added acmc command line wrapper for entire toolkit moving parameter passing...

added acmc command line wrapper for entire toolkit moving parameter passing from trud, omop and main into acmc so that they are not just functions. Still work to do on parse.py which includes command line arguments and does nto need to as this should all be in the arg parser configuration. Refactored trud and omop so that the paths are all constants, and also check that the directories required exist as it was failing on requiring the code directory.