feat(terminal): add worktree support for terminals

apps/backend/cli/batch_commands.py

@@ -184,7 +184,7 @@ def handle_batch_cleanup_command(project_dir: str, dry_run: bool = True) -> bool
         True if successful
     """
     specs_dir = Path(project_dir) / ".auto-claude" / "specs"
-    worktrees_dir = Path(project_dir) / ".worktrees"
+    worktrees_dir = Path(project_dir) / ".auto-claude" / "worktrees" / "tasks"
 
     if not specs_dir.exists():
         print_status("No specs directory found", "info")
@@ -209,7 +209,7 @@ def handle_batch_cleanup_command(project_dir: str, dry_run: bool = True) -> bool
             print(f"  - {spec_name}")
             wt_path = worktrees_dir / spec_name
             if wt_path.exists():
-                print(f"    └─ .worktrees/{spec_name}/")
+                print(f"    └─ .auto-claude/worktrees/tasks/{spec_name}/")
         print()
         print("Run with --no-dry-run to actually delete")
 

apps/backend/cli/utils.py

@@ -82,7 +82,7 @@ def find_spec(project_dir: Path, spec_identifier: str) -> Path | None:
                     return spec_folder
 
     # Check worktree specs (for merge-preview, merge, review, discard operations)
-    worktree_base = project_dir / ".worktrees"
+    worktree_base = project_dir / ".auto-claude" / "worktrees" / "tasks"
     if worktree_base.exists():
         # Try exact match in worktree
         worktree_spec = (

apps/backend/core/workspace.py

@@ -4,7 +4,7 @@
 =============================================
 
 Handles workspace isolation through Git worktrees, where each spec
-gets its own isolated worktree in .worktrees/{spec-name}/.
+gets its own isolated worktree in .auto-claude/worktrees/tasks/{spec-name}/.
 
 This module has been refactored for better maintainability:
 - Models and enums: workspace/models.py

apps/backend/core/workspace/__init__.py

@@ -4,7 +4,7 @@
 =============================
 
 Handles workspace isolation through Git worktrees, where each spec
-gets its own isolated worktree in .worktrees/{spec-name}/.
+gets its own isolated worktree in .auto-claude/worktrees/tasks/{spec-name}/.
 
 This package provides:
 - Workspace setup and configuration

apps/backend/core/workspace/finalization.py

@@ -169,7 +169,15 @@ def handle_workspace_choice(
         if staging_path:
             print(highlight(f"  cd {staging_path}"))
         else:
-            print(highlight(f"  cd {project_dir}/.worktrees/{spec_name}"))
+            worktree_path = get_existing_build_worktree(project_dir, spec_name)
+            if worktree_path:
+                print(highlight(f"  cd {worktree_path}"))
+            else:
+                print(
+                    highlight(
+                        f"  cd {project_dir}/.auto-claude/worktrees/tasks/{spec_name}"
+                    )
+                )
 
         # Show likely test/run commands
         if staging_path:
@@ -232,7 +240,15 @@ def handle_workspace_choice(
         if staging_path:
             print(highlight(f"  cd {staging_path}"))
         else:
-            print(highlight(f"  cd {project_dir}/.worktrees/{spec_name}"))
+            worktree_path = get_existing_build_worktree(project_dir, spec_name)
+            if worktree_path:
+                print(highlight(f"  cd {worktree_path}"))
+            else:
+                print(
+                    highlight(
+                        f"  cd {project_dir}/.auto-claude/worktrees/tasks/{spec_name}"
+                    )
+                )
         print()
         print("When you're ready to add it:")
         print(highlight(f"  python auto-claude/run.py --spec {spec_name} --merge"))

apps/backend/core/workspace/git_utils.py

@@ -222,10 +222,16 @@ def get_existing_build_worktree(project_dir: Path, spec_name: str) -> Path | Non
     Returns:
         Path to the worktree if it exists for this spec, None otherwise
     """
-    # Per-spec worktree path: .worktrees/{spec-name}/
-    worktree_path = project_dir / ".worktrees" / spec_name
-    if worktree_path.exists():
-        return worktree_path
+    # New path first
+    new_path = project_dir / ".auto-claude" / "worktrees" / "tasks" / spec_name
+    if new_path.exists():
+        return new_path
+
+    # Legacy fallback
+    legacy_path = project_dir / ".worktrees" / spec_name
+    if legacy_path.exists():
+        return legacy_path
+
     return None
 
 

apps/backend/core/workspace/models.py

@@ -249,7 +249,7 @@ def get_next_spec_number(self) -> int:
         max_number = max(max_number, self._scan_specs_dir(main_specs_dir))
 
         # 2. Scan all worktree specs
-        worktrees_dir = self.project_dir / ".worktrees"
+        worktrees_dir = self.project_dir / ".auto-claude" / "worktrees" / "tasks"
         if worktrees_dir.exists():
             for worktree in worktrees_dir.iterdir():
                 if worktree.is_dir():

apps/backend/core/worktree.py

@@ -4,7 +4,7 @@
 =============================================
 
 Each spec gets its own worktree:
-- Worktree path: .worktrees/{spec-name}/
+- Worktree path: .auto-claude/worktrees/tasks/{spec-name}/
 - Branch name: auto-claude/{spec-name}
 
 This allows:
@@ -48,14 +48,14 @@ class WorktreeManager:
     """
     Manages per-spec Git worktrees.
 
-    Each spec gets its own worktree in .worktrees/{spec-name}/ with
+    Each spec gets its own worktree in .auto-claude/worktrees/tasks/{spec-name}/ with
     a corresponding branch auto-claude/{spec-name}.
     """
 
     def __init__(self, project_dir: Path, base_branch: str | None = None):
         self.project_dir = project_dir
         self.base_branch = base_branch or self._detect_base_branch()
-        self.worktrees_dir = project_dir / ".worktrees"
+        self.worktrees_dir = project_dir / ".auto-claude" / "worktrees" / "tasks"
         self._merge_lock = asyncio.Lock()
 
     def _detect_base_branch(self) -> str:
@@ -194,7 +194,7 @@ def _unstage_gitignored_files(self) -> None:
 
     def setup(self) -> None:
         """Create worktrees directory if needed."""
-        self.worktrees_dir.mkdir(exist_ok=True)
+        self.worktrees_dir.mkdir(parents=True, exist_ok=True)
 
     # ==================== Per-Spec Worktree Methods ====================
 
@@ -478,14 +478,12 @@ def list_all_worktrees(self) -> list[WorktreeInfo]:
         """List all spec worktrees."""
         worktrees = []
 
-        if not self.worktrees_dir.exists():
-            return worktrees
-
-        for item in self.worktrees_dir.iterdir():
-            if item.is_dir():
-                info = self.get_worktree_info(item.name)
-                if info:
-                    worktrees.append(info)
+        if self.worktrees_dir.exists():
+            for item in self.worktrees_dir.iterdir():
+                if item.is_dir():
+                    info = self.get_worktree_info(item.name)
+                    if info:
+                        worktrees.append(info)
 
         return worktrees
 
@@ -587,81 +585,12 @@ def get_test_commands(self, spec_name: str) -> list[str]:
 
         return commands
 
-    # ==================== Backward Compatibility ====================
-    # These methods provide backward compatibility with the old single-worktree API
-
-    def get_staging_path(self) -> Path | None:
-        """
-        Backward compatibility: Get path to any existing spec worktree.
-        Prefer using get_worktree_path(spec_name) instead.
-        """
-        worktrees = self.list_all_worktrees()
-        if worktrees:
-            return worktrees[0].path
-        return None
-
-    def get_staging_info(self) -> WorktreeInfo | None:
-        """
-        Backward compatibility: Get info about any existing spec worktree.
-        Prefer using get_worktree_info(spec_name) instead.
-        """
-        worktrees = self.list_all_worktrees()
-        if worktrees:
-            return worktrees[0]
-        return None
-
-    def merge_staging(self, delete_after: bool = True) -> bool:
-        """
-        Backward compatibility: Merge first found worktree.
-        Prefer using merge_worktree(spec_name) instead.
-        """
-        worktrees = self.list_all_worktrees()
-        if worktrees:
-            return self.merge_worktree(worktrees[0].spec_name, delete_after)
-        return False
-
-    def remove_staging(self, delete_branch: bool = True) -> None:
-        """
-        Backward compatibility: Remove first found worktree.
-        Prefer using remove_worktree(spec_name) instead.
-        """
-        worktrees = self.list_all_worktrees()
-        if worktrees:
-            self.remove_worktree(worktrees[0].spec_name, delete_branch)
-
-    def get_or_create_staging(self, spec_name: str) -> WorktreeInfo:
-        """
-        Backward compatibility: Alias for get_or_create_worktree.
-        """
-        return self.get_or_create_worktree(spec_name)
-
-    def staging_exists(self) -> bool:
-        """
-        Backward compatibility: Check if any spec worktree exists.
-        Prefer using worktree_exists(spec_name) instead.
-        """
-        return len(self.list_all_worktrees()) > 0
-
-    def commit_in_staging(self, message: str) -> bool:
-        """
-        Backward compatibility: Commit in first found worktree.
-        Prefer using commit_in_worktree(spec_name, message) instead.
-        """
-        worktrees = self.list_all_worktrees()
-        if worktrees:
-            return self.commit_in_worktree(worktrees[0].spec_name, message)
-        return False
-
-    def has_uncommitted_changes(self, in_staging: bool = False) -> bool:
+    def has_uncommitted_changes(self, spec_name: str | None = None) -> bool:
         """Check if there are uncommitted changes."""
-        worktrees = self.list_all_worktrees()
-        if in_staging and worktrees:
-            cwd = worktrees[0].path
-        else:
-            cwd = None
+        cwd = None
+        if spec_name:
+            worktree_path = self.get_worktree_path(spec_name)
+            if worktree_path.exists():
+                cwd = worktree_path
         result = self._run_git(["status", "--porcelain"], cwd=cwd)
         return bool(result.stdout.strip())
-
-
-# Keep STAGING_WORKTREE_NAME for backward compatibility in imports
-STAGING_WORKTREE_NAME = "auto-claude"

apps/backend/merge/git_utils.py

@@ -27,29 +27,11 @@ def find_worktree(project_dir: Path, task_id: str) -> Path | None:
     Returns:
         Path to the worktree, or None if not found
     """
-    # Check common locations
-    worktrees_dir = project_dir / ".worktrees"
+    worktrees_dir = project_dir / ".auto-claude" / "worktrees" / "tasks"
     if worktrees_dir.exists():
-        # Look for worktree with task_id in name
         for entry in worktrees_dir.iterdir():
             if entry.is_dir() and task_id in entry.name:
                 return entry
-
-    # Try git worktree list
-    try:
-        result = subprocess.run(
-            ["git", "worktree", "list", "--porcelain"],
-            cwd=project_dir,
-            capture_output=True,
-            text=True,
-            check=True,
-        )
-        for line in result.stdout.split("\n"):
-            if line.startswith("worktree ") and task_id in line:
-                return Path(line.split(" ", 1)[1])
-    except subprocess.CalledProcessError:
-        pass
-
     return None
 
 

apps/backend/merge/timeline_git.py

@@ -189,7 +189,14 @@ def get_worktree_file_content(self, task_id: str, file_path: str) -> str:
             task_id.replace("task-", "") if task_id.startswith("task-") else task_id
         )
 
-        worktree_path = self.project_path / ".worktrees" / spec_name / file_path
+        worktree_path = (
+            self.project_path
+            / ".auto-claude"
+            / "worktrees"
+            / "tasks"
+            / spec_name
+            / file_path
+        )
         if worktree_path.exists():
             try:
                 return worktree_path.read_text(encoding="utf-8")

apps/backend/prompts/github/pr_codebase_fit_agent.md

@@ -6,6 +6,23 @@ You are a focused codebase fit review agent. You have been spawned by the orches
 
 Ensure new code integrates well with the existing codebase. Check for consistency with project conventions, reuse of existing utilities, and architectural alignment. Focus ONLY on codebase fit - not security, logic correctness, or general quality.
 
+## CRITICAL: PR Scope and Context
+
+### What IS in scope (report these issues):
+1. **Codebase fit issues in changed code** - New code not following project patterns
+2. **Missed reuse opportunities** - "Existing `utils.ts` has a helper for this"
+3. **Inconsistent with PR's own changes** - "You used `camelCase` here but `snake_case` elsewhere in the PR"
+4. **Breaking conventions in touched areas** - "Your change deviates from the pattern in this file"
+
+### What is NOT in scope (do NOT report):
+1. **Pre-existing inconsistencies** - Old code that doesn't follow patterns
+2. **Unrelated suggestions** - Don't suggest patterns for code the PR didn't touch
+
+**Key distinction:**
+- ✅ "Your new component doesn't follow the existing pattern in `components/`" - GOOD
+- ✅ "Consider using existing `formatDate()` helper instead of new implementation" - GOOD
+- ❌ "The old `legacy/` folder uses different naming conventions" - BAD (pre-existing)
+
 ## Codebase Fit Focus Areas
 
 ### 1. Naming Conventions

apps/backend/prompts/github/pr_finding_validator.md

@@ -4,13 +4,32 @@ You are a finding re-investigator. For each unresolved finding from a previous P
 
 Your job is to prevent false positives from persisting indefinitely by actually reading the code and verifying the issue exists.
 
+## CRITICAL: Check PR Scope First
+
+**Before investigating any finding, verify it's within THIS PR's scope:**
+
+1. **Check if the file is in the PR's changed files list** - If not, likely out-of-scope
+2. **Check if the line number exists** - If finding cites line 710 but file has 600 lines, it's hallucinated
+3. **Check for PR references in commit messages** - Commits like `fix: something (#584)` are from OTHER PRs
+
+**Dismiss findings as `dismissed_false_positive` if:**
+- The finding references a file NOT in the PR's changed files list AND is not about impact on that file
+- The line number doesn't exist in the file (hallucinated)
+- The finding is about code from a merged branch commit (not this PR's work)
+
+**Keep findings valid if they're about:**
+- Issues in code the PR actually changed
+- Impact of PR changes on other code (e.g., "this change breaks callers in X")
+- Missing updates to related code (e.g., "you updated A but forgot B")
+
 ## Your Mission
 
 For each finding you receive:
-1. **READ** the actual code at the file/line location using the Read tool
-2. **ANALYZE** whether the described issue actually exists in the code
-3. **PROVIDE** concrete code evidence for your conclusion
-4. **RETURN** validation status with evidence
+1. **VERIFY SCOPE** - Is this file/line actually part of this PR?
+2. **READ** the actual code at the file/line location using the Read tool
+3. **ANALYZE** whether the described issue actually exists in the code
+4. **PROVIDE** concrete code evidence for your conclusion
+5. **RETURN** validation status with evidence
 
 ## Investigation Process
 
@@ -122,12 +141,19 @@ Rate your confidence based on how certain you are:
 
 Watch for these patterns that often indicate false positives:
 
-1. **Sanitization elsewhere**: Input is validated/sanitized before reaching the flagged code
-2. **Internal-only code**: Code only handles trusted internal data, not user input
-3. **Framework protection**: Framework provides automatic protection (e.g., ORM parameterization)
-4. **Dead code**: The flagged code is never executed in the current codebase
-5. **Test code**: The issue is in test files where it's acceptable
-6. **Misread syntax**: Original reviewer misunderstood the language syntax
+1. **Non-existent line number**: The line number cited doesn't exist or is beyond EOF - hallucinated finding
+2. **Merged branch code**: Finding is about code from a commit like `fix: something (#584)` - another PR
+3. **Pre-existing issue, not impact**: Finding flags old bug in untouched code without showing how PR changes relate
+4. **Sanitization elsewhere**: Input is validated/sanitized before reaching the flagged code
+5. **Internal-only code**: Code only handles trusted internal data, not user input
+6. **Framework protection**: Framework provides automatic protection (e.g., ORM parameterization)
+7. **Dead code**: The flagged code is never executed in the current codebase
+8. **Test code**: The issue is in test files where it's acceptable
+9. **Misread syntax**: Original reviewer misunderstood the language syntax
+
+**Note**: Findings about files outside the PR's changed list are NOT automatically false positives if they're about:
+- Impact of PR changes on that file (e.g., "your change breaks X")
+- Missing related updates (e.g., "you forgot to update Y")
 
 ## Common Valid Issue Patterns