CI: add pre-commit config

[sweetytweety2406-wq]

Summary

Adds a pre-commit configuration to provide local quality checks consistent with the project's CI. Also documents how to install and use pre-commit.

Changes

• Added .pre-commit-config.yaml
• Configured Ruff, MyPy, and Bandit pre-commit hooks
• Updated Development.md with pre-commit installation and usage instructions
• Fixed a typing issue in src/modeldock/adapters/registry/bundled.py required for MyPy to pass

Testing

• Ran pre-commit run --all-files
• Verified:
  • ✅ Ruff
  • ✅ Ruff Format
  • ✅ MyPy
  • ✅ Bandit

Checklist

• Branch named per Git Workflow (feature/, fix/, docs/, refactor/, test/, chore/)
• Not developed on main
• Code follows AGENT.md coding standards (type hints, Pydantic v2, no generic Exception, no business logic in CLI)
• domain/ and ports/ stay pure (no I/O, no framework imports)
• Quality gates pass locally: ruff, mypy --strict, bandit, pytest
• Docs updated if behavior changed
• pyproject.toml and src/modeldock/__init__.py versions match (if release-related)

Closes #135