Consolidate configuration files into pyproject.toml

[paxcalpt]

Summary

• Consolidated 3 configuration files into pyproject.toml to reduce base directory clutter
• Moved _typos.toml → [tool.typos] sections in pyproject.toml
• Moved .bandit → [tool.bandit] section in pyproject.toml
• Moved src/mermaid-config.json → [tool.mermaid] section in pyproject.toml
• Updated noxfile.py to use ruff instead of deprecated black/flake8 commands
• Updated .pre-commit-config.yaml to remove references to deleted config files

Benefits

• Cleaner project structure: Removes 3 configuration files from base directory
• Better maintainability: All Python tool configuration centralized in pyproject.toml
• Modern tooling: Updated to use ruff instead of deprecated black/flake8
• Standards compliance: Follows Python packaging standards for tool configuration

Test plan

• Verified ruff check and ruff format work correctly with new configuration
• Verified typos spell checker reads config from pyproject.toml
• Verified bandit security scanner uses pyproject.toml config
• Verified nox -s lint and nox -s format sessions work correctly
• Verified all pre-commit hooks pass with updated configuration

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