Replace brittle Python deps with native bindings

[theGreatHerrLebert]

Summary

• replace brittle Python-side IO and numeric dependencies with native Rust/PyO3 bindings
• add mzML and MGF reading through mzdata and sync sagepy with the updated sage-core fork API
• add PR CI for Python 3.11, 3.12, and 3.13 and expand Python tests, including sage compatibility coverage

Validation

• local Python 3.13 env: python -m pytest -q -> 97 passed
• trace-based execution now covers the core Python FDR, PEP, and TMT modules that were previously untested
• CI workflow added to build sagepy-connector and run the Python suite on PRs and main pushes