Merge pull request #1928 from RosettaCommons/Cyrus/mergetarget
From Steven Lewis:
This is mostly small features I did in in the summer/fall of 2016 and never got around to testing and PRing until just now.
Features:
* smlewis/fix_README - improving the front README, based on a better understanding of our forking policy, thanks to @aleaverfay @kwikwag
* smlewis/FT_clangstatic_fix - fix a clangstatic bug @roccomoretti pointed out (it was a copy paste error)
* smlewis/cyrus/ss_printer_for_commons - fixes to the HELIX/SHEET printer so that the records are ordered properly in large/multichain structures where the numbering restarts per chain. This integration test (secondary_structure_output) will change, as it now has a long enough input to have triggered this bug.
smlewis/cyrus/LoopLengthChange_restype: LoopLengthChange takes a residue type char for what to insert/ Resolves RC issue RosettaCommons/main#1700. Adds integration test.
smlewis/cyrus/actccm_atompair_bounded - AddConstraintsToCurrentConformationMover constraint choice improvements. Adds integration test. This code already had an integration test testing different aspects of the Mover; I made a second test so that it multithreads more efficiently.