Bug fix in Molecule::removeAtom

Since m_formalCharges.size() is always equal to itself this line
would only work once and segfault when two calls to clearAtoms()
occurred in the same instance of Avogadro2.

Change-Id: I110ff44a4103c08f382d4af7f1d87cb25de99881
Merge branch 'moleculeFix' into spg

Change-Id: Id0b99bf7804a4ba4450a6ab6dca86a8f62f45191
Build menu phase 1

Supercell builder now works. I'd like to adjust the clipping planes
and rotation origin after building the supercell.

Change-Id: Icb216757b0f6cfa36d34441d22afe94cc914261f
build menu phase 2

Slab building now works.

I had to transpose the surfaceMatrix initalization from that in
Avogadro 1. I'm not sure why, but this matches the output unit cell
that I get from the slab builder in Avogadro 1.

Change-Id: I9ee7d90f6664633c7f6c12cb198165152ff66d4e