Fully fix PR#683. Don't fully clear the molecule when loading WFN.

All orbitals and other cubes were cleared on loading WFN. Instead
just remove atoms, bonds, etc. which will be reset with the WFN
analysis. Preserves orbital cubes, as expected by users.

Change-Id: I4df8af45d59a351f52ae0d308130950b4c9482c1
Merge topic 'FIX_qtaim-MO-clearing' into master

e3c574c7 Fully fix PR#683. Don't fully clear the molecule when loading WFN.