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/.pi-map.md

@@ -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/FastAPI with PostgreSQL (Alembic migrations), multi-stage Docker containerization with socket access, uv package management, and Cloudflare tunneling integration.
+Async Python/FastAPI backend with PostgreSQL (asyncpg), Alembic migrations, multi-stage Docker deployment with Cloudflare tunneling, uv package management, and containerized orchestration with database dependency waiting.
 ## tags
 docker, alembic, python, database, fastapi, postgresql, asyncpg, uvicorn
 ## symbols