Get labels and weighted atoms before editing bounds matrix

This was all done in a single method. Separating it
will help if new families need them to be edited.
Add double-ended setup to setupMolecules method

It only set up molecules for the group additive estimator.
That's not corrected.
Fix checking of double-ended steps

The methods would return if they failed, but this
wouldn't affect if the next step went ahead. This has
been corrected.
Exclude temporarily tetra-valent nitrogen from QM in Gaussian

Cherry-picked from 579b75f
Consistent logging and source comments

Cherry-picked from f2cd41a0c
Modify qm/main to store files in method subfolders

Also includes some default values for other options.
The tests have been updated to match the modified
QMCalculator settings.