Removed the copy of libmsr from the repo. Now downloading it from its official repository.

Fixes to file path parsing in utils.C
Fixed bug with PAPIMeasure where nested measurements were not being collected
Make makefiles more robust

Added support for inheritable inputs

Commented out collection of output buffers in lulesh since that didn't end up being very useful. Replaced with total energy
Clearer warnings/errors
Merge remote-tracking branch 'origin/gbDevelop' into gregDevelop
Fixed compile refresh so it doesn't abort if kulfi has not previously been compiled

Fixed bugs in PAPIMeasure
Removed unused logging
Removed some logging output
Merge branch 'gbDevelop' of https://github.com/bronevet/sight into gbDevelop
Adjusted computation of cache miss rates
Merge remote-tracking branch 'origin/gbDevelop' into gregDevelop
Small fixes