fix: stage config-profile mounts as directories so ~/.config stays writable

- Switch apply_resolved_profile from per-file bind mounts to one
  directory-level bind mount per ResolvedMount target.
- Stage all configured files under instance_dir/mounts/<sanitized_target>
  and bind-mount that directory, so Docker no longer creates a root-owned
  parent directory such as ~/.config.
- Propagate read-only mode ('ro') as the 'readonly' flag on volume entries.
- Update unit tests to expect directory-level mounts and add coverage for
  readonly/writable flags.

Quality gates: python3 -m py_compile, pytest (313 passed, 34 skipped),
npm run typecheck, npm run lint.

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

@@ -4,7 +4,7 @@ dir: apps/api/src
 index: apps/api/src/.pi-map.index.md
 
 ## role
-Core application package for the Headquarter API, handling configuration, database connectivity, structured logging, and FastAPI application initialization.
+Core application package for the Headquarter API, providing 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 application package for the Headquarter API, handling configuration, databa
 - 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 architecture with environment-based Pydantic config, async SQLAlchemy with retry patterns, structured JSON logging with correlation IDs, and modular FastAPI setup with middleware and background services.
+Layered architecture with environment-based Pydantic config, async SQLAlchemy with retry patterns, structured JSON logging with correlation ID tracking, and modular FastAPI setup with middleware pipeline.
 ## tags
 src, database, logging, call:logger.info, api, middleware, fastapi, filter
 ## symbols