Fix two bugs with NCAAs and the PackerTask, change behavior of EMPTY
Adds a new Resfile action called RESET and changes behavior of EMPTY. Previously, once a position became a NCAA, it could not be mutated back to a CAA. Also, once a NCAA was enabled at a position, it could not be disabled. The RESET action enables all CAAs at a position like the default state when a ResidueLevelTask is created. This allows the PIKAA action to behave properly. The RESET action also disables any NCAAs that have been enabled, allowing you to reenable any you want turn on using the NC action. The behavior of EMPTY has been changed to also disables any NCAAs that have been enabled, allowing you to reenable any you want turn on.
To design both CAAs and NCAAs at the same position use RESET, for example...
5 A RESET NC HLU PIKAA AVL
To design just NCAAs use EMPTY, for example...
5 A EMPTY NC HLU
This fix has the packer tack comparing interchange ability group rather than AA type to determine if we are designing at a position. The hydroxyproline patches had to change slightly so that they did not produce a residue type with identical AA and varient types, I believe this was a bug. Additioanl syntactic changes to the packer task to get around some complicated pointer assignment when used with std::list::erase.
Unit test status: [Pass]
Integration test status: [1]
[posttranslational_io]: decrease in the number of rotmaers during packing from the HYP bug