refactor: extract Pydantic schemas into schemas/ subpackages

Extract inline Pydantic models from 9 API routers into dedicated
schema modules under schemas/:

- schemas/tool/tool_type.py — ToolTypeCreate, ToolTypeUpdate, etc.
- schemas/tool/tool_instance.py — CreateInstanceRequest, StartInstanceRequest
- schemas/config/config_profile.py — ConfigProfileCreate, ConfigProfileUpdate,
  ConfigProfileResponse, DefaultProfilesUpdate, ValidateGitUrlRequest, etc.
- schemas/system/health.py — DatabaseHealth, DiskHealth, HealthResponse, etc.
- schemas/user/user.py — UserProfileResponse, UserProfileUpdate
- schemas/user/user_config.py — UserConfigResponse, UserConfigUpdate
- schemas/project/project.py — ProjectCreate, ProjectUpdate, etc.
- schemas/project/ssh_key.py — SSHKeyCreate, SSHKeyResponse, etc.
- schemas/project/git_repository.py — GitRepositoryCreate, etc.

API routers now import from src.schemas.* instead of defining inline.
Net change: -548 lines across 16 files.

Quality gates: py_compile passed, ruff passed on all 18 files.

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

@@ -1 +1,17 @@
-"""System module."""
+"""System schemas module."""
+
+from src.schemas.system.health import (
+    DatabaseHealth,
+    DatabaseHealthResponse,
+    DiskHealth,
+    HealthChecks,
+    HealthResponse,
+)
+
+__all__ = [
+    "DatabaseHealth",
+    "DatabaseHealthResponse",
+    "DiskHealth",
+    "HealthChecks",
+    "HealthResponse",
+]