Simplify Makefile: consolidate format/lint/check into fewer targets
- Rewrite `make format` to auto-fix (black/isort) then report remaining
issues (flake8/mypy) in one command
- Rewrite `make ci` as the single pre-push check (format + lint + test)
- Remove redundant targets: lint, lint-*, check, *-verbose, check-all, pre-push
- Add proper exclusions (.venv, scratch, logs, build) to all tools:
- .flake8: add exclude list (was scanning .venv packages)
- pyproject.toml: add excludes for black, isort, mypy
- Update AGENTS.md quick reference to match
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>