Merge pull request #895 from RosettaCommons/vmullig/removeSPs
Removing all Lua scripting support from the codebase
Certain key classes seem to have a second type of owning pointer defined, apparently for use with the Lua scripting hooks. This creates confusion, particularly for new developers, who might think that they should be using, for example, PoseSPs instead of PoseOPs. These owning pointers are hard-coded to be boost::shared_ptrs (unlike our owning pointers, which could be std::shared_ptrs, boost::shared_ptrs, or something else, depending on compilation settings).
This pull request tears 'em all out so that they're not cluttering up our codebase and confusing new developers.
UPDATE: This pull request now has the goal of ripping out all of the Lua hooks. Lua scripting was never implemented well, and has not been maintained since the original author left the Baker lab; it is almost certainly no longer a functional feature of Rosetta, and it is certainly one that no one uses. If I'm going to reduce useless codebase cluster, I might as well not bother with half-measures. (Plus, it actually turned out to be easier to solve the SP issue by tearing out all of the Lua stuff, since the SPs were mainly only used in the Lua code and this way I don't have to convert them all to OPs.)