Picked-group-fdr

- 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

- Add filename column for andromeda2pin
- Update mokapot to 0.10.0
- Update packages in poetry.lock
- Fix docker package version in greeter

- Skip lfq if only 1 experiment is present
- Fix organism fasta parsing
- Added fractionated sample support for sage
- Fix update_fragpipe_results