⚡ Bolt: Optimize file loading with streaming I/O

[erayfirat]

💡 What: Replaced memory-intensive file reading (read().decode()) with streaming io.TextIOWrapper in app.py.
🎯 Why: Loading large MGF/mzTab files caused excessive memory usage by creating multiple in-memory copies (bytes, string, buffer). This optimization reduces memory footprint and startup time.
📊 Impact: Reduces peak memory usage during file loading by preventing full-file in-memory duplication.
🔬 Measurement: Verified with new regression test tests/test_streaming_io.py that confirms pyteomics parsers work correctly with streaming wrappers. Existing integration tests passed.
Misc: Updated .gitignore to exclude __pycache__ and *.pyc.

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PR created automatically by Jules for task 611152263640603441 started by @erayfirat

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