feat: tool definition manifest system (PR 1)

- Add ToolDefinitionManifest model with base image versioning
- Add manifest compiler: Dockerfile + Compose generation from JSON manifests
- Add permission fixer: post-start chown/chmod for mount policies
- Add tool definition CRUD API with live compile preview endpoint
- Integrate manifest-based startup flow in start_instance
- Add Alembic migration with data conversion for pi-agent
- Add 48 unit tests for manifest compiler, permission fixer, docker service
- Keep backward compatibility with legacy dockerfile_template/compose_template

Migration: applied successfully. Pi-agent converted to manifest.
Quality gates: pytest (146 passed, 4 pre-existing unrelated failures)

apps/api/src/main.py

@@ -18,6 +18,7 @@ from src.api.instance_proxy import router as instance_proxy_router
 from src.api.config_folders import router as config_folders_router
 from src.api.config_profiles import router as config_profiles_router
 from src.api.tool_configs import router as tool_configs_router
+from src.api.tool_definitions import router as tool_definitions_router
 from src.api.tool_instances import router as tool_instances_router
 from src.api.tool_instances import sessions_router
 from src.api.tool_types import router as tool_types_router
@@ -66,7 +67,9 @@ def _sanitize_validation_errors(errors):
             "type": error.get("type"),
             "loc": error.get("loc"),
             "msg": error.get("msg"),
-            "input": str(error.get("input")) if error.get("input") is not None else None,
+            "input": str(error.get("input"))
+            if error.get("input") is not None
+            else None,
         }
         # Convert ctx to safe format
         ctx = error.get("ctx")
@@ -110,10 +113,12 @@ async def on_startup():
     if not db_ready:
         logger.error("Database initialization failed. Shutting down.")
         import sys
+
         sys.exit(1)
 
     logger.info("Startup complete.")
 
+
 app.include_router(health_router)
 app.include_router(auth_router)
 app.include_router(dashboard_router)
@@ -123,6 +128,7 @@ app.include_router(ssh_keys_router)
 app.include_router(git_repositories_router)
 app.include_router(user_config_router)
 app.include_router(tool_types_router)
+app.include_router(tool_definitions_router)
 app.include_router(config_folders_router)
 app.include_router(config_profiles_router)
 app.include_router(tool_instances_router)