Merge of several important changes from personal branch: (1) fix to geom_sol derivatives, needed for RNA, (2) removal of 'incorrect_deriv' options from hbonds, not in use anymore, (3) code to allow parsing of residue chains and numbers from tags like 'A:5-20', used now in stepwise assembly/monte carlo to read in 'conventional' chains and numbering from FASTA files, (4) cleanup of directory structure in protocols/stepwise/, including combination of all legacy/ subdirs into one subdir. Integration tests checked, and only RNA and swa/swm tests change, except maybe for order of tracer output from match tests.