make local debug_flags 64 bits

It was originally 32-bits so none of the tests for the flag
DEBUG_FLAG_CPU_FREQ in step_mgr.c worked at all.
scontrol show step to show cpu-freq

Previously it was printing a bunch of garbage
set step default cpu-freq to job values (if any)
some redundant code from srun was removed
Cosmetic changes to cpu-freq logic

No changes in logic
Make test more robust if CPU slow

This test failed once due to a low CPU frequency. Change the logic
to lessen the impact of a low frequency.