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- Fix error on Windows.
- Fix for MSFragger 3.2.
- Better support for terminal and protein-terminal variable modifications in input.
- By default, support both "DECOY_" and "rev_" decoy prefixes.
- Improve error messaging on data reading.
- Support whole directories instead of file lists on command line.
- Save clustering figures to a single multi-page PDF for each input file.
- Better account for configured variable modifications in recommending variable modifications.