RCG: some calculations were made out of order.

createDiagsFile.pm wass created as a refactoring of the feCodeGen.pl for writing the parts connections file.

Some global variables that were altered in this file were treated as locals, so the changes did not propagate back to feCodeGen.pl. This led to incorrect assessment that subsystems had no inputs, which meant subsystems could be processed before their inputs, introducing a one cycle delay.