Shor's CNOT and Toffoli control / target input ordering fix.
Shor's CNOT and Toffoli control / target input ordering fix.

epiqc/ScaffCC,epiqc/ScaffCC,epiqc/ScaffCC,epiqc/ScaffCC,epiqc/ScaffCC,epiqc/ScaffCC,epiqc/ScaffCC,epiqc/ScaffCC,epiqc/ScaffCC