chore: remove legacy and redundant files
- Remove .flake8 (replaced by ruff)
- Remove .pylintrc (replaced by ruff)
- Remove pip-audit.toml (redundant, runs via CI/pre-commit)
- Remove backend/.gitkeep, routes/.gitkeep, services/.gitkeep (dirs now populated)
- Remove .specify/constitution.md (duplicate of .specify/memory/constitution.md)