A common cleanup for the transition of the auxiliaries directory from cvs to git

- added pointer into the new directory structure (auxiliaries/shapes/*) in doSM.py and doMSSM.py.
- made both doSM.py and doMSSM.py executable by that way.
- small adaptation needed in summer13* file where the directory name for vhtt changed to VHTT.
- removed init.py functions and config files in scripts, data, setup as these are obsolete now.