Make update_options an always-run when compiling
To avoid compilation problems when someone updated options_rosetta.py and
forgets to run update_options.sh, add the running of update_options.sh to
the compilation process, for both scons and cmake. It should no longer be
necessary to run update_options.sh manually when you change options_rosetta.py
(though it shouldn't hurt anytyhing if you still want to). The additional
time added should be minimal (fraction of a second).
In conjunction, remove the autogenerated files from being tracked with git,
and fix a few places which depended on autogenerated files which were
removed/changed.
Tested compilation with both scons and cmake, and with a fresh checkout.
No compilation issues seen locally.
NOTE: If you have a compilation scheme that doesn't use our standard scons/cmake
builds (or a non-compilation use that uses the autogenerated options files),
you may need to add update_options.sh to your build scheme.
(I have done this already for BuildDocs.sh and make_ctags.sh)