Core: Add functionality to also run single MC file from command line
Core: Added ability to set output directories for root and batch files via command line
Core: Give preference to command line setting for output directories for root and batch files, and provide default for batch files directory to avoid crash when not set in batch mode
Core: Fixed command line option for MC datafile to clear config TreeFile lines
Edited farming scripts to use new command line options. This eliminates the need for cloning the config files and allows both experiment and MC data to use the same scripts. Also made them a little smarter in looking for files and directories
Merge branch 'A2GoAT'