When restoring from a checkpoint, the simulation used to use file handles from
the checkpoint. This disallows multiple separate restore simulations from using
separate input and output files and directories, and plays havoc when the
checkpointed file locations may have changed. Add handling to allow the command
line specified files to be used as input/output for the restored simulation
(Note: this is the similar functionality to FS mode for output and error).
6a49dee3f3