Fix raw pointer use in core::util::add_cutpoint_variants()
Meilerlab Powercoding with Alyssa Lokits
This addresses the core of bug 0000336 - removing the raw pointer use in
core::util::add_cutpoint_variants() and remove_cutpoint_variants(). It also
starts in on the comments made by Justin Porter, replacing core::util::add_cutpoint_variants()
use with core::util::pose::correctly_add_cutpoint_variants()
Attempts to fold in some of the other add_cutpoints/add_chainbreaks were made,
but we ran out of time prior to debugging them.
No test changes (aside from currently failing ones) expected.