Carbohydrates: mostly database updates
This merge includes some addition of ATOM_ALIASes, a new sugar topology file,
(so that I can load in sialyl-Lewis X,) and some sugar pilot app updates to
reflect the recent options system clean-up.
It also adds a formal +1 charge to all lower terminus peptide residues.
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Unit test status: Not Run (no C++ code changed)
Integration test status: 1 test change
carbohydrates: expected, due to the +1 on peptide lower termini