - Stage or unstage files in a worktree
+ *
+ * Supports two operations:
+ * 1. Stage files: `git add <files>` (adds files to the staging area)
+ * 2. Unstage files: `git reset HEAD -- <files>` (removes files from staging area)
+ *
+ * Note: Git repository validation (isGitRepo) is handled by
+ * the requireGitRepoOnly middleware in index.ts
+ */
+
+import type { Request, Response } from 'express';
+import { getErrorMessage, logError } from '../common.js';
+import { execGitCommand } from '../../../lib/git.js';
+
+export function createStageFilesHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { worktreePath, files, operation } = req.body as {
+        worktreePath: string;
+        files: string[];
+        operation: 'stage' | 'unstage';
+      };
+
+      if (!worktreePath) {
+        res.status(400).json({
+          success: false,
+          error: 'worktreePath required',
+        });
+        return;
+      }
+
+      if (!files || files.length === 0) {
+        res.status(400).json({
+          success: false,
+          error: 'files array required and must not be empty',
+        });
+        return;
+      }
+
+      if (operation !== 'stage' && operation !== 'unstage') {
+        res.status(400).json({
+          success: false,
+          error: 'operation must be "stage" or "unstage"',
+        });
+        return;
+      }
+
+      if (operation === 'stage') {
+        // Stage the specified files
+        await execGitCommand(['add', '--', ...files], worktreePath);
+      } else {
+        // Unstage the specified files
+        await execGitCommand(['reset', 'HEAD', '--', ...files], worktreePath);
+      }
+
+      res.json({
+        success: true,
+        result: {
+          operation,
+          filesCount: files.length,
+        },
+      });
+    } catch (error) {
+      logError(error, `${(req.body as { operation?: string })?.operation ?? 'stage'} files failed`);
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/worktree/routes/stash-apply.ts

@@ -54,7 +54,7 @@ export function createStashApplyHandler(events: EventEmitter) {
       const result = await applyOrPop(worktreePath, idx, { pop }, events);
 
       if (!result.success) {
-        logError(new Error(result.error ?? 'Stash apply failed'), 'Stash apply failed');
+        // applyOrPop already logs the error internally via logError — no need to double-log here
         res.status(500).json({ success: false, error: result.error });
         return;
       }