Add scripts for measuring the instrumentation overhead and hw perf counters
ct_main note about setup for ROI support
ct_runtime - Initial ROI support in runtime
Run script - add time parameter and further nas support

There is a time parameter, which is prepended to the instrumentation run.
The NAS support now includes running with pin.
Harmony - revisions to harmony backend to improve modeling of parallelism
Middle - include note about how to change middle layer to compute order after writing