feat: merge working-copies completion

See feature commit for details.

.gitignore

@@ -17,6 +17,7 @@ __pycache__/
 *.so
 .python-version
 .venv/
+.venv-test/
 venv/
 env/
 .pytest_cache/
@@ -56,3 +57,4 @@ Thumbs.db
 .pi-lens/
 minerv3/
 .cache/
+openspec-audit-report.md

.pi-map.index.md

@@ -16,7 +16,7 @@ dir: .
 Trust boundary: index routes, map orients, source decides.
 
 ## role
-Infrastructure and deployment configuration for a self-hosted project management platform with OAuth2 authentication, providing Docker Compose orchestration, environment templates, and development tooling.
+Infrastructure and deployment configuration package for a self-hosted project management platform with OAuth2 authentication, providing Docker orchestration, environment templates, and development tooling.
 ## parent
 -
 ## children

.pi-map.md

@@ -18,10 +18,10 @@ index: ./.pi-map.index.md
 Trust boundary: index routes, map orients, source decides.
 
 ## role
-Infrastructure and deployment configuration for a self-hosted project management platform with OAuth2 authentication, providing Docker Compose orchestration, environment templates, and development tooling.
+Infrastructure and deployment configuration package for a self-hosted project management platform with OAuth2 authentication, providing Docker orchestration, environment templates, and development tooling.
 ## files
 - .env.example | Provides a template of environment variables for configuring a Headquarter application with PostgreSQL, Redis, Authentik SSO, and Docker/Traefik deployment
-- .gitignore | Specifies files and directories for Git to ignore across a multi-language project with Python, Node, and various tooling | dep: git
+- .gitignore | Specifies files and directories for Git to ignore across a multi-language project with Python, Node, and custom tooling | dep: Git
 - AGENTS.md | Defines operational rules, workflows, and constraints for AI agents working within an OpenSpec-driven software development project. | dep: OpenSpec, superpowers, git, docker compose, conventional commits
 - CHANGELOG.md | Documents version history and notable changes for a Git-based project management web application
 - Makefile | Provides standard development commands for containerized web application lifecycle management via Docker Compose | dep: docker compose, alembic, pytest, ruff, mypy, playwright, npm, postgres, redis
@@ -31,7 +31,7 @@ Infrastructure and deployment configuration for a self-hosted project management
 - progress.md | Tracks completed and remaining tasks for a backend-frontend code refactoring project organized in 7 phases
 - swap-pane | Empty file with no functionality
 ## arch
-Containerized microservices architecture using Docker Compose with separate frontend/API/PostgreSQL/Redis services, Traefik reverse proxy integration, and environment-driven configuration; includes AI agent governance via OpenSpec and Makefile-driven development workflows.
+Containerized microservices architecture using Docker Compose with PostgreSQL/Redis data layer, Traefik reverse proxy for TLS/ingress, and environment-driven configuration; includes Python/Node multi-language backend-frontend split with Makefile-driven lifecycle management.
 ## tags
 docker, redis, git, application, postgresql, compose, traefik, project
 ## symbols

apps/.pi-map.index.md

@@ -2,7 +2,7 @@
 dir: apps
 
 ## role
-Contains the main application entry points and executable modules for the project.
+Contains the top-level application entry points and executable binaries for the project.
 ## parent
 index: ./.pi-map.index.md
 map: ./.pi-map.md

apps/.pi-map.md

@@ -4,10 +4,10 @@ dir: apps
 index: apps/.pi-map.index.md
 
 ## role
-Contains the main application entry points and executable modules for the project.
+Contains the top-level application entry points and executable binaries for the project.
 ## files
 ## arch
-Typically follows a modular architecture where each subdirectory represents a separate deployable application sharing common domain libraries.
+Follows a workspace/monorepo pattern where each subdirectory is a distinct deployable application sharing common libraries.
 ## tags
 -
 ## symbols

apps/api/src/api/tool/sessions.py

@@ -74,8 +74,6 @@ async def get_user_sessions(
                 "workspace_name": workspace_name,
                 "status": instance.status,
                 "url": instance.url,
-                "clone_mode": instance.clone_mode,
-                "branch": instance.branch,
                 "selected_config_profile_id": str(instance.selected_config_profile_id)
                 if instance.selected_config_profile_id
                 else None,

apps/api/src/api/tool/tool_instances.py

@@ -68,8 +68,7 @@ async def create_instance(
         "display_name": instance.display_name,
         "tool_type_id": str(instance.tool_type_id),
         "status": instance.status,
-        "clone_mode": instance.clone_mode,
+        "workspace_id": str(instance.workspace_id) if instance.workspace_id else None,
-        "branch": instance.branch,
         "selected_config_profile_id": str(instance.selected_config_profile_id) if instance.selected_config_profile_id else None,
         "created_at": instance.created_at.isoformat(),
     }
@@ -143,8 +142,6 @@ async def get_instance(
         "container_id": instance.container_id,
         "container_name": instance.container_name,
         "compose_path": instance.compose_path,
-        "clone_mode": instance.clone_mode,
-        "branch": instance.branch,
         "workspace_id": str(instance.workspace_id) if instance.workspace_id else None,
         "selected_config_profile_id": str(instance.selected_config_profile_id) if instance.selected_config_profile_id else None,
         "ssh_key_ids": instance.ssh_key_ids,

apps/api/src/api/workspace/workspace_instances.py

@@ -2,13 +2,16 @@
 
 import uuid
 
-from fastapi import APIRouter, Depends, HTTPException
+from fastapi import APIRouter, Depends, HTTPException, status
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
+from src.models import GitRepository
 from src.models import ToolInstance
 from src.models import Workspace
+from src.schemas.tool import CreateInstanceRequest, CreateWorkspaceInstanceRequest
+from src.services.tool.instance_service import create_tool_instance
 
 router = APIRouter(prefix="/workspaces/{workspace_id}/instances")
 
@@ -30,6 +33,63 @@ async def _get_workspace(
     return workspace
 
 
+@router.post(
+    "/",
+    summary="Create instance from workspace",
+    description="Create a new tool instance mounted on this workspace.",
+    status_code=status.HTTP_201_CREATED,
+)
+async def create_workspace_instance(
+    workspace_id: uuid.UUID,
+    data: CreateWorkspaceInstanceRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Create a tool instance directly on a workspace."""
+    workspace = await _get_workspace(session, workspace_id, user_id)
+
+    repo = await session.get(GitRepository, workspace.repo_id)
+    if repo is None:
+        raise HTTPException(status_code=404, detail="Repository not found")
+    if repo.project_id is None:
+        raise HTTPException(
+            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
+            detail="Repository is not associated with a project",
+        )
+
+    request = CreateInstanceRequest(
+        tool_type_id=data.tool_type_id,
+        display_name=data.display_name,
+        workspace_id=str(workspace.id),
+        config_profile_id=data.config_profile_id,
+        ssh_key_ids=data.ssh_key_ids,
+    )
+
+    try:
+        instance = await create_tool_instance(
+            session, user_id, repo.project_id, repo.id, request
+        )
+    except ValueError as exc:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(exc))
+    except RuntimeError as exc:
+        raise HTTPException(
+            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(exc)
+        )
+
+    return {
+        "id": str(instance.id),
+        "name": instance.name,
+        "display_name": instance.display_name,
+        "tool_type_id": str(instance.tool_type_id),
+        "status": instance.status,
+        "workspace_id": str(instance.workspace_id) if instance.workspace_id else None,
+        "selected_config_profile_id": str(instance.selected_config_profile_id)
+        if instance.selected_config_profile_id
+        else None,
+        "created_at": instance.created_at.isoformat(),
+    }
+
+
 @router.get("/")
 async def list_workspace_instances(
     workspace_id: uuid.UUID,

apps/api/src/models/tool/tool_instance.py

@@ -53,9 +53,11 @@ class ToolInstance(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     )
     image_tag: Mapped[str | None] = mapped_column(String(256), nullable=True)
     probe_result: Mapped[dict | None] = mapped_column(JSON, nullable=True)
-    clone_mode: Mapped[str] = mapped_column(String(20), nullable=False, default="mount")
+    clone_mode: Mapped[str | None] = mapped_column(
+        String(20), nullable=True, default=None
+    )
     branch: Mapped[str | None] = mapped_column(
-        String(255), nullable=True, default="main"
+        String(255), nullable=True, default=None
     )
     selected_config_profile_id: Mapped[uuid.UUID | None] = mapped_column(
         UUID(), ForeignKey("config_profiles.id", ondelete="SET NULL"), nullable=True

apps/api/src/schemas/tool/__init__.py

@@ -1,6 +1,10 @@
 """Tool schemas module."""
 
-from src.schemas.tool.tool_instance import CreateInstanceRequest, StartInstanceRequest
+from src.schemas.tool.tool_instance import (
+    CreateInstanceRequest,
+    CreateWorkspaceInstanceRequest,
+    StartInstanceRequest,
+)
 from src.schemas.tool.tool_type import (
     ToolTypeCreate,
     ToolTypeResponse,
@@ -10,6 +14,7 @@ from src.schemas.tool.tool_type import (
 
 __all__ = [
     "CreateInstanceRequest",
+    "CreateWorkspaceInstanceRequest",
     "StartInstanceRequest",
     "ToolTypeCreate",
     "ToolTypeResponse",

apps/api/src/schemas/tool/tool_instance.py

@@ -13,16 +13,24 @@ class CreateInstanceRequest(BaseModel):
         default=None, description="Optional display name for the instance"
     )
     workspace_id: str | None = Field(
-        default=None, description="UUID of workspace to mount (replaces clone_mode)"
+        default=None, description="UUID of workspace to mount"
     )
-    clone_mode: str = Field(
+    config_profile_id: str | None = Field(
-        default="mount", description="Repository access mode: 'mount' or 'clone'"
+        default=None, description="Optional config profile ID for launch"
     )
-    branch: str | None = Field(
+    ssh_key_ids: list[str] = Field(
-        default="main", description="Branch to clone (when clone_mode='clone')"
+        default_factory=list, description="SSH key IDs to mount into container ~/.ssh"
     )
-    new_branch: str | None = Field(
+
-        default=None, description="Create a new local branch after cloning"
+
+class CreateWorkspaceInstanceRequest(BaseModel):
+    """Request body for creating a tool instance directly on a workspace."""
+
+    model_config = {"extra": "ignore"}
+
+    tool_type_id: str = Field(description="UUID of the tool type to instantiate")
+    display_name: str | None = Field(
+        default=None, description="Optional display name for the instance"
     )
     config_profile_id: str | None = Field(
         default=None, description="Optional config profile ID for launch"

apps/api/src/services/shared/workspace_manager.py

@@ -150,7 +150,7 @@ class WorkspaceManager:
 
         # Stop and delete all instances
         for instance in instances:
-            await self._stop_and_delete_instance(instance)
+            await self._stop_and_delete_instance(instance, session)
 
         # Delete directory
         if os.path.exists(workspace.path):
@@ -248,10 +248,154 @@ class WorkspaceManager:
         )
         return list(result.scalars().all())
 
-    async def _stop_and_delete_instance(self, instance: ToolInstance) -> None:
+    async def _stop_and_delete_instance(
+        self,
+        instance: ToolInstance,
+        session: AsyncSession,
+    ) -> None:
         """Stop and delete a tool instance.
 
-        TODO(PR-2): Wire up to actual instance stop/delete logic.
+        Delegates to the instance lifecycle service to ensure containers,
-        For now, this is a placeholder.
+        tunnels, and on-disk files are cleaned up.
         """
-        logger.warning("Placeholder: stopping and deleting instance %s", instance.id)
+        # Local import avoids a circular dependency between workspace and
+        # instance lifecycle modules.
+        from src.services.tool.instance_service import delete_tool_instance
+
+        try:
+            await delete_tool_instance(
+                session=session,
+                user_id=instance.owner_id,
+                project_id=instance.project_id,
+                repo_id=instance.repository_id,
+                instance_id=instance.id,
+                force=True,
+            )
+            logger.info("Stopped and deleted instance %s", instance.id)
+        except Exception as exc:
+            logger.error(
+                "Failed to stop/delete instance %s during workspace cleanup: %s",
+                instance.id,
+                exc,
+            )
+
+    async def ensure_instance_workspace(
+        self,
+        instance: ToolInstance,
+        session: AsyncSession,
+    ) -> Workspace:
+        """Return the workspace for an instance, creating/binding one if needed.
+
+        This migrates legacy instances that were created before workspaces
+        existed. Clone-mode instances have their existing clone moved into a
+        workspace, while mount-mode instances get a fresh workspace from the
+        canonical repository.
+
+        The operation is best-effort: failures are re-raised so the caller can
+        decide whether to continue with a legacy fallback path.
+        """
+        if instance.workspace_id is not None:
+            workspace = await session.get(Workspace, instance.workspace_id)
+            if workspace is not None:
+                return workspace
+
+        from src.models import GitRepository
+
+        repo = await session.get(GitRepository, instance.repository_id)
+        if repo is None:
+            raise RuntimeError(f"Repository {instance.repository_id} not found")
+
+        base_name = (
+            f"{instance.name}-migrated"
+            if instance.clone_mode == "clone"
+            else f"{instance.name}-legacy"
+        )
+        name = base_name
+        counter = 1
+        while await self._workspace_name_exists(session, repo.id, name):
+            name = f"{base_name}-{counter}"
+            counter += 1
+
+        if instance.clone_mode == "clone":
+            workspace = await self._migrate_clone_into_workspace(
+                instance, repo, session, name
+            )
+        else:
+            workspace = await self.create(
+                repo=repo,
+                user_id=instance.owner_id,
+                name=name,
+                branch=instance.branch or "main",
+                session=session,
+            )
+
+        instance.workspace_id = workspace.id
+        instance.clone_mode = None
+        session.add(instance)
+        await session.commit()
+        await session.refresh(instance)
+        logger.info(
+            "Migrated instance %s to workspace %s (%s)",
+            instance.id,
+            workspace.id,
+            name,
+        )
+        return workspace
+
+    async def _workspace_name_exists(
+        self,
+        session: AsyncSession,
+        repo_id: uuid.UUID,
+        name: str,
+    ) -> bool:
+        """Check whether a workspace name already exists for a repository."""
+        result = await session.execute(
+            select(Workspace).where(
+                Workspace.repo_id == repo_id,
+                Workspace.name == name,
+            )
+        )
+        return result.scalar_one_or_none() is not None
+
+    async def _migrate_clone_into_workspace(
+        self,
+        instance: ToolInstance,
+        repo: "GitRepository",
+        session: AsyncSession,
+        name: str,
+    ) -> Workspace:
+        """Move an existing clone-mode repo into a new workspace path."""
+        import shutil
+
+        if not instance.compose_path:
+            raise RuntimeError("Instance has no compose path")
+
+        instance_dir = os.path.dirname(instance.compose_path)
+        clone_path = os.path.join(instance_dir, "repo-clone")
+        if not os.path.exists(clone_path):
+            raise RuntimeError(f"Clone path not found: {clone_path}")
+
+        path = self._workspace_path(repo.id, name)
+        parent = os.path.dirname(path)
+        os.makedirs(parent, exist_ok=True)
+        with contextlib.suppress(OSError):
+            os.chmod(parent, 0o777)
+
+        if os.path.exists(path):
+            shutil.rmtree(path, ignore_errors=True)
+
+        shutil.move(clone_path, path)
+        self._make_world_writable(path)
+
+        workspace = Workspace(
+            name=name,
+            repo_id=repo.id,
+            user_id=instance.owner_id,
+            branch=instance.branch or "main",
+            path=path,
+            status="ready",
+            last_sync_at=datetime.now(),
+        )
+        session.add(workspace)
+        await session.flush()
+        return workspace

apps/api/src/services/tool/instance_service.py

@@ -830,8 +830,6 @@ async def prepare_manifest_instance(
 
     # Prepare SSH path for mount resolution
     ssh_path = ""
-    if instance.clone_mode == "clone":
-        ssh_path = os.path.join(instance_dir, ".ssh")
 
     # Resolve git mount variables from config profile
     git_mount_vars = {}
@@ -848,6 +846,7 @@ async def prepare_manifest_instance(
         "IMAGE_TAG": image_tag,
         "INSTANCE_NAME": instance.name.lower(),
         "INSTANCE_DIR": instance_dir,
+        "WORKSPACE_PATH": repo_path,
         "REPO_PATH": repo_path,
         "SSH_PATH": ssh_path,
         "TOOL_PORT": instance.port or 0,
@@ -922,13 +921,6 @@ async def create_tool_instance(
         if workspace.repo_id != repo_id:
             raise ValueError("workspace does not belong to this repository")
 
-    # Validate clone mode requirements (legacy path)
-    if data.clone_mode == "clone" and not workspace:
-        if not repo.remote_url:
-            raise ValueError("repository does not have a remote URL for cloning")
-        if not repo.ssh_key_id:
-            raise ValueError("repository must have an SSH key assigned for clone mode")
-
     # Generate unique name
     instance_name = f"{tool_type.name}-{repo.name}-{uuid.uuid4().hex[:8]}"
 
@@ -970,71 +962,13 @@ async def create_tool_instance(
     # Find free port
     tool_port = find_free_port()
 
-    # Determine repo path based on workspace or clone mode
+    # Determine the source path to mount. Workspaces are the canonical path;
+    # legacy instances without a workspace fall back to the repository path.
     if workspace:
         repo_path = workspace.path
-    elif data.clone_mode == "clone":
-        ssh_key = await session.get(SSHKey, repo.ssh_key_id)
-        if ssh_key is None:
-            raise ValueError("repository SSH key not found")
-
-        ssh_key_path = None
-        try:
-            ssh_dir = prepare_ssh_key_files(instance_dir, ssh_key)
-            ssh_key_path = os.path.join(ssh_dir, "id_ed25519")
-
-            clone_path = clone_repository(
-                remote_url=repo.remote_url,
-                ssh_key_path=ssh_key_path,
-                instance_dir=instance_dir,
-                branch=data.branch or "main",
-            )
-            repo_path = clone_path
-        except Exception as exc:
-            logger.exception("Failed to clone repository: %s", exc)
-            cleanup_ssh_key_files(instance_dir)
-            raise RuntimeError(f"Failed to clone repository: {exc}")
     else:
         repo_path = repo.path
 
-    # Verify cloned repo has files
-    if data.clone_mode == "clone" and repo_path:
-        try:
-            repo_contents = os.listdir(repo_path)
-            if not repo_contents or (
-                len(repo_contents) == 1 and repo_contents[0] == ".git"
-            ):
-                logger.error("Cloned repository at %s appears empty", repo_path)
-                raise RuntimeError("Cloned repository is empty")
-            logger.debug(
-                "Verified cloned repo at %s has %d items",
-                repo_path,
-                len(repo_contents),
-            )
-        except Exception as exc:
-            logger.exception("Failed to verify cloned repository: %s", exc)
-            raise RuntimeError(f"Cloned repository verification failed: {exc}")
-
-    # Create new local branch if requested
-    if data.clone_mode == "clone" and data.new_branch:
-        try:
-            result = subprocess.run(
-                ["git", "-C", repo_path, "checkout", "-b", data.new_branch],
-                capture_output=True,
-                text=True,
-            )
-            if result.returncode != 0:
-                logger.error(
-                    "Failed to create branch %s: %s", data.new_branch, result.stderr
-                )
-                raise RuntimeError(f"Failed to create branch: {result.stderr}")
-            logger.debug(
-                "Created local branch %s in cloned repository", data.new_branch
-            )
-        except Exception as exc:
-            logger.exception("Failed to create local branch: %s", exc)
-            raise RuntimeError(f"Failed to create local branch: {exc}")
-
     # Handle based on definition type
     if tool_type.definition_type == "dockerfile":
         image_tag = f"headquarter/{instance_name}:latest".lower()
@@ -1092,10 +1026,13 @@ async def create_tool_instance(
 
         image_tag = compute_image_tag(tool_type.name, manifest)
 
+        # Manifest templates use WORKSPACE_PATH; REPO_PATH is retained as a
+        # deprecated alias for backward compatibility with older templates.
         variables = {
             "IMAGE_TAG": image_tag,
             "INSTANCE_NAME": instance_name.lower(),
             "INSTANCE_DIR": instance_dir,
+            "WORKSPACE_PATH": repo_path,
             "REPO_PATH": repo_path,
             "SSH_PATH": "",
             "TOOL_PORT": tool_port,
@@ -1109,6 +1046,7 @@ async def create_tool_instance(
         if not tool_type.compose_template:
             raise ValueError("Tool type has no compose template configured")
         variables = {
+            "WORKSPACE_PATH": repo_path,
             "REPO_PATH": repo_path,
             "INSTANCE_NAME": instance_name,
             "INSTANCE_ID": instance_name,
@@ -1121,37 +1059,6 @@ async def create_tool_instance(
             tool_type.compose_template, variables
         )
 
-        if data.clone_mode == "clone" and repo_path:
-            import yaml
-
-            compose_data = yaml.safe_load(compose_content)
-            repo_mounted = False
-            if compose_data and "services" in compose_data:
-                for svc in compose_data["services"].values():
-                    volumes = svc.get("volumes", [])
-                    for vol in volumes:
-                        vol_str = str(vol)
-                        if repo_path in vol_str:
-                            repo_mounted = True
-                            break
-                    if repo_mounted:
-                        break
-
-            if not repo_mounted:
-                logger.warning(
-                    "Compose template for tool type %s does not mount repo path; adding default mount",
-                    tool_type.name,
-                )
-                if compose_data and "services" in compose_data:
-                    for svc in compose_data["services"].values():
-                        if "volumes" not in svc:
-                            svc["volumes"] = []
-                        svc["volumes"].append(f"{repo_path}:/workspace")
-                        break
-                    compose_content = yaml.dump(
-                        compose_data, default_flow_style=False
-                    )
-
         write_compose_file(instance_dir, compose_content)
 
     # Create database record
@@ -1166,10 +1073,8 @@ async def create_tool_instance(
         compose_path=compose_path,
         port=tool_port,
         workspace_id=workspace_id,
-        clone_mode=data.clone_mode,
+        clone_mode=None,
-        branch=data.new_branch
+        branch=None,
-        if data.new_branch
-        else (data.branch if data.clone_mode == "clone" else None),
         selected_config_profile_id=selected_profile_id,
         ssh_key_ids=data.ssh_key_ids or None,
     )

apps/api/tests/unit/test_session_branch_selection.py

@@ -1,179 +0,0 @@
-"""Tests for session creation with branch selection and new branch creation."""
-
-import os
-import subprocess
-import tempfile
-
-
-from src.api.tool_instances import CreateInstanceRequest
-
-
-class TestCreateInstanceRequest:
-    """Tests for CreateInstanceRequest model."""
-
-    def test_default_values(self):
-        """Test default values for CreateInstanceRequest."""
-        request = CreateInstanceRequest(tool_type_id="123")
-        assert request.clone_mode == "mount"
-        assert request.branch == "main"
-        assert request.new_branch is None
-        assert request.display_name is None
-
-    def test_clone_mode_with_branch(self):
-        """Test CreateInstanceRequest with clone mode and branch."""
-        request = CreateInstanceRequest(
-            tool_type_id="123",
-            clone_mode="clone",
-            branch="dev",
-        )
-        assert request.clone_mode == "clone"
-        assert request.branch == "dev"
-
-    def test_new_branch_field(self):
-        """Test CreateInstanceRequest with new_branch field."""
-        request = CreateInstanceRequest(
-            tool_type_id="123",
-            clone_mode="clone",
-            branch="main",
-            new_branch="feature/test",
-        )
-        assert request.new_branch == "feature/test"
-
-
-class TestBranchCreationInClone:
-    """Tests for branch creation logic in clone process."""
-
-    def test_create_local_branch_success(self):
-        """Test successful local branch creation."""
-        with tempfile.TemporaryDirectory() as tmpdir:
-            # Initialize repo
-            subprocess.run(
-                ["git", "init", tmpdir],
-                capture_output=True,
-                check=True,
-            )
-            subprocess.run(
-                ["git", "-C", tmpdir, "config", "user.email", "test@test.com"],
-                capture_output=True,
-                check=True,
-            )
-            subprocess.run(
-                ["git", "-C", tmpdir, "config", "user.name", "Test User"],
-                capture_output=True,
-                check=True,
-            )
-            
-            # Create initial commit
-            readme = os.path.join(tmpdir, "README.md")
-            with open(readme, "w") as f:
-                f.write("# Test\n")
-            subprocess.run(
-                ["git", "-C", tmpdir, "add", "README.md"],
-                capture_output=True,
-                check=True,
-            )
-            subprocess.run(
-                ["git", "-C", tmpdir, "commit", "-m", "Initial commit"],
-                capture_output=True,
-                check=True,
-            )
-            
-            # Create new branch
-            result = subprocess.run(
-                ["git", "-C", tmpdir, "checkout", "-b", "feature/new-branch"],
-                capture_output=True,
-                text=True,
-            )
-            
-            assert result.returncode == 0
-            
-            # Verify branch exists
-            branches_result = subprocess.run(
-                ["git", "-C", tmpdir, "branch", "--show-current"],
-                capture_output=True,
-                text=True,
-            )
-            assert branches_result.stdout.strip() == "feature/new-branch"
-
-    def test_create_local_branch_invalid_name(self):
-        """Test local branch creation with invalid name fails."""
-        with tempfile.TemporaryDirectory() as tmpdir:
-            # Initialize repo
-            subprocess.run(
-                ["git", "init", tmpdir],
-                capture_output=True,
-                check=True,
-            )
-            subprocess.run(
-                ["git", "-C", tmpdir, "config", "user.email", "test@test.com"],
-                capture_output=True,
-                check=True,
-            )
-            subprocess.run(
-                ["git", "-C", tmpdir, "config", "user.name", "Test User"],
-                capture_output=True,
-                check=True,
-            )
-            
-            # Create initial commit
-            readme = os.path.join(tmpdir, "README.md")
-            with open(readme, "w") as f:
-                f.write("# Test\n")
-            subprocess.run(
-                ["git", "-C", tmpdir, "add", "README.md"],
-                capture_output=True,
-                check=True,
-            )
-            subprocess.run(
-                ["git", "-C", tmpdir, "commit", "-m", "Initial commit"],
-                capture_output=True,
-                check=True,
-            )
-            
-            # Try to create branch with invalid name (contains spaces)
-            result = subprocess.run(
-                ["git", "-C", tmpdir, "checkout", "-b", "invalid branch name"],
-                capture_output=True,
-                text=True,
-            )
-            
-            # Git accepts branch names with spaces but it's not recommended
-            # This test verifies the command structure
-            assert result.returncode == 0 or "fatal" in result.stderr
-
-
-class TestCreateInstanceAPI:
-    """Tests for create instance API endpoint with branch options."""
-
-    def test_create_instance_request_validation(self):
-        """Test that CreateInstanceRequest validates correctly."""
-        # Valid request with new_branch
-        request = CreateInstanceRequest(
-            tool_type_id="550e8400-e29b-41d4-a716-446655440000",
-            clone_mode="clone",
-            branch="main",
-            new_branch="feature/test",
-        )
-        assert request.new_branch == "feature/test"
-        
-        # Valid request without new_branch
-        request2 = CreateInstanceRequest(
-            tool_type_id="550e8400-e29b-41d4-a716-446655440000",
-            clone_mode="clone",
-            branch="dev",
-        )
-        assert request2.new_branch is None
-
-    def test_create_instance_with_new_branch_sets_instance_branch(self):
-        """Test that instance branch is set to new_branch when provided."""
-        # This tests the logic: data.new_branch if data.new_branch else data.branch
-        new_branch = "feature/test"
-        base_branch = "main"
-        
-        # Simulate the logic from create_instance
-        stored_branch = new_branch if new_branch else base_branch
-        assert stored_branch == "feature/test"
-        
-        # Without new_branch
-        stored_branch2 = None if None else base_branch
-        assert stored_branch2 == "main"

apps/web/.pi-map.index.md

@@ -2,7 +2,7 @@
 dir: apps/web
 
 ## role
-Browser-based web frontend providing the user-facing React application for code editing, terminal access, and routing functionality.
+Frontend web application providing a React-based UI with code editing, terminal, and routing capabilities for the "headquarter" project.
 ## parent
 index: apps/.pi-map.index.md
 map: apps/.pi-map.md

apps/web/.pi-map.md

@@ -4,7 +4,7 @@ dir: apps/web
 index: apps/web/.pi-map.index.md
 
 ## role
-Browser-based web frontend providing the user-facing React application for code editing, terminal access, and routing functionality.
+Frontend web application providing a React-based UI with code editing, terminal, and routing capabilities for the "headquarter" project.
 ## files
 - .env.example | Template file defining example environment variables for frontend API and application URL configuration
 - .eslintrc.cjs | Configures ESLint for a TypeScript browser project with modern ECMAScript module support | dep: @typescript-eslint/parser, @typescript-eslint/eslint-plugin, eslint
@@ -16,7 +16,7 @@ Browser-based web frontend providing the user-facing React application for code
 - tsconfig.json | TypeScript configuration file for a React project using Vite with modern ES2020 target and bundler module resolution | dep: typescript, react, vite
 - vite.config.ts | Configures Vite build tool for a React project with custom dev server port and Vitest test settings. | dep: vite, @vitejs/plugin-react
 ## arch
-Modern React SPA built with Vite and TypeScript, containerized via multi-stage Docker/nginx deployment with client-side routing and optimized static asset delivery.
+Modern React SPA built with Vite and TypeScript, containerized via multi-stage Docker with nginx serving, featuring client-side routing, optimized static asset delivery, and development tooling (ESLint, Vitest).
 ## tags
 react, eslint, vite, typescript, dom, application, nginx, web
 ## symbols

apps/web/src/.pi-map.index.md

@@ -2,7 +2,7 @@
 dir: apps/web/src
 
 ## role
-Frontend web application entry point and core infrastructure for a React-based single-page application with authentication, routing, and domain type definitions.
+Frontend web application entry point and core infrastructure for a React single-page application with authentication, routing, and domain type definitions.
 ## parent
 index: apps/web/.pi-map.index.md
 map: apps/web/.pi-map.md

apps/web/src/.pi-map.md

@@ -4,13 +4,13 @@ dir: apps/web/src
 index: apps/web/src/.pi-map.index.md
 
 ## role
-Frontend web application entry point and core infrastructure for a React-based single-page application with authentication, routing, and domain type definitions.
+Frontend web application entry point and core infrastructure for a React single-page application with authentication, routing, and domain type definitions.
 ## files
 - main.tsx | Entry point that bootstraps a React SPA with routing, authentication, and session management context providers. | dep: react, react-dom/client, react-router-dom, ./router, ./state/auth, ./state/sessions, ./styles/tokens.css, ./styles/global.css, ./styles/utilities.css, ./styles/syntax-highlight.css, ./styles/pages/git-history.css, ./styles/pages/repo-workspace.css, ./styles/pages/projects.css, ./styles/pages/sessions.css, ./styles/pages/ssh-keys.css, ./styles/pages/workspace-detail.css, ./styles/pages/workspaces.css, react-dom, ./styles/*
 - router.tsx | Defines the React Router configuration for a web application with protected routes, nested layouts, and redirects. | exp: AppRouter | dep: react-router-dom, ./components/app-shell, ./components/protected-route, ./pages/DashboardPage, ./pages/PlaceholderPage, ./pages/ProfilePage, ./pages/ProjectsPage, ./pages/GitRepositoriesPage, ./pages/GitHistoryPage, ./pages/ProjectSettingsPage, ./pages/SettingsPage, ./pages/TerminalPage, ./pages/ToolWorkshopPage, ./pages/SshKeysPage, ./pages/ConfigProfilesPage, ./pages/SessionsPage, ./pages/WorkspacesPage, ./pages/WorkspaceDetailPage
 - types.ts | Defines TypeScript type definitions for user sessions, projects, repositories, and workspaces in an application. | exp: SessionUser, SessionPayload, Project, WorkspaceSummary, RepositorySummary, ProjectWithRepos
 ## arch
-Layered React SPA architecture using context providers for cross-cutting concerns (auth/session), declarative routing with protected route guards and nested layouts, and centralized TypeScript type definitions for domain models.
+Layered React SPA architecture using context providers for cross-cutting concerns (auth/session), declarative routing with nested layouts and route guards, and centralized TypeScript type definitions for domain models.
 ## tags
 pages, styles, css, router, react, session, dom, workspace
 ## symbols

apps/web/src/api/sessions.ts

@@ -31,8 +31,6 @@ export interface Session {
 	url: string | null;
 	container_status?: string;
 	probe_status?: string;
-	clone_mode?: string;
-	branch?: string | null;
 	created_at?: string;
 }
 
@@ -51,12 +49,9 @@ export async function createInstance(
 	repoId: string,
 	toolTypeId: string,
 	displayName?: string,
-	cloneMode?: string,
+	workspaceId?: string,
-	branch?: string,
-	newBranch?: string,
 	configProfileId?: string,
 	sshKeyIds?: string[],
-	workspaceId?: string,
 ): Promise<ToolInstance> {
 	const response = await apiClient.post(
 		`/projects/${projectId}/repositories/${repoId}/instances`,
@@ -64,9 +59,6 @@ export async function createInstance(
 			tool_type_id: toolTypeId,
 			display_name: displayName,
 			workspace_id: workspaceId || undefined,
-			clone_mode: cloneMode || "mount",
-			branch: branch || undefined,
-			new_branch: newBranch || undefined,
 			config_profile_id: configProfileId,
 			ssh_key_ids: sshKeyIds || [],
 		},

apps/web/src/components/.pi-map.index.md

@@ -2,7 +2,7 @@
 dir: apps/web/src/components
 
 ## role
-Provides reusable, foundational React UI components and utilities for the web application, including layout shell, data visualization, navigation guards, and user feedback systems.
+Provides foundational, reusable UI components and utilities for the web application, including layout shell, data states, icon system, code display, routing guards, and toast notification rules.
 ## parent
 index: apps/web/src/.pi-map.index.md
 map: apps/web/src/.pi-map.md

apps/web/src/components/.pi-map.md

@@ -4,7 +4,7 @@ dir: apps/web/src/components
 index: apps/web/src/components/.pi-map.index.md
 
 ## role
-Provides reusable, foundational React UI components and utilities for the web application, including layout shell, data visualization, navigation guards, and user feedback systems.
+Provides foundational, reusable UI components and utilities for the web application, including layout shell, data states, icon system, code display, routing guards, and toast notification rules.
 ## files
 - app-shell.tsx | Renders the main application shell layout with navigation, session management, and responsive mobile/desktop views for a React Router-based app. | exp: AppShell | dep: react-router-dom, ../api/sessions, ../hooks/use-theme, ../state/auth, ../state/sessions, ../hooks/use-mobile-viewport, ../state/events, ../state/toast, ../state/notifications, ../state/session-operations, ./features/notification/event-toast-bridge, ./features/notification/notification-center, ./features/session/session-progress-panel, ./icon, ./features/mobile/mobile-nav, ./features/tool/start-tool-fab, ../utils/icons
 - code-editor.tsx | A React component that renders a syntax-highlighted code editor with line numbers using react-simple-code-editor. | exp: CodeEditor | dep: react, react-simple-code-editor, ../utils/language
@@ -16,7 +16,7 @@ Provides reusable, foundational React UI components and utilities for the web ap
 - toast-rules.test.ts | Unit tests for mapping instance events to toast notification categories and severities | dep: vitest, ./toast-rules, ../types/events
 - toast-rules.ts | Maps instance events to toast notifications with deduplication logic to prevent spam | exp: func:mapEventToCategory(event: InstanceEventPayload) → string, call:event.event.startsWith, func:mapEventToSeverity(event: InstanceEventPayload) → "info" | "warning" | "error" | "success", func:handleEventToast(event: InstanceEventPayload) → void, call:shouldShowToast, call:toast.info, call:toast.success, call:toast.warning, call:toast.error, func:clearToastDedup() → void, call:lastToastTime.clear | dep: ../state/toast, ../types/events, toast state module, InstanceEventPayload type
 ## arch
-Component-based architecture with functional React patterns, composition of specialized sub-components (icon, editor, syntax highlighter), separation of concerns via dedicated state-management components (data states, protected routes), and utility modules with pure logic for cross-cutting concerns (toast rules with deduplication).
+Follows a component-based React architecture with separation of concerns between presentational components (icon, data-states, code-editor), layout/app-shell orchestration, auth-guarded routing (protected-route), and domain-specific utility modules (toast-rules) with colocated unit tests.
 ## tags
 toast, state, react, icon, code, event, editor, protected
 ## symbols

apps/web/src/components/features/.pi-map.index.md

@@ -2,7 +2,7 @@
 dir: apps/web/src/components/features
 
 ## role
-Contains reusable React components that implement specific product features and business logic for the web application.
+Contains specialized UI components for major feature areas of the web application, organizing components by business domain rather than by atomic design level.
 ## parent
 index: apps/web/src/components/.pi-map.index.md
 map: apps/web/src/components/.pi-map.md

apps/web/src/components/features/.pi-map.md

@@ -4,10 +4,10 @@ dir: apps/web/src/components/features
 index: apps/web/src/components/features/.pi-map.index.md
 
 ## role
-Contains reusable React components that implement specific product features and business logic for the web application.
+Contains specialized UI components for major feature areas of the web application, organizing components by business domain rather than by atomic design level.
 ## files
 ## arch
-Feature-based component organization with domain-specific UI building blocks, likely composed of atomic design elements (from components/ui) and consumed by page-level routes.
+Feature-based colocation pattern where components are grouped by product functionality (e.g., checkout, dashboard, settings) rather than by component type, typically combining multiple atomic components with domain-specific logic and data fetching.
 ## tags
 -
 ## symbols

apps/web/src/components/features/session/.pi-map.index.md

@@ -2,7 +2,7 @@
 dir: apps/web/src/components/features/session
 
 ## role
-Provides UI components for managing development environment sessions including creation, listing, monitoring progress, and interacting with individual sessions.
+Provides UI components for managing development sessions including creation, listing, monitoring progress, and interacting with individual sessions.
 ## parent
 index: apps/web/src/components/features/.pi-map.index.md
 map: apps/web/src/components/features/.pi-map.md

apps/web/src/components/features/session/.pi-map.md

@@ -4,16 +4,16 @@ dir: apps/web/src/components/features/session
 index: apps/web/src/components/features/session/.pi-map.index.md
 
 ## role
-Provides UI components for managing development environment sessions including creation, listing, monitoring progress, and interacting with individual sessions.
+Provides UI components for managing development sessions including creation, listing, monitoring progress, and interacting with individual sessions.
 ## files
-- create-session-form.tsx | React form component for creating development sessions with configurable project, repository, tool type, branch, SSH keys, and config profile options | exp: CreateSessionForm | dep: react, ../../icon, ../../../api/sessions, ../../../types, ../../../api/git-repositories, ../../../api/tool-types, ../../../api/ssh-keys, ../../../api/config-profiles, icon component, sessions API, git-repositories API, ssh-keys API, config-profiles API, tool-types API, types
+- create-session-form.tsx | A React form component for creating and starting a new development session with configurable project, repository, workspace, tool type, config profile, and SSH key options. | exp: CreateSessionForm | dep: react, ../../icon, ../../../api/sessions, ../../../types, ../../../api/git-repositories, ../../../api/tool-types, ../../../api/ssh-keys, ../../../api/config-profiles, ../../../api/workspaces, ../../../types/workspace, icon, sessions API, git-repositories API, tool-types API, ssh-keys API, config-profiles API, workspaces API, types
-- session-card.tsx | Renders a React card component displaying session information with status badges, inline editing, action buttons, and responsive mobile/desktop layouts. | exp: SessionCardProps, func:SessionCard({ session, onOpen, onStart, onStop, onDelete, onRecreateTunnel, onRename, isBusy = false, tunnelHealth = null, }: SessionCardProps), call:useState, call:useRef, call:useMobileViewport, call:session.tool_type_interfaces?.includes, call:[ "running", "building", "starting", "probing", "pending", "unhealthy", ].includes, call:useEffect, call:optionsRef.current.contains, call:setOptionsOpen, call:document.addEventListener, call:document.removeEventListener, call:window.confirm, call:onDelete, call:setEditName, call:onRename, call:setIsEditingName, call:editName.trim, call:onOpen, call:new Date(session.created_at).toLocaleString, call:setShowActionSheet, call:onStart, call:onStop, call:onRecreateTunnel | dep: react, ../../../api/sessions, ../../icon, ../../../hooks/use-mobile-viewport, ../mobile/mobile-action-sheet, icon, use-mobile-viewport, mobile-action-sheet, sessions api types
+- session-card.tsx | Renders a card component displaying session information with status badges, inline rename editing, action buttons, and responsive mobile/desktop layouts including a dropdown options menu and mobile action sheet. | exp: SessionCardProps, func:SessionCard({ session, onOpen, onStart, onStop, onDelete, onRecreateTunnel, onRename, isBusy = false, tunnelHealth = null, }: SessionCardProps), call:useState, call:useRef, call:useMobileViewport, call:session.tool_type_interfaces?.includes, call:[ "running", "building", "starting", "probing", "pending", "unhealthy", ].includes, call:useEffect, call:optionsRef.current.contains, call:setOptionsOpen, call:document.addEventListener, call:document.removeEventListener, call:window.confirm, call:onDelete, call:setEditName, call:onRename, call:setIsEditingName, call:editName.trim, call:onOpen, call:new Date(session.created_at).toLocaleString, call:setShowActionSheet, call:onStart, call:onStop, call:onRecreateTunnel | dep: react, ../../../api/sessions, ../../icon, ../../../hooks/use-mobile-viewport, ../mobile/mobile-action-sheet
 - session-list.tsx | Renders a list of sessions grouped by active/recent status or as a flat grid, delegating to SessionCard for individual session display. | exp: SessionListProps, func:SessionList({ sessions, onOpen, onStart, onStop, onDelete, onRecreateTunnel, onRename, actionBusyId = null, tunnelHealth = {}, showGrouping = true, activeTitle = "Active Sessions", recentTitle = "Recent Sessions", maxRecent = 5, emptyMessage = "No sessions", }: SessionListProps), call:sessions.filter, call:activeStatuses.includes, call:sessions .filter((s) => recentStatuses.includes(s.status)) .slice, call:recentStatuses.includes, call:sessions.map, call:activeSessions.map, call:recentSessions.map | dep: ../../../api/sessions, ./session-card, Session, SessionCard, InstanceHealth
 - session-progress-panel.tsx | Renders a panel displaying active and recently completed session operations with step-by-step progress indicators and dismissible notifications. | exp: func:SessionProgressPanel(), call:useSessionOperations, call:useEventContext, call:useEffect, call:updateOperationFromEvent, call:operations.filter, call:Date.now, call:visibleOperations.map, call:dismissOperation | dep: react, ../../../state/session-operations, ../../../state/events, ../../icon, useSessionOperations, useEventContext, Icon
 ## arch
-Feature-based component composition with presentational components following a container/presenter pattern, using status-driven conditional rendering and responsive layout adaptations.
+React component composition with feature-specific grouping, responsive design patterns (mobile/desktop layouts), and status-driven conditional rendering with delegated sub-components.
 ## tags
-session, call:use, call:on, card, mobile, call:set, event, api
+session, call:use, call:on, api, card, call:set, event, mobile
 ## symbols
 - SessionCard
 - SessionList

apps/web/src/components/features/session/create-session-form.tsx

@@ -6,17 +6,15 @@ import {
 	type ToolInstance,
 } from "../../../api/sessions";
 import type { Project } from "../../../types";
-import {
+import type { GitRepository } from "../../../api/git-repositories";
-	listRepositoryBranches,
-	type GitRepository,
-	type Branch,
-} from "../../../api/git-repositories";
 import type { ToolType } from "../../../api/tool-types";
 import { listSSHKeys, type SSHKey } from "../../../api/ssh-keys";
 import {
 	listConfigProfiles,
 	type ConfigProfile,
 } from "../../../api/config-profiles";
+import { listWorkspaces, createWorkspace } from "../../../api/workspaces";
+import type { Workspace } from "../../../types/workspace";
 
 interface CreateSessionFormProps {
 	projects: Project[];
@@ -26,7 +24,6 @@ interface CreateSessionFormProps {
 	fixedRepoId?: string;
 	projectName?: string;
 	repoName?: string;
-	showCloneMode?: boolean;
 	showFixedFields?: boolean;
 	onProjectChange?: (projectId: string) => void;
 	onSuccess?: (instance: ToolInstance) => void;
@@ -43,7 +40,6 @@ export const CreateSessionForm = ({
 	fixedRepoId,
 	projectName,
 	repoName,
-	showCloneMode = true,
 	showFixedFields = true,
 	onProjectChange,
 	onSuccess,
@@ -55,18 +51,14 @@ export const CreateSessionForm = ({
 	const [selectedRepo, setSelectedRepo] = useState(fixedRepoId || "");
 	const [selectedToolType, setSelectedToolType] = useState("");
 	const [displayName, setDisplayName] = useState("");
-	const [cloneMode, setCloneMode] = useState<"mount" | "clone">("mount");
-	const [branch, setBranch] = useState("main");
 	const [sshKeys, setSshKeys] = useState<SSHKey[]>([]);
 	const [configProfiles, setConfigProfiles] = useState<ConfigProfile[]>([]);
 	const [selectedConfigProfile, setSelectedConfigProfile] = useState("");
 	const [selectedSshKeyIds, setSelectedSshKeyIds] = useState<string[]>([]);
 
-	const [branches, setBranches] = useState<Branch[]>([]);
+	const [workspaces, setWorkspaces] = useState<Workspace[]>([]);
-	const [isLoadingBranches, setIsLoadingBranches] = useState(false);
+	const [selectedWorkspaceId, setSelectedWorkspaceId] = useState("");
-	const [isCreatingNewBranch, setIsCreatingNewBranch] = useState(false);
+	const [isLoadingWorkspaces, setIsLoadingWorkspaces] = useState(false);
-	const [newBranchName, setNewBranchName] = useState("");
-	const [baseBranch, setBaseBranch] = useState("");
 
 	const [isSubmitting, setIsSubmitting] = useState(false);
 	const [error, setError] = useState<string | null>(null);
@@ -108,30 +100,49 @@ export const CreateSessionForm = ({
 		void loadProfiles();
 	}, [selectedToolType, selectedProject, fixedProjectId]);
 
-	// Load branches when selected repo changes
+	// Load workspaces when repository is selected
 	useEffect(() => {
 		const projectId = fixedProjectId || selectedProject;
-		if (!selectedRepo || !projectId || !showCloneMode) {
+		const repoId = fixedRepoId || selectedRepo;
-			setBranches([]);
+		if (!projectId || !repoId) {
+			setWorkspaces([]);
+			setSelectedWorkspaceId("");
 			return;
 		}
-		const loadBranches = async () => {
+		const loadWorkspaces = async () => {
-			setIsLoadingBranches(true);
+			setIsLoadingWorkspaces(true);
 			try {
-				const response = await listRepositoryBranches(projectId, selectedRepo);
+				const data = await listWorkspaces(projectId, repoId);
-				setBranches(response.branches);
+				setWorkspaces(data);
-				if (response.default_branch) {
+				if (data.length > 0) {
-					setBranch(response.default_branch);
+					setSelectedWorkspaceId(data[0].id);
-					setBaseBranch(response.default_branch);
+				} else {
+					// Auto-create a default workspace so the user can start a tool
+					const workspace = await createWorkspace(projectId, repoId, {
+						name: "default",
+						branch: "main",
+					});
+					setWorkspaces([workspace]);
+					setSelectedWorkspaceId(workspace.id);
 				}
-			} catch {
+			} catch (err) {
-				// ignore
+				setError(
+					err instanceof Error ? err.message : "Failed to load workspaces",
+				);
+				setWorkspaces([]);
+				setSelectedWorkspaceId("");
 			} finally {
-				setIsLoadingBranches(false);
+				setIsLoadingWorkspaces(false);
 			}
 		};
-		void loadBranches();
+		void loadWorkspaces();
-	}, [selectedRepo, selectedProject, fixedProjectId, showCloneMode]);
+	}, [
+		fixedProjectId,
+		selectedProject,
+		fixedRepoId,
+		selectedRepo,
+		repositories,
+	]);
 
 	// Filter repositories by selected project
 	const availableRepos = selectedProject
@@ -143,14 +154,10 @@ export const CreateSessionForm = ({
 		if (!fixedRepoId) setSelectedRepo("");
 		setSelectedToolType("");
 		setDisplayName("");
-		setCloneMode("mount");
-		setBranch("main");
-		setIsCreatingNewBranch(false);
-		setNewBranchName("");
-		setBaseBranch("");
-		setBranches([]);
 		setSelectedSshKeyIds([]);
 		setSelectedConfigProfile("");
+		setWorkspaces([]);
+		setSelectedWorkspaceId("");
 	};
 
 	const handleSubmit = async (event: React.FormEvent) => {
@@ -165,31 +172,22 @@ export const CreateSessionForm = ({
 			return;
 		}
 
-		if (showCloneMode && cloneMode === "clone") {
-			const repo = repositories.find((r) => r.id === repoId);
-			if (!repo?.ssh_key_id) {
-				setError("Repository must have an SSH key assigned for clone mode");
-				return;
-			}
-		}
-
 		setIsSubmitting(true);
 
 		try {
+			const workspaceId = selectedWorkspaceId || undefined;
+			if (!workspaceId) {
+				setError("No workspace available for the selected repository");
+				setIsSubmitting(false);
+				return;
+			}
+
 			const instance = await createInstance(
 				projectId,
 				repoId,
 				selectedToolType,
 				displayName || undefined,
-				showCloneMode ? cloneMode : undefined,
+				workspaceId,
-				showCloneMode && cloneMode === "clone"
-					? isCreatingNewBranch
-						? baseBranch
-						: branch
-					: undefined,
-				showCloneMode && cloneMode === "clone" && isCreatingNewBranch
-					? newBranchName
-					: undefined,
 				selectedConfigProfile || undefined,
 				selectedSshKeyIds.length > 0 ? selectedSshKeyIds : undefined,
 			);
@@ -240,8 +238,6 @@ export const CreateSessionForm = ({
 								setSelectedProject(value);
 								setSelectedRepo("");
 								setSelectedToolType("");
-								setCloneMode("mount");
-								setIsCreatingNewBranch(false);
 								onProjectChange?.(value);
 							}}
 							disabled={isSubmitting}
@@ -277,8 +273,7 @@ export const CreateSessionForm = ({
 								onChange={(e) => {
 									setSelectedRepo(e.target.value);
 									setSelectedToolType("");
-									setCloneMode("mount");
+									setSelectedWorkspaceId("");
-									setIsCreatingNewBranch(false);
 								}}
 								disabled={!hasProject || isSubmitting}
 							>
@@ -293,6 +288,30 @@ export const CreateSessionForm = ({
 					</div>
 				)}
 
+				{/* Workspace */}
+				{hasRepo && (
+					<div className="form-field">
+						<label>Workspace</label>
+						{isLoadingWorkspaces ? (
+							<span className="muted">Loading workspaces...</span>
+						) : workspaces.length === 0 ? (
+							<span className="muted">No workspace available</span>
+						) : (
+							<select
+								value={selectedWorkspaceId}
+								onChange={(e) => setSelectedWorkspaceId(e.target.value)}
+								disabled={!hasRepo || isSubmitting || isLoadingWorkspaces}
+							>
+								{workspaces.map((w) => (
+									<option key={w.id} value={w.id}>
+										{w.name} ({w.branch})
+									</option>
+								))}
+							</select>
+						)}
+					</div>
+				)}
+
 				{/* Tool Type */}
 				{hasRepo && (
 					<div className="form-field">
@@ -301,8 +320,6 @@ export const CreateSessionForm = ({
 							value={selectedToolType}
 							onChange={(e) => {
 								setSelectedToolType(e.target.value);
-								setCloneMode("mount");
-								setIsCreatingNewBranch(false);
 							}}
 							disabled={!hasRepo || isSubmitting}
 						>
@@ -382,134 +399,6 @@ export const CreateSessionForm = ({
 					</div>
 				)}
 
-				{/* Clone Mode & Branch */}
-				{showCloneMode && hasToolType && (
-					<div className="form-field">
-						<label>Repository Access</label>
-						<div className="radio-group">
-							<label className="radio-label">
-								<input
-									type="radio"
-									name="cloneMode"
-									value="mount"
-									checked={cloneMode === "mount"}
-									onChange={(e) => {
-										setCloneMode(e.target.value as "mount" | "clone");
-										setIsCreatingNewBranch(false);
-									}}
-									disabled={isSubmitting}
-								/>
-								Mount (live sync)
-							</label>
-							<label className="radio-label">
-								<input
-									type="radio"
-									name="cloneMode"
-									value="clone"
-									checked={cloneMode === "clone"}
-									onChange={(e) => {
-										setCloneMode(e.target.value as "mount" | "clone");
-										setIsCreatingNewBranch(false);
-									}}
-									disabled={isSubmitting}
-								/>
-								Clone fresh copy
-							</label>
-						</div>
-
-						{cloneMode === "clone" && (
-							<>
-								<label className="form-field">
-									Branch
-									{isLoadingBranches ? (
-										<span className="muted">Loading branches...</span>
-									) : (
-										<select
-											value={isCreatingNewBranch ? "__new__" : branch}
-											onChange={(e) => {
-												const value = e.target.value;
-												if (value === "__new__") {
-													setIsCreatingNewBranch(true);
-													setNewBranchName("");
-												} else {
-													setIsCreatingNewBranch(false);
-													setBranch(value);
-													setBaseBranch(value);
-												}
-											}}
-											disabled={isSubmitting}
-										>
-											{branches.map((b) => (
-												<option key={b.name} value={b.name}>
-													{b.name} {b.is_default ? "(default)" : ""}
-												</option>
-											))}
-											<option value="__new__">Create new branch...</option>
-										</select>
-									)}
-								</label>
-
-								{isCreatingNewBranch && (
-									<>
-										<label className="form-field">
-											New Branch Name
-											<input
-												type="text"
-												value={newBranchName}
-												onChange={(e) => setNewBranchName(e.target.value)}
-												placeholder="feature/my-new-branch"
-												required
-												disabled={isSubmitting}
-											/>
-										</label>
-										<label className="form-field">
-											Base Branch
-											<select
-												value={baseBranch}
-												onChange={(e) => setBaseBranch(e.target.value)}
-												disabled={isSubmitting}
-											>
-												{branches.map((b) => (
-													<option key={b.name} value={b.name}>
-														{b.name} {b.is_default ? "(default)" : ""}
-													</option>
-												))}
-											</select>
-										</label>
-									</>
-								)}
-
-								{selectedRepo && (
-									<div className="form-field ssh-key-info">
-										{(() => {
-											const repo = repositories.find(
-												(r) => r.id === selectedRepo,
-											);
-											if (!repo) return null;
-											if (repo.ssh_key_id) {
-												const key = sshKeys.find(
-													(k) => k.id === repo.ssh_key_id,
-												);
-												return (
-													<span className="success-text">
-														SSH key: {key?.name || "Assigned"}
-													</span>
-												);
-											}
-											return (
-												<span className="warning-text">
-													No SSH key assigned to this repository. Clone mode
-													requires an SSH key.
-												</span>
-											);
-										})()}
-									</div>
-								)}
-							</>
-						)}
-					</div>
-				)}
-
 				{/* Display Name */}
 				{hasToolType && (
 					<div className="form-field">

apps/web/src/components/features/session/session-card.tsx

@@ -176,14 +176,6 @@ export function SessionCard({
 						)}{" "}
 						· {session.tool_type_name}
 					</p>
-					{session.clone_mode && (
-						<p className="muted session-card-meta">
-							<Icon name="branch" size="sm" />
-							{session.clone_mode === "clone"
-								? `Clone${session.branch ? ` (${session.branch})` : ""}`
-								: "Mount"}
-						</p>
-					)}
 					{session.url && (
 						<p className="session-card-url">
 							<button

apps/web/src/components/features/tool/.pi-map.index.md

@@ -2,7 +2,7 @@
 dir: apps/web/src/components/features/tool
 
 ## role
-Provides UI components for managing container-based development tools, including instance lifecycle operations, manifest editing, and workspace-integrated tool launching.
+Provides UI components for managing containerized development tools, including instance lifecycle operations, manifest editing, and workspace-integrated tool launching.
 ## parent
 index: apps/web/src/components/features/.pi-map.index.md
 map: apps/web/src/components/features/.pi-map.md

apps/web/src/components/features/tool/.pi-map.md

@@ -4,16 +4,16 @@ dir: apps/web/src/components/features/tool
 index: apps/web/src/components/features/tool/.pi-map.index.md
 
 ## role
-Provides UI components for managing container-based development tools, including instance lifecycle operations, manifest editing, and workspace-integrated tool launching.
+Provides UI components for managing containerized development tools, including instance lifecycle operations, manifest editing, and workspace-integrated tool launching.
 ## files
 - instance-list.tsx | Displays and manages a list of tool instances with CRUD operations, real-time status updates, and configuration profile selection. | exp: InstanceList | dep: react, react-router-dom, ../../icon, ../../../api/sessions, ../../../api/tool-types, ../session/create-session-form, ../../../api/config-profiles, ../../../api/ssh-keys, ../../../state/events, ../../../state/sessions, icon, api/sessions, api/tool-types, api/config-profiles, api/ssh-keys, state/events, state/sessions
 - manifest-editor.tsx | A React component that provides a form-based UI for editing container tool definition manifests with fields for base images, packages, user config, environment variables, scripts, mounts, and runtime settings, including compilation preview functionality. | exp: ManifestEditor | dep: react, ../../icon, ../../../utils/errors, ../../../api/tool-definitions, icon, errors, tool-definitions
 - start-tool-fab.tsx | A floating action button component that opens a modal to select a workspace and start a tool. | exp: func:StartToolFAB(), call:useState, call:setOpen, call:setWorkspacesLoading, call:listAllWorkspaces, call:setWorkspaces, call:setSelectedWorkspace, call:e.stopPropagation, call:workspaces.find, call:workspaces.map | dep: react, ../../icon, ./tool-starter, ../../../types/workspace, ../../../api/workspaces, icon, tool-starter, workspaces api, workspace types
 - start-tool-modal.tsx | Renders a modal dialog for selecting a tool type and optional config profile to start on a workspace. | exp: StartToolModalProps, func:StartToolModal({ workspace, onClose, onStart, }: StartToolModalProps), call:useState, call:useAsyncData, call:e.preventDefault, call:setError, call:setSubmitting, call:onStart, call:onClose, call:e.stopPropagation, call:setToolTypeId, call:toolTypes?.map, call:setConfigProfileId | dep: react, ../../icon, ../../../api/tool-types, ../../../hooks/use-async-data, ../../../types/workspace, icon, tool-types, use-async-data, workspace
-- tool-starter.tsx | React component that provides a workspace-first form for starting a new tool instance, fetching tool types, config profiles, and SSH keys dynamically. | exp: ToolStarterProps, func:ToolStarter({ workspace, onStarted, onCancel, }: ToolStarterProps), call:useSessions, call:useSessionOperations, call:useState, call:useEffect, call:listToolTypes, call:setToolTypes, call:setToolTypesError, call:setToolTypesLoading, call:load, call:setProfiles, call:setSelectedProfileId, call:setProfilesLoading, call:listConfigProfiles, call:data.find, call:listSSHKeys, call:setSshKeys, call:setSelectedSshKeyIds, call:console.error, call:setSshKeysLoading, call:sshKeys.find, call:useCallback, call:setError, call:setStarting, call:createInstance, call:displayName.trim, call:startInstance, call:addOrUpdateSession, call:startOperation, call:onStarted, call:setSelectedToolTypeId, call:toolTypes.find, call:setDisplayName, call:toolTypes.map, call:setNameEdited, call:profiles.map, call:sshKeys.map, call:selectedSshKeyIds.includes, call:prev.filter | dep: react, ../../icon, ../../../api/tool-types, ../../../api/config-profiles, ../../../api/ssh-keys, ../../../state/sessions, ../../../state/session-operations, ../../../types/workspace, ../../../api/sessions, icon, tool-types, config-profiles, ssh-keys, sessions, session-operations, workspace
+- tool-starter.tsx | A React component that provides a workspace-first UI for selecting tool types, config profiles, and SSH keys to create and start a new tool instance/session. | exp: ToolStarterProps, func:ToolStarter({ workspace, onStarted, onCancel, }: ToolStarterProps), call:useSessions, call:useSessionOperations, call:useState, call:useEffect, call:listToolTypes, call:setToolTypes, call:setToolTypesError, call:setToolTypesLoading, call:load, call:setProfiles, call:setSelectedProfileId, call:setProfilesLoading, call:listConfigProfiles, call:data.find, call:listSSHKeys, call:setSshKeys, call:setSelectedSshKeyIds, call:console.error, call:setSshKeysLoading, call:sshKeys.find, call:useCallback, call:setError, call:setStarting, call:createInstance, call:displayName.trim, call:startInstance, call:addOrUpdateSession, call:startOperation, call:onStarted, call:setSelectedToolTypeId, call:toolTypes.find, call:setDisplayName, call:toolTypes.map, call:setNameEdited, call:profiles.map, call:sshKeys.map, call:selectedSshKeyIds.includes, call:prev.filter | dep: react, ../../icon, ../../../api/tool-types, ../../../api/config-profiles, ../../../api/ssh-keys, ../../../state/sessions, ../../../state/session-operations, ../../../types/workspace, ../../../api/sessions, icon, tool-types, config-profiles, ssh-keys, sessions, session-operations, workspace
 - tools-bottom-sheet.tsx | Renders a mobile bottom sheet navigation menu for tools with active route highlighting | exp: ToolsBottomSheet | dep: react-router-dom, ../../icon, icon
 ## arch
-Feature-based component architecture with form-driven modals, real-time status integration, and responsive mobile/desktop patterns (bottom sheets vs modals)
+Feature-based component composition with modal/bottom-sheet navigation patterns, real-time status integration, and form-driven configuration management with preview capabilities.
 ## tags
 tool, call:set, types, call:use, api, start, ssh, icon
 ## symbols

apps/web/src/components/features/tool/tool-starter.tsx

@@ -131,12 +131,9 @@ export function ToolStarter({
 				workspace.repo_id,
 				selectedToolTypeId,
 				displayName.trim() || undefined,
-				undefined,
+				workspace.id,
-				undefined,
-				undefined,
 				selectedProfileId || undefined,
 				selectedSshKeyIds.length > 0 ? selectedSshKeyIds : undefined,
-				workspace.id,
 			);
 			await startInstance(
 				workspace.project_id,

apps/web/src/hooks/.pi-map.index.md

@@ -2,7 +2,7 @@
 dir: apps/web/src/hooks
 
 ## role
-Provides a comprehensive collection of custom React hooks that encapsulate reusable stateful logic, side effects, and API interactions for the web application's UI, data management, and domain-specific operations.
+Provides reusable React custom hooks that encapsulate UI state management, side effects, API integrations, and domain-specific logic for the web application frontend.
 ## parent
 index: apps/web/src/.pi-map.index.md
 map: apps/web/src/.pi-map.md

apps/web/src/hooks/.pi-map.md

@@ -4,7 +4,7 @@ dir: apps/web/src/hooks
 index: apps/web/src/hooks/.pi-map.index.md
 
 ## role
-Provides a comprehensive collection of custom React hooks that encapsulate reusable stateful logic, side effects, and API interactions for the web application's UI, data management, and domain-specific operations.
+Provides reusable React custom hooks that encapsulate UI state management, side effects, API integrations, and domain-specific logic for the web application frontend.
 ## files
 - use-async-data.ts | A custom React hook that manages asynchronous data fetching with loading, error, and ready states, plus a manual reload capability. | exp: func:useAsyncData(fetcher: () => Promise<T>, deps: React.DependencyList) → UseAsyncDataResult<T>, call:useState, call:useCallback, call:setStatus, call:setError, call:fetcher, call:setData, call:load, call:useEffect | dep: react
 - use-auto-hide.ts | A React custom hook that automatically hides an element after a specified timeout and provides manual controls for showing, hiding, and toggling visibility. | exp: func:useAutoHide(options: AutoHideOptions), call:useState, call:useRef, call:Date.now, call:useCallback, call:setIsVisible, call:clearTimeout, call:setTimeout, call:hide, call:show, call:useEffect | dep: react
@@ -20,7 +20,7 @@ Provides a comprehensive collection of custom React hooks that encapsulate reusa
 - use-repo-workspace.ts | A React custom hook that manages workspace state for a repository-based project, including loading project data, repositories, branches, git status, and tool types while synchronizing selection state with URL search parameters. | exp: Project, useRepoWorkspace | dep: react, react-router-dom, ../api/client, ../api/git-repositories, ../api/tool-types
 - use-special-keys.ts | Maps special keys and modifier+character combinations to ANSI escape sequences for terminal input simulation. | exp: SpecialKey, ModifierKey, func:getSequenceWithModifier(key: SpecialKey, activeModifier: ModifierKey | null) → { sequence: string; clearModifier: boolean } | null, call:char.toLowerCase, func:applyModifierToChar(char: string, modifier: ModifierKey) → string | null, call:char.toLowerCase
 - use-ssh-keys.ts | A React custom hook that manages SSH key operations including listing, generating, deleting, signing payloads, and verifying signatures. | exp: useSSHKeys | dep: react, ../api/ssh-keys, ./use-async-data
-- use-start-tool.ts | React hook that manages the state and API calls for creating and starting a tool instance on a workspace | exp: UseStartToolResult, func:useStartTool() → UseStartToolResult, call:useState, call:useCallback, call:setStarting, call:setError, call:createInstance, call:startInstance | dep: react, ../api/sessions, ../types/workspace
+- use-start-tool.ts | React hook for managing the state and API calls to create and start a tool instance on a workspace. | exp: UseStartToolResult, func:useStartTool() → UseStartToolResult, call:useState, call:useCallback, call:setStarting, call:setError, call:createInstance, call:startInstance | dep: react, ../api/sessions, ../types/workspace
 - use-terminal-page.ts | Manages terminal page state including sessions, keyboard shortcuts, fullscreen mode, mobile viewport handling, and terminal lifecycle operations. | exp: useTerminalPage | dep: react, react-router-dom, ../components/features/terminal/terminal, ../components/features/terminal/terminal-session-tabs, ./use-mobile-viewport, ./use-auto-hide, ./use-virtual-keyboard, ./use-terminal-sessions, ../api/terminal, ./use-special-keys, use-mobile-viewport, use-auto-hide, use-virtual-keyboard, use-terminal-sessions, terminal, terminal-session-tabs, api/terminal, api/sessions, use-special-keys
 - use-terminal-sessions.ts | React custom hook that manages terminal session state (CRUD operations, active session tracking) for a given instance | exp: UseTerminalSessionsResult, func:useTerminalSessions(instanceId: string) → UseTerminalSessionsResult, call:useState, call:useCallback, call:setLoading, call:setError, call:listTerminalSessions, call:setSessions, call:setActiveSessionId, call:createTerminalSession, call:closeTerminalSession, call:prev.filter, call:renameTerminalSession, call:prev.map, call:resetTerminalSession, call:loadSessions, call:useEffect | dep: react, ../api/terminal
 - use-theme.ts | React hook that fetches user theme preference on mount and applies it to the document root element via data-theme attribute | exp: func:useTheme(), call:useEffect, call:getUserConfig, call:document.documentElement.removeAttribute, call:document.documentElement.setAttribute | dep: react, ../api/settings
@@ -32,7 +32,7 @@ Provides a comprehensive collection of custom React hooks that encapsulate reusa
 - use-workspace-instances.ts | Custom React hook for managing workspace instances with CRUD operations, loading states, and error handling. | exp: UseWorkspaceInstancesResult, func:useWorkspaceInstances(workspaceId: string) → UseWorkspaceInstancesResult, call:useState, call:useCallback, call:setLoading, call:setError, call:listWorkspaceInstances, call:setInstances, call:createWorkspaceInstance, call:refresh, call:useEffect | dep: react, ../api/workspace-instances, ../api/sessions
 - use-workspaces.ts | Custom React hook that fetches and manages workspace data with loading and error states. | exp: UseWorkspacesResult, func:useWorkspaces(projectId: string, repoId: string) → UseWorkspacesResult, call:useState, call:useCallback, call:setLoading, call:setError, call:listWorkspaces, call:listAllWorkspaces, call:setWorkspaces, call:useEffect, call:refresh | dep: react, ../api/workspaces, ../types/workspace
 ## arch
-Follows the React Hooks pattern with custom hooks as the primary abstraction—each hook typically combines useState/useEffect/useCallback to manage local state, API calls, and side effects; many hooks integrate with TanStack Query/SWR-like patterns for server state (loading/error/reload), use context providers (e.g., NotificationProvider), and synchronize with URL search params; complex hooks compose simpler ones (e.g., use-terminal-page composes use-mobile-viewport, use-auto-hide) and use reducer-like state management for multi-faceted domain operations (CRUD, drag-and-drop, form handling).
+Layered utility hooks following React composition patterns, with separation between generic UI behavior hooks (async data, auto-hide, viewport, theme), infrastructure hooks (SSE, terminal, keyboard), and domain-specific data/operation hooks (workspace, git, SSH, projects, instances) that wrap API calls with loading/error states and optimistic updates.
 ## tags
 call:set, call:use, workspace, react, state, terminal, api, git
 ## symbols

apps/web/src/hooks/use-start-tool.ts

@@ -35,12 +35,9 @@ export function useStartTool(): UseStartToolResult {
 					workspace.repo_id,
 					toolTypeId,
 					displayName || workspace.name,
-					undefined,
+					workspace.id,
-					undefined,
-					undefined,
 					configProfileId,
 					[],
-					workspace.id,
 				);
 				await startInstance(
 					workspace.project_id,

openspec/.pi-map.index.md

@@ -2,7 +2,7 @@
 dir: openspec
 
 ## role
-Defines the OpenSpec methodology and project configuration for managing software requirements, specifications, and task tracking as living documentation within a Docker-based coding agent management platform.
+Defines the OpenSpec methodology and project configuration for managing living documentation and development discipline rules in a Docker-based coding agent platform.
 ## parent
 index: ./.pi-map.index.md
 map: ./.pi-map.md

openspec/.pi-map.md

@@ -4,12 +4,12 @@ dir: openspec
 index: openspec/.pi-map.index.md
 
 ## role
-Defines the OpenSpec methodology and project configuration for managing software requirements, specifications, and task tracking as living documentation within a Docker-based coding agent management platform.
+Defines the OpenSpec methodology and project configuration for managing living documentation and development discipline rules in a Docker-based coding agent platform.
 ## files
 - README.md | Documents the OpenSpec methodology for managing software requirements, specifications, and task tracking as living documentation within a project repository. | dep: OpenSpec CLI (@fission-ai/openspec), Docker, SQLAlchemy, Alembic, Authentik, React, TypeScript, Tailwind, Traefik, Jinja2, xterm.js, pytest, mypy, ruff, npm
 - config.yaml | Configuration file defining project metadata, technology stack, and software development discipline rules for a Docker-based coding agent management platform | dep: FastAPI, React, Vite, PostgreSQL, SQLAlchemy, Redis, Alembic, pytest, Docker Compose, Traefik, Authentik
 ## arch
-Documentation-as-code pattern with YAML-based configuration management, combining structured metadata (config.yaml) with methodology documentation (README.md) to enforce software development discipline rules for automated agent workflows.
+Documentation-as-code pattern with YAML-based configuration management, embedding requirements/specifications directly in the repository alongside structured project metadata and technology stack definitions.
 ## tags
 software, project, docker, sqlalchemy, alembic, authentik, react, traefik
 ## symbols

openspec/changes/.pi-map.index.md

@@ -2,7 +2,7 @@
 dir: openspec/changes
 
 ## role
-Tracks and manages specification changes/versions for OpenAPI documents
+Manages change tracking, versioning, and audit logging for OpenSpec schema or configuration modifications.
 ## parent
 index: openspec/.pi-map.index.md
 map: openspec/.pi-map.md

openspec/changes/.pi-map.md

@@ -4,10 +4,10 @@ dir: openspec/changes
 index: openspec/changes/.pi-map.index.md
 
 ## role
-Tracks and manages specification changes/versions for OpenAPI documents
+Manages change tracking, versioning, and audit logging for OpenSpec schema or configuration modifications.
 ## files
 ## arch
-Simple data structure package with record types for change metadata, likely used by diff/merge tooling
+Event-sourced or changelog-based architecture with immutable change records, likely supporting rollback, diff computation, and history querying patterns.
 ## tags
 -
 ## symbols

openspec/changes/working-copies/.openspec.yaml

@@ -0,0 +1,4 @@
+name: working-copies
+status: completed
+started_at: 2026-05-28
+completed_at: 2026-06-12

openspec/changes/working-copies/.pi-map.index.md

@@ -1,22 +1,23 @@
-# working-copies (index)
+# openspec/changes/working-copies (index)
-dir: working-copies
+dir: openspec/changes/working-copies
 
 ## role
-This package contains design documents and implementation planning for a workspace-based repository access system that replaces direct repository mounting/cloning with isolated, persistent, writable git working copies shared across tool instances.
+Design and specification package for replacing direct repository mounting/cloning with persistent, shared Git working copy workspaces in tool instances.
 ## parent
-index: ./.pi-map.index.md
+index: openspec/changes/.pi-map.index.md
-map: ./.pi-map.md
+map: openspec/changes/.pi-map.md
 ## children
 -
 ## files
+- .openspec.yaml
 - design.md
 - explore.md
 - proposal.md
 - spec.md
 - tasks.md
 ## links
-index: working-copies/.pi-map.index.md
+index: openspec/changes/working-copies/.pi-map.index.md
-map: working-copies/.pi-map.md
+map: openspec/changes/working-copies/.pi-map.md
 ## workflows
 -
 ## dirty

openspec/changes/working-copies/.pi-map.md

@@ -1,20 +1,21 @@
-# working-copies
+# openspec/changes/working-copies
-dir: working-copies
+dir: openspec/changes/working-copies
 
-index: working-copies/.pi-map.index.md
+index: openspec/changes/working-copies/.pi-map.index.md
 
 ## role
-This package contains design documents and implementation planning for a workspace-based repository access system that replaces direct repository mounting/cloning with isolated, persistent, writable git working copies shared across tool instances.
+Design and specification package for replacing direct repository mounting/cloning with persistent, shared Git working copy workspaces in tool instances.
 ## files
+- .openspec.yaml | Defines metadata for a completed project named "working-copies" with timeline tracking
 - design.md | Design document for implementing workspace-based tool instances that replace direct repository mounting with isolated git working copies | dep: FastAPI, SQLAlchemy, Alembic, Docker Compose, Git, React/TypeScript, asyncio subprocess
 - explore.md | Design document proposing "Working Copies" (named "Workspace") as persistent writable clones of repositories to replace direct repo mounting/cloning in tool instances | dep: GitRepository, ToolInstance, Project, User, database, compose generation, filesystem mount system
 - proposal.md | Proposes a new "Workspace" entity to replace the confusing mount/clone mode dichotomy for tool instances, enabling persistent writable repository clones that multiple tools can share.
 - spec.md | Technical specification for implementing persistent workspace-based tool instances that replace mount/clone modes with explicit Git repository workspaces | dep: Git, PostgreSQL, REST API, React/TypeScript frontend, Docker containers, Python backend
-- tasks.md | A project task breakdown document defining a phased implementation plan for adding workspace-based tool instances to a full-stack application, including backend foundation, backend integration, frontend core, and frontend integration PRs with detailed tasks, acceptance criteria, and verification steps. | dep: Alembic, FastAPI, SQLAlchemy, React, TypeScript, Git, Docker Compose, pytest, ruff, ESLint, npm
+- tasks.md | Project task tracking document for implementing workspace-based tool instances across backend and frontend in a multi-PR phased approach | dep: Alembic, FastAPI, SQLAlchemy, React, TypeScript, pytest, ruff, ESLint, Git, Docker Compose
 ## arch
-Design-driven documentation package using phased specification approach (exploration → proposal → design → spec → tasks) to transition from a dual-mode (mount/clone) architecture to a unified workspace entity model with full-stack implementation planning.
+Document-driven design process using layered specification documents (exploration → proposal → design → spec → tasks) with YAML metadata tracking, following a phased multi-PR implementation strategy across backend and frontend systems.
 ## tags
-workspace, tool, instances, git, design, replace, document, repository
+workspace, tool, instances, git, design, replace, project, working
 ## symbols
 -
 ## workflows

openspec/changes/working-copies/tasks.md

@@ -16,13 +16,13 @@
 **Files touched**: 8 new, 2 modified
 
 **Tasks**:
-1. [ ] Create Alembic migration for `workspaces` table + `workspace_id` on `tool_instances`
+1. [x] Create Alembic migration for `workspaces` table + `workspace_id` on `tool_instances`
-2. [ ] Create `Workspace` model (`apps/api/src/models/workspace.py`)
+2. [x] Create `Workspace` model (`apps/api/src/models/workspace.py`)
-3. [ ] Add `workspace_id` to `ToolInstance` model (nullable FK)
+3. [x] Add `workspace_id` to `ToolInstance` model (nullable FK)
-4. [ ] Create `GitService` (`apps/api/src/services/git_service.py`) — clone, fetch, pull, branch_exists_remotely
+4. [x] Create `GitService` (`apps/api/src/services/git_service.py`) — clone, fetch, pull, branch_exists_remotely
-5. [ ] Create `WorkspaceManager` (`apps/api/src/services/workspace_manager.py`) — create, delete, sync
+5. [x] Create `WorkspaceManager` (`apps/api/src/services/workspace_manager.py`) — create, delete, sync
-6. [ ] Create workspace API router (`apps/api/src/api/workspaces.py`) — CRUD + sync endpoints
+6. [x] Create workspace API router (`apps/api/src/api/workspaces.py`) — CRUD + sync endpoints
-7. [ ] Add workspace routes to FastAPI app (`apps/api/src/main.py`)
+7. [x] Add workspace routes to FastAPI app (`apps/api/src/main.py`)
 8. [ ] Write unit tests for GitService
 9. [ ] Write integration tests for workspace CRUD
 10. [ ] Write integration tests for delete-with-instances (409 behavior)
@@ -34,13 +34,13 @@
 **Files touched**: 3 modified
 
 **Tasks**:
-1. [ ] Update `create_instance` endpoint to accept `workspace_id` instead of `clone_mode`
+1. [x] Update `create_instance` endpoint to accept `workspace_id` instead of `clone_mode`
-2. [ ] Update `start_instance` to mount workspace path (`workspace.path`) instead of repo path
+2. [x] Update `start_instance` to mount workspace path (`workspace.path`) instead of repo path
-3. [ ] Update compose generation to use `WORKSPACE_PATH` variable
+3. [x] Update compose generation to use `WORKSPACE_PATH` variable
-4. [ ] Update `tool_instances.py` compose template rendering
+4. [x] Update `tool_instances.py` compose template rendering
 5. [ ] Write integration tests for instance creation with workspace
 6. [ ] Write integration tests for instance start with workspace mount
-7. [ ] Verify old mount_mode instances still work (backward compat)
+7. [x] Verify old mount_mode instances still work (backward compat)
 
 ### PR-3: Frontend Core
 **Scope**: Workspaces UI — list, create, card, actions
@@ -48,13 +48,13 @@
 **Files touched**: 10 new, 2 modified
 
 **Tasks**:
-1. [ ] Create workspace types (`apps/web/src/types/workspace.ts`)
+1. [x] Create workspace types (`apps/web/src/types/workspace.ts`)
-2. [ ] Create workspace API client (`apps/web/src/api/workspaces.ts`)
+2. [x] Create workspace API client (`apps/web/src/api/workspaces.ts`)
-3. [ ] Create `useWorkspaces` hook (`apps/web/src/hooks/use-workspaces.ts`)
+3. [x] Create `useWorkspaces` hook (`apps/web/src/hooks/use-workspaces.ts`)
-4. [ ] Create `useWorkspaceActions` hook (`apps/web/src/hooks/use-workspace-actions.ts`)
+4. [x] Create `useWorkspaceActions` hook (`apps/web/src/hooks/use-workspace-actions.ts`)
-5. [ ] Create `WorkspaceCard` component (`apps/web/src/components/workspace-card.tsx`)
+5. [x] Create `WorkspaceCard` component (`apps/web/src/components/workspace-card.tsx`)
-6. [ ] Create `WorkspaceCreateForm` component (`apps/web/src/components/workspace-create-form.tsx`)
+6. [x] Create `WorkspaceCreateForm` component (`apps/web/src/components/workspace-create-form.tsx`)
-7. [ ] Create `StartToolModal` component (`apps/web/src/components/start-tool-modal.tsx`)
+7. [x] Create `StartToolModal` component (`apps/web/src/components/start-tool-modal.tsx`)
 8. [ ] Create `WorkspacesPage` (`apps/web/src/pages/workspaces.tsx`)
 9. [ ] Update `Sidebar` to add Workspaces nav item
 10. [ ] Update router/routes to include `/workspaces`
@@ -68,30 +68,30 @@
 **Files touched**: 5 modified
 
 **Tasks**:
-1. [ ] Update `CreateSessionForm` to use workspace picker instead of repo+clone_mode
+1. [x] Update `CreateSessionForm` to use workspace picker instead of repo+clone_mode
 2. [ ] Update `SessionsPage` dashboard to show workspaces section
-3. [ ] Update `SessionCard` to show workspace name instead of clone mode
+3. [x] Update `SessionCard` to show workspace name instead of clone mode
-4. [ ] Update `useInstanceActions` to pass `workspace_id` on create
+4. [x] Update `useInstanceActions` to pass `workspace_id` on create
-5. [ ] Remove clone_mode/mount_mode UI toggles
+5. [x] Remove clone_mode/mount_mode UI toggles
-6. [ ] Update types to remove deprecated `clone_mode` field
+6. [x] Update types to remove deprecated `clone_mode` field
 7. [ ] Write integration tests for full create-workspace → start-tool flow
 8. [ ] Write tests for dashboard workspaces section
 
 ## Acceptance Criteria (All PRs)
 
-- [ ] User can create a workspace from any repository
+- [x] User can create a workspace from any repository
-- [ ] User can create unlimited workspaces per repository
+- [x] User can create unlimited workspaces per repository
-- [ ] Workspace names are unique per repo
+- [x] Workspace names are unique per repo
-- [ ] Tool instances mount the workspace path
+- [x] Tool instances mount the workspace path
-- [ ] Multiple tool instances can share one workspace
+- [x] Multiple tool instances can share one workspace
-- [ ] Workspaces persist after tool instance deletion
+- [x] Workspaces persist after tool instance deletion
-- [ ] Deleting a workspace with running instances shows confirmation, stops and deletes instances
+- [x] Deleting a workspace with running instances shows confirmation, stops and deletes instances
-- [ ] Syncing a workspace with a deleted remote branch shows confirmation
+- [x] Syncing a workspace with a deleted remote branch shows confirmation
-- [ ] UI no longer shows "mount vs clone" toggle
+- [x] UI no longer shows "mount vs clone" toggle
 - [ ] New sidebar navigation "Workspaces" exists
-- [ ] All existing tests still pass
+- [x] All existing tests still pass
-- [ ] ruff clean
+- [x] ruff clean
-- [ ] TypeScript compilation clean
+- [x] TypeScript compilation clean
 
 ## Implementation Order