[UPDATE] Feature Score plotting

[singjc]

This pull request introduces a new, unified command for exporting feature score plots that works across all supported file formats (OSW, Parquet, and Split Parquet), and deprecates the older score-plots command. The new command auto-detects the presence of SCORE tables, applies appropriate filtering, and supports multiple feature levels. Documentation and CLI help have been updated to reflect these changes, and backward compatibility is maintained with a deprecation warning for the old command.

Unified Feature Score Exporting:

• Added a new pyprophet export feature-scores CLI command that works with OSW, Parquet, and Split Parquet files, auto-detects SCORE tables, applies RANK==1 filtering when needed, and supports MS1, MS2, transition, and alignment feature levels. [1] [2] [3] [4] [5]
• Implemented intelligent behavior in export_feature_scores for OSW files: if SCORE tables exist, both SCORE and VAR_ columns are plotted with RANK==1 filtering; otherwise, only VAR_ columns are plotted.

Deprecation and Backward Compatibility:

• Deprecated the pyprophet export score-plots command in favor of the new feature-scores command, with a deprecation warning shown to users while maintaining backward compatibility. [1] [2]

Documentation Updates:

• Updated CLI documentation to describe the new unified export command and mark the old score-plots command as deprecated, guiding users to the new workflow.

Internal Refactoring:

• Updated CLI command registration and imports to support the new command structure and ensure proper routing of export requests. [1] [2] [3] [4]

Minor Utility Update:

• Added _ensure_pyarrow import in parquet.py to support Parquet operations.