add apply_rotation to Makefile
If a function is likely to be used elsewhere, move it to utilities

Also move vector definition to utilities and fill out rotn_comp.c
concatenate all mesh-alignment related files to align.cpp

this will be the new focus for work, now that the component pieces
have been testing and not found wanting
Make significant process on converting align_meshes.cpp to use C++

By necessity, I have the entirety of C++ available to me, so it makes
sense to reap the benefits.
remove compile errors and clear mistakes from align_meshes.cpp