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Normalize MR ids after command argument parsing

Merged Marco Clemencic requested to merge 75-fix-normalization-of-mr-ids into master

we still have people tricked by #75 (closed), so I decided to have a look at the code and I found that the fix was easy.

I also took the occasion to correctly set the default groups for Gaudi and Gaussino.

Closes #75 (closed)

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