Picked-group-fdr

- Fix nondeterministic behavior of decouple_connected_proteins

- Add --protein_group_fdr_threshold flag to set the protein group-level FDR cutoff for the rescuing procedure and logging messages
- Fix compatibility with Oktoberfest's new ProForma N-terminal notation
- Improved ProForma sequence format support
- Support new oktoberfest psmid with optional scan event number
- Use --psm_fdr_cutoff for "Peptide counts (unique)" column

- Switch to modified peptide instead of peptide in fragpipe parsing functions
- Make peptide flanking characters consistent across search engines. Fixes bug with percolator input used with --peptide_protein_map

- Less strict llvmlite dependency
- Add functionality to requantify fragpipe combined_protein.tsv
- Fix random number seed for mokapot
- Major refactoring and linting of multiple scripts
- Add system tests
- Fix peptide_protein_map input option for quantification.py
- Refactor picked_group_fdr.py, add some unit tests
- Add --suppress_missing_peptide_warning to all relevant modules
- Add readthedocs documentation
- Allow combining multiple Sage or FragPipe searches

- Revert return type to List for ProteinGroups.get_protein_groups

- Fix check for peptides not assigned to any protein group
- Fix for docker interactive mode