Move code for managing mdrun -cpi and -append

Move code for managing mdrun -cpi and -append

Prepares for refactoring to simplify and fix this handling. Kept logic
peculiar to handling mdrun command-line options near other such code.
Renamed functions to better suit their roles. Renamed bAppend
variables, in particular to separate the role of "the user asked for
appending" from "whether mdrun is actually going to do appending."

Change-Id: I063138a49d210e92cebe19e290dc6a0e7b72b1cf