ci: enforce ruff+black formatting, fix all 50 lint errors, add pre-commit hooks

[DeepRatAI]

Summary

Closes #11

Enforces ruff check and black --check across the entire codebase. All 50 ruff errors fixed, all 113 files pass black formatting. CI lint job already runs without continue-on-error (was updated in earlier session).

Changes

Lint Fixes (50 errors → 0)

Rule	Count	Fix
F821	12	Added missing imports: logging, Specialty, ErrorCode (TYPE_CHECKING). Fixed bug: memory_service → service parameter
F841	10	Removed/prefixed unused variables: state, ttft_ms, start_time, html_lang, logger, span, etc.
B007	7	Prefixed unused loop variables with underscore
B905	5	Added strict=False to zip() calls
E741	4	Renamed ambiguous variable l → lab/lv in comprehensions
B904	3	Added from e to re-raised HTTPException
E712	2	Use is True instead of == True (1 fix, 1 noqa for SQLAlchemy)
I001	1	Auto-fixed import sorting
C401	1	Set comprehension instead of set(generator)
B027	1	Added noqa for intentional non-abstract empty method

Config Updates

• pyproject.toml: Migrated ruff config from deprecated top-level to [tool.ruff.lint] section
• .pre-commit-config.yaml: New file — Black, Ruff, Bandit, file hygiene hooks

Files Modified (23 total)

• 15 source files under src/medex/
• 5 test files
• 1 config file (pyproject.toml)
• 1 new config file (.pre-commit-config.yaml)
• 1 init file (api/__init__.py — import sorting)

Bug Found & Fixed

controller.py:622 had self.memory_service = memory_service instead of self.memory_service = service — the parameter service was being ignored, using the instance attribute name as a variable reference (which would fail at runtime). This is a real bug caught by F821.

Verification

ruff check src/ tests/
# All checks passed!

black --check src/ tests/
# All done! 113 files would be left unchanged.

Pre-commit Setup

pip install pre-commit
pre-commit install
# Future commits will auto-check formatting