Replace module-level singletons in api.py with FastAPI app state
Problem
`pyrite/server/api.py` caches `_config`, `_db`, and `_kb_service` as module-level globals. While FastAPI DI rebuilds them if dependencies change, this pattern creates test isolation risk — tests that don't properly reset these globals can interfere with each other, especially under parallel execution (`pytest-xdist`).
Solution
Move singleton state into FastAPI `app.state` instead of module-level variables. This makes lifecycle explicit (tied to app instance), simplifies test overrides via `app.dependency_overrides`, and eliminates the risk of stale state leaking across tests.