fix many warnings
fix many warnings

removed loops over multiple files per process - that feature was dead

yangf4/phasta,matthb2/phasta,matthb2/phasta,PHASTA/phasta,matthb2/phasta,yangf4/phasta,yangf4/phasta,PHASTA/phasta,PHASTA/phasta,SCOREC/phasta,SCOREC/phasta,SCOREC/phasta