Big merge -- a few little improvements for entire code, and several important updates specifically for stepwise assembly and monte carlo code. All integration tests checked very carefully. In terms of affecting lots of apps: (1) Patch linker text is now ':', not '_p:', which was more verbose and (I found) confusing; (2) Number of default residue types has been reduced a lot, by putting patches under '-patch_selector' flags, and a warning message is triggered if a dev starts a patch explosion; (3) got rid of silly warning message from hbonds about DonorStrength.csv missing. Also, fixed an initialized variable in LigandConformation class caught by instability in cstfile_to_theozyme_pdb test (and by valgrind). In SWA/SWM, almost everything is seamlessly unified between RNA & protein modeling so that RNA/protein (and more general cases, including ligands & metal ions) can be easily set up within the stepwise framework, finally.