Move the checkstyle to [Ruff](https://docs.astral.sh/ruff/)

[shivam15s]

This PR has code contributed by Devin

Migration to Ruff

This PR migrates our code style tooling from flake8+isort+black to Ruff, which provides:

• 10-100x faster linting and formatting
• Drop-in replacement for all current tools
• Built-in caching for better CI performance
• Single configuration file in pyproject.toml

Changes

• Added Ruff configuration in pyproject.toml maintaining current rules:
  • Line length: 120
  • Ignored rules: E501, B006, E731, A002, E203
  • Import sorting with isort compatibility
  • Black-compatible formatting
• Updated Makefile checkstyle target to use Ruff
• Removed obsolete .flake8 and .isort.cfg
• Reformatted 112 files across the codebase:
  • Fixed import sorting and organization
  • Standardized import grouping (stdlib -> third-party -> local)
  • Maintained existing code style and formatting preferences
  • No logical code changes, only style improvements

Testing

• Verified all changes locally:
  • make checkstyle passes successfully
  • Import sorting matches project conventions
  • Formatting maintains code readability
• CI Status:
  • ✓ Checkstyle checks pass
  • ℹ️ Test failures are unrelated (Modal authentication issue)
  • No changes to code logic, only formatting changes

Note: The test failures in CI are due to missing Modal authentication tokens and are unrelated to this migration. The checkstyle checks pass successfully, confirming our formatting changes are correct.

Link to Devin run: https://app.devin.ai/sessions/efa14454ce01434d883d9394e3c525f8

[ByronHsu]

Crazy