chore: track all project map and index files

Add generated .pi-map.md and .pi-map.index.md files across the repository
so the project navigation maps are shared and versioned. These artifacts
are maintained by project_map_init/patch/validate and must be kept in
sync with source edits.

Note: .cache/ remains ignored (added in previous commit).

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

@@ -0,0 +1,28 @@
+# apps/api/src/services/shared (index)
+dir: apps/api/src/services/shared
+
+## role
+Provides reusable, cross-cutting infrastructure services for the API including I/O safety, container operations, user notifications, request tracing, and workspace lifecycle management.
+## parent
+index: apps/api/src/services/.pi-map.index.md
+map: apps/api/src/services/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- correlation.py
+- file_service.py
+- notification_service.py
+- permission_fixer.py
+- readiness_probe.py
+- ssh_keys.py
+- tunnel.py
+- workspace_manager.py
+## links
+index: apps/api/src/services/shared/.pi-map.index.md
+map: apps/api/src/services/shared/.pi-map.md
+## workflows
+- change shared behavior
+  read: __init__.py, correlation.py, file_service.py
+## dirty
+-

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

@@ -0,0 +1,35 @@
+# apps/api/src/services/shared
+dir: apps/api/src/services/shared
+
+index: apps/api/src/services/shared/.pi-map.index.md
+
+## role
+Provides reusable, cross-cutting infrastructure services for the API including I/O safety, container operations, user notifications, request tracing, and workspace lifecycle management.
+## files
+- __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
+- permission_fixer.py | Applies mount and SSH permission policies inside running Docker containers by executing chown/chmod commands via docker exec as root. | exp: class:PermissionFixError, func:apply_mount_permissions(container_id: str, mounts: list[dict], timeout) → list[dict[str, Any]], call:mount.get, call:logger.debug, call:results.append, call:_run_in_container, call:str, call:logger.warning, func:_exec_and_log(container_id: str, command: list[str], timeout: int, description: str) → str, call:logger.debug, call:" ".join, call:subprocess.run, call:result.stdout.strip, call:result.stderr.strip, raise:PermissionFixError, func:apply_ssh_permissions(container_id: str, ssh_target: str, container_user: str, timeout) → dict[str, Any], call:_exec_and_log, call:logger.info, call:str, call:logger.warning, func:_run_in_container(container_id: str, command: list[str], timeout: int) → None, call:subprocess.run, raise:PermissionFixError, func:check_root_user_available(container_id: str, timeout) → bool, call:_run_in_container | dep: logging, subprocess, typing
+- 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 workspace lifecycle operations including creation, deletion, synchronization, and validation for git repository workspaces. | exp: class:SyncResult, class:WorkspaceHasInstancesError, method:__init__(self, instances: list[dict]) → None, call:super().__init__, call:len, class:WorkspaceManager, method:_workspace_path(self, repo_id: uuid.UUID, name: str) → str, call:os.path.join, call:str, method:create(self, repo: GitRepository, user_id: uuid.UUID, name: str, branch, session) → Workspace, call:self._workspace_path, call:os.path.dirname, call:os.makedirs, call:contextlib.suppress, call:os.chmod, call:logger.info, call:os.path.exists, call:logger.warning, call:shutil.rmtree, 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: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) → None, call:logger.warning | dep: contextlib, logging, os, shutil, stat, uuid, dataclasses, datetime, typing, sqlalchemy, src.models, src.services.git.git_service, src.services.shared.ssh_keys, sqlalchemy.ext.asyncio
+## arch
+Modular service-oriented architecture with async singletons, context variable-based state propagation, path traversal defense, Docker container exec abstraction, and strict ownership-based isolation boundaries.
+## tags
+error, get, key, call:self., src, call:ssh, at.is, call:session.execute
+## symbols
+- CorrelationIdMiddleware
+- FileEntry
+- FileService
+- NotificationService
+- PermissionFixError
+- SyncResult
+- WorkspaceHasInstancesError
+- WorkspaceManager
+## workflows
+- change shared behavior
+  read: __init__.py, correlation.py, file_service.py
+## dirty
+-