Rename CMake options and C macros to use PUMI_ prefix

[bobpaw]

Rename CMake options and C macros to use PUMI_ prefix

I prefixed lots of options with PUMI_ and renamed variables/options with the SCOREC_ prefix which are not created by bob.cmake. In general I set the default value for options like PUMI_ENABLE_SIMMETRIX to ${ENABLE_SIMMETRIX} which allows us to remain somewhat backward compatible and also inherit the selection from parent projects by default.

To find things that needed to be changed, I used the following searches:

git grep '\WENABLE' :^Doxyfile.in :^Doxyfile_internal.in
git grep '\WHAS' :^Doxyfile.in :^Doxyfile_internal.in
git grep '\WHAVE' :^Doxyfile.in :^Doxyfile_internal.in
git grep '\WUSE' :^Doxyfile.in :^Doxyfile_internal.in

I removed the private compile definition -DHAVE_SIMADVMESHING from phasta/CMakeLists.txt and some test exes and replaced it with the PUMI_HAS_SIMADVMESHING macro in apf_sim/apf_simConfig.h. There are some options which are left, specifically Simmetrix things like SIM_PARASOLID, SIM_ACIS, etc that I wasn't sure how we wanted to deal with yet.

An exception that I did not remove is ENABLE_VIZ in test/CMakeLists.txt:

https://github.com/SCOREC/core/blob/debc743406347f85368ee82cf6544b655a9f00cb/test/CMakeLists.txt#L63-L65

I think test/viz.cc can be removed, but Dan forgot to in 0c607cff2db9148c853fbb88704fcb7da06b0ac1.

I did not yet change the project name to SCOREC because I wanted to make sure all of these changes work.

Leaving in draft mode for now because there are a few things (Phasta HAVE_CLOCK_/USE_PCU_TIME, LION_COMPRESS, etc) left that I did not get to or am not sure if need to be updated.

Closes #337. Closes #477.