Update and bug-fix the MakeInFiles_sample.py script to represent what I've run to generate source data processing job files.
Don't build dependencies on 'clean'
Fix bug that was leaving dangling -L flags
Fix mkl flags on hopper
Update makefile to build partial static build.

Execute with:

make BUILD_STATIC=yes

which will build a partially static build.  Also sets rpath to:
$ORIGIN/../lib to allow the executable to be called in principle
without setting LD_LIBRARY_PATH.
Fixing bug ignoring "which"
Merge branch 'makefile_bugfixes' of git://github.com/mgmarino/StandaloneRefitter into mgmarino-makefile_bugfixes
Edison's static librt has _dl_cpuclock_offset undefined, and I couldn't locate it -- forcing it to be dynamic seems to solve the problem.