refactor: consolidate mypy and ruff config into pyproject.toml

[sooperset]

Description

This PR consolidates the configuration for MyPy and Ruff into the central pyproject.toml file, following modern Python packaging standards (PEP 518/621). The separate mypy.ini, ruff.toml, and .pylintrc files are removed to reduce root directory clutter and improve project organization. All relevant settings are now under [tool.mypy] and [tool.ruff] in pyproject.toml.

Fixes: # (see PLAN.md for context)

Changes

• Migrated all MyPy settings from mypy.ini to [tool.mypy] in pyproject.toml
• Migrated all Ruff settings from ruff.toml to [tool.ruff] in pyproject.toml
• Deleted mypy.ini, ruff.toml, and .pylintrc from the project root
• Updated pyproject.toml to include all previous configuration, preserving overrides and per-file ignores
• No changes to runtime code or functionality

Testing

• Unit tests added/updated
• Integration tests passed
• Manual checks performed:
  • Ran ruff check . and ruff format . to verify Ruff uses the new config
  • Ran mypy . to verify MyPy uses the new config
  • Ran pre-commit run --all-files to ensure hooks work with consolidated config
  • Verified all tests pass and linting is enforced as before

Checklist

• Code follows project style guidelines (linting passes).
• Tests added/updated for changes.
• All tests pass locally.
• Documentation updated (if needed).