Tweaks to get reliable system operation

changed counter_pattern from a 32-bit entity to a 64-bit entity
Tweaks to get reliable system operation

permuted test and normal data to satisfy recorder requirements
Tweaks to get reliable system operation

Fix an error which caused the Fra,eMi,_register to not be periodically reset by one_PPS_PIC_Adv
Tweaks to get reliable system operation

permuted header to satisfy recorder requirements
fixed data going to capture registers which was messed up by above permutation
did a little clean up on process parameters and "rising_edge" call
Tweaks to get reliable system operation

Separated the generation and checking of TIME0
Tweaks to get reliable system operation

cleaned up a few timing and signal dependencies issues to guarantee synchronizationto rising edge of TE
Tweaks to get reliable system operation

added clocked capture of RunTG and RunFM to avoid metastable operation
added clean capture of TE
swapped connections of TIME0 with TIME1 in a few places