All user-facing scripts now require Python 3 and expose --help via argparse. Highlights:
- extract_lowscore_decoys*.py: argparse, Python 3 fixes, alias hints in --help
- cluster scripts (r2c, rfc, c2c): alias hints, cluster_info hint on no-args
- rosetta_submit.py, rna_denovo_setup.py: argparse + full 2to3
- Library modules (amino_acids, read_pdb, rosetta_exe, make_tag): main for CLI self-documentation
- easy_cat.py: argparse + Python 3
Drops Python 2 support.