new parser and first stab at condorisation

MR to address two separate but related issues:

• argument parsing : allow parsing from command line only (i.e. all arguments may be passed as command line arguments), command line + ini file, ini file only, and also build in defaults into Parameters such that the user can pass only what they really want to modify.
• condorisation : add a dagfile writing routine (starting from the new argument parsing method) and a default submission file. the write_dag python script also takes care of setting up a minimal folder tree.

missing will update

• new unit test for Parameters
• -h support for all passable arguments
• write_dag argument parser (do we want this? I think we do...)