Implement resolution truncation between scaling and refinement

[dennisbrookner]

This PR:

• corrects a previous bug/poor behavior where following scaling, the unit cell from the "off" data was used for both datasets. Now, following SCALEIT, the unit cell from the "on" mtz is manually restored.
• Following SCALEIT, both mtzs ("off" and "scaled on") are truncated to have matching resolution.
• various changes to the rigid-body refinement wrapper to ensure compatibility between all utilities.

I also continued work on the file cleanup functionality. This will be finished in a future PR which includes a more radical overhaul of how paths are handled.

[dennisbrookner]

I also added a _validate_environment helper utility which provides a more useful error message for when phenix and/or CCP4 is not active.