Fix missing base_model_with_deprecations.py and update pyproject.toml

- Restore base_model_with_deprecations.py file that was accidentally deleted
- Update pyproject.toml assemble task to use uv run instead of deleted shell script
- Regenerate models and JSON schema with working build process
- Resolves ModuleNotFoundError that was causing pytest failures

Co-Authored-By: AJ Steers <[email protected]>

Author: devin-ai-integration[bot]