Compatibility breaking changes we eventually want to do

[mcocdawc]

• [ ] implement a diff_Zmat for representing the difference between Z-matrices, similar to a time-delta.
• [ ] Make CleanDihedralOrientation's default true
• [ ] Get rid of the use_lookup argument and explicitly pass bond dictionaries.
• [ ] Change behaviour of align to make the translation to the reference molecule. @nwhel