fix: clone workspace into repo-named subdirectory directly

Git clone with an explicit destination puts the working copy directly into
that directory; it does not create a repo-named subdirectory. The previous
change assumed the opposite, so workspaces ended up at
/data/working-copies/{workspace_id}/ with the repo contents mixed in,
causing a 500 when the expected repo-named subdirectory was missing.

- Build the target path as /data/working-copies/{workspace_id}/{repo_name}/
  and pass it directly to GitService.clone
- Remove stale directory detection and fallback logic that is no longer
  needed
- Keep diagnostic logging around git clone failures

Quality gates:
- pytest tests/unit: 219 passed
- mypy: clean on changed files

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

@@ -2,7 +2,7 @@
 dir: apps/api
 
 ## role
-Self-hosted FastAPI backend API that manages projects, git repositories, and development tools via Docker instances.
+FastAPI backend API that manages projects, git repositories, and development tools through Docker containers with PostgreSQL persistence.
 ## parent
 index: apps/.pi-map.index.md
 map: apps/.pi-map.md

apps/api/.pi-map.md

@@ -4,7 +4,7 @@ dir: apps/api
 index: apps/api/.pi-map.index.md
 
 ## role
-Self-hosted FastAPI backend API that manages projects, git repositories, and development tools via Docker instances.
+FastAPI backend API that manages projects, git repositories, and development tools through Docker containers with PostgreSQL persistence.
 ## files
 - .dockerignore | Specifies files and directories to exclude from Docker build context to reduce image size and avoid copying unnecessary files into containers. | dep: Docker
 - Dockerfile | Multi-stage Docker build for a Python application with Docker socket access, Cloudflare tunneling, and database dependency waiting | dep: python:3.11-slim, gcc, libpq-dev, docker-ce-cli, docker-compose-plugin, cloudflared, uvicorn, pyproject.toml dependencies
@@ -14,7 +14,7 @@ Self-hosted FastAPI backend API that manages projects, git repositories, and dev
 - uv.lock | Lock file for the uv Python package manager that pins exact dependency versions and their artifact hashes for reproducible installations | dep: uv, Python 3.11+, aiosqlite, alembic, annotated-doc, annotated-types, anyio, ast-serialize, asyncpg, and many other PyPI packages
 - wait-for-db.sh | Wait for a PostgreSQL database to become available before executing a command, with configurable retry logic. | dep: nc (netcat), sh (POSIX shell), sleep
 ## arch
-Async Python backend with FastAPI, PostgreSQL via Alembic migrations, multi-stage Docker containerization with Cloudflare tunneling, and uv-based dependency management.
+Async Python microservice using FastAPI, SQLAlchemy/Alembic for migrations, multi-stage Docker builds with Docker-in-Docker socket access, Cloudflare tunneling, and uv for dependency management.
 ## tags
 docker, alembic, python, database, fastapi, postgresql, asyncpg, uvicorn
 ## symbols

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

@@ -2,7 +2,7 @@
 dir: apps/api/src
 
 ## role
-Core backend API package for the "Headquarter" service, providing application bootstrap, configuration, database connectivity, and structured logging infrastructure.
+Core backend API package for the "Headquarter" service, handling configuration, database connectivity, structured logging, and FastAPI application initialization.
 ## parent
 index: apps/api/.pi-map.index.md
 map: apps/api/.pi-map.md

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

@@ -4,7 +4,7 @@ dir: apps/api/src
 index: apps/api/src/.pi-map.index.md
 
 ## role
-Core backend API package for the "Headquarter" service, providing application bootstrap, configuration, database connectivity, and structured logging infrastructure.
+Core backend API package for the "Headquarter" service, handling configuration, database connectivity, structured logging, and FastAPI application initialization.
 ## files
 - __init__.py | Marks the directory as a Python package for the Headquarter API.
 - config.py | Defines application configuration settings with environment-based overrides using Pydantic, including database URLs, service domains, OAuth/Authentik integration, JWT/session settings, and computed properties for environment-specific behavior. | exp: class:Settings, func:build_database_url(user: str, password: str, host: str, port: int, database: str) → str | dep: pydantic, pydantic_settings
@@ -12,7 +12,7 @@ Core backend API package for the "Headquarter" service, providing application bo
 - logging_config.py | Configures structured JSON logging with correlation ID injection, custom formatters, and HTTP request/exception middleware for a FastAPI application. | exp: class:CorrelationIdFilter, method:filter(self, record: logging.LogRecord) → bool, call:get_correlation_id, class:JSONFormatter, method:format(self, record: logging.LogRecord) → str, call:self.formatTime, call:record.getMessage, call:getattr, call:self.formatException, call:json.dumps, method:formatTime(self, record: logging.LogRecord, datefmt) → str, call:time.strftime, call:time.gmtime, class:RequestLoggingMiddleware, method:dispatch(self, request: Request, call_next: Callable) → Response, call:time.time, call:logger.info, call:call_next, call:int, call:logger.error, call:type, call:traceback.format_exc, class:ExceptionLoggingMiddleware, method:dispatch(self, request: Request, call_next: Callable) → Response, call:call_next, call:logger.critical, call:traceback.format_exc, func:configure_logging(level) → None, call:JSONFormatter, call:logging.StreamHandler, call:console_handler.setFormatter, call:console_handler.addFilter, call:CorrelationIdFilter, call:root_logger.setLevel, call:logging.getLogger("uvicorn").setLevel, call:logging.getLogger("uvicorn.access").setLevel, call:logging.getLogger("sqlalchemy.engine").setLevel, call:logger.info, call:logging.getLevelName | dep: json, logging, sys, time, traceback, collections.abc, fastapi, starlette.middleware.base, src.services.shared.correlation
 - main.py | Initializes and configures a FastAPI application for the "Headquarter API" with database setup, middleware, routing, and background services. | exp: func:_sanitize_validation_errors(errors), call:error.get, call:str, call:ctx.items, call:isinstance, call:type, call:sanitized.append, func:validation_exception_handler(request: Request, exc: RequestValidationError), call:exc.errors, call:logger.warning, call:_sanitize_validation_errors, call:JSONResponse, func:on_startup(), call:logger.info, call:init_database, call:logger.error, call:sys.exit, call:_health_monitor.start, call:seed_builtin_tool_types, func:on_shutdown(), call:logger.info, call:_health_monitor.stop | dep: logging, os, fastapi, fastapi.exceptions, fastapi.middleware.cors, fastapi.responses, fastapi.staticfiles, src.api.config, src.api.project, src.api.system, src.api.tool, src.api.user, src.api.workspace, src.config, src.models, src.database, src.logging_config, src.seeds.builtin_tool_types, src.services.instance, src.services.shared, sys, src.api.*
 ## arch
-Layered FastAPI application architecture using Pydantic settings with environment overrides, async SQLAlchemy with Alembic migrations, dependency injection via lifespan context, and middleware-based cross-cutting concerns (correlation ID tracking, JSON logging, request/exception handling).
+Layered architecture with environment-driven Pydantic config, async SQLAlchemy with retry resilience, structured JSON logging with correlation ID tracking, and modular FastAPI bootstrap with middleware/routing composition.
 ## tags
 src, database, logging, call:logger.info, api, middleware, fastapi, filter
 ## symbols

apps/api/src/services/.pi-map.index.md

@@ -2,7 +2,7 @@
 dir: apps/api/src/services
 
 ## role
-This package serves as a Python namespace marker for the services layer in the API application, indicating a modular architecture where business logic services are organized as a subpackage.
+Marks the `services` directory as a Python package for organizing business logic and service-layer modules.
 ## parent
 index: apps/api/src/.pi-map.index.md
 map: apps/api/src/.pi-map.md

apps/api/src/services/.pi-map.md

@@ -4,11 +4,11 @@ dir: apps/api/src/services
 index: apps/api/src/services/.pi-map.index.md
 
 ## role
-This package serves as a Python namespace marker for the services layer in the API application, indicating a modular architecture where business logic services are organized as a subpackage.
+Marks the `services` directory as a Python package for organizing business logic and service-layer modules.
 ## files
 - __init__.py | Empty file with no functionality
 ## arch
-Standard Python package structure using __init__.py for namespace declaration, following conventional layered architecture with services separated into their own directory for future dependency injection and domain logic encapsulation.
+Standard Python package structure using `__init__.py` to define an importable namespace, following conventional layered architecture with an empty initializer awaiting future service modules.
 ## tags
 init, empty, functionality
 ## symbols

apps/api/src/services/shared/.pi-map.index.md

@@ -2,7 +2,7 @@
 dir: apps/api/src/services/shared
 
 ## role
-Provides common infrastructure services used across the API backend, including security, I/O, container operations, and workspace lifecycle management.
+Provides common, cross-cutting backend services used by multiple API components for security, infrastructure, and user-facing operations.
 ## parent
 index: apps/api/src/services/.pi-map.index.md
 map: apps/api/src/services/.pi-map.md

apps/api/src/services/shared/.pi-map.md

@@ -4,9 +4,9 @@ dir: apps/api/src/services/shared
 index: apps/api/src/services/shared/.pi-map.index.md
 
 ## role
-Provides common infrastructure services used across the API backend, including security, I/O, container operations, and workspace lifecycle management.
+Provides common, cross-cutting backend services used by multiple API components for security, infrastructure, and user-facing operations.
 ## files
-- __init__.py | Re-exports shared service classes and functions from a services package to provide a unified public API | dep: correlation, file_service, notification_service, permission_fixer, readiness_probe, ssh_keys, tunnel, workspace_manager
+- __init__.py | Re-exports shared service classes and functions from a services package to provide a unified public API | dep: src.services.shared.correlation, src.services.shared.file_service, src.services.shared.notification_service, src.services.shared.permission_fixer, src.services.shared.readiness_probe, src.services.shared.ssh_keys, src.services.shared.tunnel, src.services.shared.workspace_manager, correlation, file_service, notification_service, permission_fixer, readiness_probe, ssh_keys, tunnel, workspace_manager
 - correlation.py | Provides async correlation ID tracking via context variables and FastAPI middleware for request tracing. | exp: class:CorrelationIdMiddleware, method:dispatch(self, request: Request, call_next), call:request.headers.get, call:str, call:uuid.uuid4, call:CORRELATION_ID.set, call:call_next, call:CORRELATION_ID.reset, func:get_correlation_id() → str, call:CORRELATION_ID.get, call:str, call:uuid.uuid4 | dep: contextvars, uuid, fastapi, starlette.middleware.base, fastapi.Request, starlette.middleware.base.BaseHTTPMiddleware
 - file_service.py | Provides safe file operations (list, read, write) scoped within a workspace directory with path traversal protection. | exp: class:FileEntry, class:FileService, method:list_directory(self, workspace: Workspace, relative_path) → list[FileEntry], call:os.path.join, call:os.path.normpath, call:abs_path.startswith, call:os.path.exists, call:sorted, call:os.listdir, call:os.path.isdir, call:os.path.getsize, call:os.path.isfile, call:entries.append, call:FileEntry, call:rel.replace, call:entries.sort, call:e.name.lower, raise:ValueError, method:read_file(self, workspace: Workspace, relative_path: str) → str, call:self._resolve_path, call:os.path.isfile, call:open, call:f.read, raise:FileNotFoundError, raise:ValueError, method:write_file(self, workspace: Workspace, relative_path: str, content: str) → None, call:self._resolve_path, call:os.makedirs, call:os.path.dirname, call:open, call:f.write, call:logger.info, method:_resolve_path(self, workspace: Workspace, relative_path: str) → str, call:os.path.normpath, call:os.path.join, call:abs_path.startswith, raise:ValueError | dep: logging, os, dataclasses, src.models, src.models.Workspace
 - notification_service.py | Provides an async singleton service for creating, listing, reading, and dismissing user-owned notifications with strict ownership isolation. | exp: class:NotificationService, method:create_notification(self, session: AsyncSession, user_id: uuid.UUID, category: str, severity: str, title: str, message, source_type, source_id, metadata) → Notification, call:Notification, call:session.add, call:session.commit, call:session.refresh, method:list_notifications(self, session: AsyncSession, user_id: uuid.UUID, limit, offset, unread_only, mute_categories) → tuple[list[Notification], int], call:Notification.dismissed_at.is_, call:where_clauses.append, call:Notification.read_at.is_, call:Notification.category.not_in, call:select(func.count()).select_from(Notification).where, call:func.count, call:session.execute, call:total_result.scalar_one, call:select(Notification) .where(*where_clauses) .order_by(Notification.created_at.desc()) .limit(limit) .offset, call:Notification.created_at.desc, call:list, call:items_result.scalars().all, method:get_unread_count(self, session: AsyncSession, user_id: uuid.UUID) → int, call:select(func.count()) .select_from(Notification) .where, call:func.count, call:Notification.read_at.is_, call:Notification.dismissed_at.is_, call:session.execute, call:result.scalar_one, method:mark_read(self, session: AsyncSession, notification_id: uuid.UUID, user_id: uuid.UUID) → Notification, call:self._get_owned_notification, call:datetime.now, call:session.commit, call:session.refresh, method:mark_all_read(self, session: AsyncSession, user_id: uuid.UUID) → int, call:update(Notification) .where( Notification.user_id == user_id, Notification.read_at.is_(None), Notification.dismissed_at.is_(None), ) .values, call:Notification.read_at.is_, call:Notification.dismissed_at.is_, call:datetime.now, call:session.execute, call:session.commit, method:dismiss_all(self, session: AsyncSession, user_id: uuid.UUID) → int, call:update(Notification) .where( Notification.user_id == user_id, Notification.dismissed_at.is_(None), ) .values, call:Notification.dismissed_at.is_, call:datetime.now, call:session.execute, call:session.commit, method:dismiss(self, session: AsyncSession, notification_id: uuid.UUID, user_id: uuid.UUID) → None, call:self._get_owned_notification, call:datetime.now, call:session.commit, method:_get_owned_notification(self, session: AsyncSession, notification_id: uuid.UUID, user_id: uuid.UUID) → Notification, call:session.get, raise:ValueError | dep: uuid, datetime, typing, sqlalchemy, sqlalchemy.engine, sqlalchemy.ext.asyncio, src.models, src.models.Notification
@@ -14,11 +14,11 @@ Provides common infrastructure services used across the API backend, including s
 - readiness_probe.py | Executes a retryable readiness probe command inside a Docker container with configurable timeout and interval | exp: func:execute_probe(container_id: str, command: str, timeout, interval) → tuple[bool, list[str]], call:asyncio.get_event_loop().time, call:logs.append, call:logger.debug, call:subprocess.run, call:result.stdout.strip, call:result.stderr.strip, call:asyncio.sleep | dep: asyncio, logging, subprocess
 - ssh_keys.py | Decrypts and writes SSH key files to instance directories for container mounting, with optional ownership configuration and SSH config generation. | exp: func:_get_fernet() → Fernet, call:Settings, call:hashlib.sha256(settings.session_secret.encode()).digest, call:settings.session_secret.encode, call:base64.urlsafe_b64encode, call:Fernet, func:_sanitize_filename(name: str) → str, call:re.sub, call:sanitized.strip, func:prepare_ssh_key_files(instance_dir: str, ssh_key, subdir, uid, gid, key_filename, write_config) → str, call:Path, call:ssh_dir.mkdir, call:_get_fernet, call:fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode, call:ssh_key.private_key_encrypted.encode, call:private_key_path.write_text, call:os.chmod, call:public_key_path.write_text, call:config_path.write_text, call:os.chown, call:logger.debug, call:logger.warning, call:os.getuid, call:str, func:write_ssh_config(ssh_dir: str, key_filenames: list[str], uid, gid) → None, call:Path, call:ssh_dir_path.mkdir, call:lines.append, call:"\n".join, call:config_path.write_text, call:os.chmod, call:os.chown, func:cleanup_ssh_key_files(instance_dir: str) → None, call:Path, call:ssh_dir.exists, call:ssh_dir.iterdir, call:file_path.unlink, call:ssh_dir.rmdir | dep: logging, os, re, pathlib, cryptography.fernet, src.config, base64, hashlib
 - tunnel.py | Re-exports Docker tunnel functions from a nested module for backward compatibility. | dep: src.services.docker.tunnel
-- workspace_manager.py | Manages the full lifecycle of development workspaces including creation via git clone, deletion with cleanup, remote sync, and migration of legacy tool instances into workspace-bound structures. | exp: class:SyncResult, class:WorkspaceHasInstancesError, method:__init__(self, instances: list[dict]) → None, call:super().__init__, call:len, class:WorkspaceManager, method:_workspace_path(self, workspace_id: uuid.UUID, repo: "GitRepository") → str, call:os.path.join, call:str, call:self._repo_directory_name, method:create(self, repo: GitRepository, user_id: uuid.UUID, name: str, branch, session) → Workspace, call:self._repo_directory_name, call:uuid.uuid4, call:os.path.join, call:str, call:logger.info, call:os.path.exists, call:logger.warning, call:shutil.rmtree, call:os.makedirs, call:contextlib.suppress, call:os.chmod, call:getattr, call:session.execute, call:select(SSHKey).where, call:result.scalar_one_or_none, call:_get_fernet, call:fernet.decrypt( ssh_key_obj.private_key_encrypted.encode() ).decode, call:ssh_key_obj.private_key_encrypted.encode, call:GitService.clone, call:logger.error, call:os.path.isdir, call:os.listdir, call:len, call:self._make_world_writable, call:Workspace, call:datetime.now, raise:ValueError, raise:RuntimeError, method:delete(self, workspace: Workspace, force, session) → None, call:self._get_instances, call:self._stop_and_delete_instance, call:os.path.exists, call:shutil.rmtree, call:logger.info, call:session.delete, raise:ValueError, raise:WorkspaceHasInstancesError, method:sync(self, workspace: Workspace, session) → SyncResult, call:logger.info, call:session.get, call:getattr, call:session.execute, call:select(SSHKey).where, call:result.scalar_one_or_none, call:_get_fernet, call:fernet.decrypt( ssh_key_obj.private_key_encrypted.encode() ).decode, call:ssh_key_obj.private_key_encrypted.encode, call:GitService.fetch, call:GitService.branch_exists_remotely, call:SyncResult, call:GitService.pull, call:self._make_world_writable, call:datetime.now, method:_make_world_writable(self, path: str) → None, call:contextlib.suppress, call:os.chmod, call:os.walk, call:os.path.join, call:os.stat, method:_get_instances(self, workspace: Workspace, session: AsyncSession) → list[ToolInstance], call:session.execute, call:select(ToolInstance).where, call:list, call:result.scalars().all, method:_stop_and_delete_instance(self, instance: ToolInstance, session: AsyncSession) → None, call:delete_tool_instance, call:logger.info, call:logger.error, method:ensure_instance_workspace(self, instance: ToolInstance, session: AsyncSession) → Workspace, call:session.get, call:self._workspace_name_exists, call:self._migrate_clone_into_workspace, call:self.create, call:session.add, call:session.commit, call:session.refresh, call:logger.info, raise:RuntimeError, method:_workspace_name_exists(self, session: AsyncSession, repo_id: uuid.UUID, name: str) → bool, call:session.execute, call:select(Workspace).where, call:result.scalar_one_or_none, method:_migrate_clone_into_workspace(self, instance: ToolInstance, repo: "GitRepository", session: AsyncSession, name: str) → Workspace, call:os.path.dirname, call:os.path.join, call:os.path.exists, call:uuid.uuid4, call:str, call:self._repo_directory_name, call:os.makedirs, call:contextlib.suppress, call:os.chmod, call:shutil.rmtree, call:shutil.move, call:self._make_world_writable, call:Workspace, call:datetime.now, call:session.add, call:session.flush, raise:RuntimeError | dep: contextlib, logging, os, shutil, stat, uuid, dataclasses, datetime, typing, sqlalchemy, src.models, src.services.git.git_service, src.services.shared.ssh_keys, src.utils.git_url_parser, sqlalchemy.ext.asyncio, src.services.tool.instance_service
+- workspace_manager.py | Manages workspace lifecycle operations including creation, deletion, synchronization, and migration of legacy tool instances into workspace-based repositories. | exp: class:SyncResult, class:WorkspaceHasInstancesError, method:__init__(self, instances: list[dict]) → None, call:super().__init__, call:len, class:WorkspaceManager, method:_workspace_path(self, workspace_id: uuid.UUID, repo: "GitRepository") → str, call:os.path.join, call:str, call:self._repo_directory_name, method:create(self, repo: GitRepository, user_id: uuid.UUID, name: str, branch, session) → Workspace, call:self._repo_directory_name, call:uuid.uuid4, call:os.path.join, call:str, call:logger.info, call:os.path.exists, call:logger.warning, call:shutil.rmtree, call:os.makedirs, call:contextlib.suppress, call:os.chmod, call:getattr, call:session.execute, call:select(SSHKey).where, call:result.scalar_one_or_none, call:_get_fernet, call:fernet.decrypt( ssh_key_obj.private_key_encrypted.encode() ).decode, call:ssh_key_obj.private_key_encrypted.encode, call:GitService.clone, call:logger.error, call:self._make_world_writable, call:Workspace, call:datetime.now, raise:ValueError, method:delete(self, workspace: Workspace, force, session) → None, call:self._get_instances, call:self._stop_and_delete_instance, call:os.path.exists, call:shutil.rmtree, call:logger.info, call:session.delete, raise:ValueError, raise:WorkspaceHasInstancesError, method:sync(self, workspace: Workspace, session) → SyncResult, call:logger.info, call:session.get, call:getattr, call:session.execute, call:select(SSHKey).where, call:result.scalar_one_or_none, call:_get_fernet, call:fernet.decrypt( ssh_key_obj.private_key_encrypted.encode() ).decode, call:ssh_key_obj.private_key_encrypted.encode, call:GitService.fetch, call:GitService.branch_exists_remotely, call:SyncResult, call:GitService.pull, call:self._make_world_writable, call:datetime.now, method:_make_world_writable(self, path: str) → None, call:contextlib.suppress, call:os.chmod, call:os.walk, call:os.path.join, call:os.stat, method:_get_instances(self, workspace: Workspace, session: AsyncSession) → list[ToolInstance], call:session.execute, call:select(ToolInstance).where, call:list, call:result.scalars().all, method:_stop_and_delete_instance(self, instance: ToolInstance, session: AsyncSession) → None, call:delete_tool_instance, call:logger.info, call:logger.error, method:ensure_instance_workspace(self, instance: ToolInstance, session: AsyncSession) → Workspace, call:session.get, call:self._workspace_name_exists, call:self._migrate_clone_into_workspace, call:self.create, call:session.add, call:session.commit, call:session.refresh, call:logger.info, raise:RuntimeError, method:_workspace_name_exists(self, session: AsyncSession, repo_id: uuid.UUID, name: str) → bool, call:session.execute, call:select(Workspace).where, call:result.scalar_one_or_none, method:_migrate_clone_into_workspace(self, instance: ToolInstance, repo: "GitRepository", session: AsyncSession, name: str) → Workspace, call:os.path.dirname, call:os.path.join, call:os.path.exists, call:uuid.uuid4, call:str, call:self._repo_directory_name, call:os.makedirs, call:contextlib.suppress, call:os.chmod, call:shutil.rmtree, call:shutil.move, call:self._make_world_writable, call:Workspace, call:datetime.now, call:session.add, call:session.flush, raise:RuntimeError | dep: contextlib, logging, os, shutil, stat, uuid, dataclasses, datetime, typing, sqlalchemy, src.models, src.services.git.git_service, src.services.shared.ssh_keys, src.utils.git_url_parser, sqlalchemy.ext.asyncio, src.services.tool.instance_service
 ## arch
-Modular service-oriented architecture with singleton async services, context variable-based request tracing, path traversal-safe file operations, Docker container exec-based operations, and git-based workspace provisioning with cleanup and migration support.
+Modular utility services following singleton and async patterns, with Docker/container integration, filesystem sandboxing, context-based request tracing, and strict resource ownership isolation.
 ## tags
-error, call:self., get, workspace, key, call:str, call:session.execute, call:ssh
+error, call:self., get, workspace, src, key, call:str, call:session.execute
 ## symbols
 - CorrelationIdMiddleware
 - FileEntry

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

@@ -104,20 +104,21 @@ class WorkspaceManager:
         repo_dir_name = self._repo_directory_name(repo)
         workspace_id = uuid.uuid4()
         parent_path = os.path.join(self.BASE_PATH, str(workspace_id))
-        clone_target = parent_path  # git clone creates {repo_dir_name}/ inside this
+        expected_path = os.path.join(parent_path, repo_dir_name)
 
         logger.info(
-            "Creating workspace: id=%s name=%s repo=%s branch=%s",
+            "Creating workspace: id=%s name=%s repo=%s branch=%s target=%s",
             workspace_id,
             name,
             repo.id,
             branch,
+            expected_path,
         )
 
         # Remove stale directory from previous failed/aborted clone
-        if os.path.exists(parent_path):
-            logger.warning("Removing stale workspace directory: %s", parent_path)
-            shutil.rmtree(parent_path, ignore_errors=True)
+        if os.path.exists(expected_path):
+            logger.warning("Removing stale workspace directory: %s", expected_path)
+            shutil.rmtree(expected_path, ignore_errors=True)
 
         os.makedirs(parent_path, exist_ok=True)
         # Ensure container users (various UIDs) can write to workspace dirs
@@ -141,7 +142,7 @@ class WorkspaceManager:
 
         try:
             await GitService.clone(
-                repo.remote_url, branch, clone_target, ssh_key=ssh_key
+                repo.remote_url, branch, expected_path, ssh_key=ssh_key
             )
         except Exception as exc:
             logger.error(
@@ -153,29 +154,6 @@ class WorkspaceManager:
             )
             raise
 
-        expected_path = os.path.join(parent_path, repo_dir_name)
-        if not os.path.isdir(expected_path):
-            # git clone can create a different directory name than expected for
-            # some URL shapes; fall back to the single directory git created.
-            entries = [
-                entry
-                for entry in os.listdir(parent_path)
-                if os.path.isdir(os.path.join(parent_path, entry))
-            ]
-            logger.info(
-                "Workspace %s: expected %s/ but found directories: %s",
-                workspace_id,
-                repo_dir_name,
-                entries,
-            )
-            if len(entries) == 1:
-                expected_path = os.path.join(parent_path, entries[0])
-            else:
-                raise RuntimeError(
-                    f"Expected git clone to create {repo_dir_name}/ under "
-                    f"{parent_path}, but found: {entries}"
-                )
-
         self._make_world_writable(expected_path)
 
         workspace = Workspace(