fix: restore CI tools and current retrieval coverage

[Amazinghorseli]

CI could not start Ruff because the development dependencies are an optional dev extra, while the workflow only installed the default dependencies. After installing the extra, the existing formatting violations and tests for the deleted Supervisor module also prevented the pipeline from passing.

• Install and retain the dev extra for lint and test commands; add the missing pytest-timeout plugin and update its lockfile entry.
• Apply the existing Ruff rules and formatting to src/ and tests/, with local-name and unused-variable cleanup. No lint rules are disabled.
• Replace stale Supervisor tests with coverage of the current query preprocessing and hybrid retrieval flow, using mocked retrieval, reranking, and LLM calls.
• Start Docker through the installed virtualenv Python instead of a nonexistent .venv/bin/uv; use Python's standard library for the health check instead of an unavailable runtime curl binary.

Validation:

• uv run --frozen --extra dev ruff check src/ tests/: passed.
• uv run --frozen --extra dev ruff format --check src/ tests/: passed.
• Python 3.11, uv run --frozen --extra dev pytest tests/ -q --tb=short --timeout=60 -p no:warnings: 39 passed.
• uv lock --check and git diff --check: passed.
• Local Uvicorn startup and HTTP health check: passed with lifespan initialization disabled; no live model requests were made.
• Full Docker build was not run locally because the Docker daemon is unavailable; the PR's existing build job will verify the image.

AI assistance: Codex helped diagnose the failures, make the changes, and verify the checks above.