Remove Sample::setMaterial member

Avoids ambiguity about where the Material is actually stored.
Refs #9842
Allow the Sample shape to be returned to its default state.

Refs #9842
Fix LoadHKL, SaveHKL and SortHKL after sample changes.

Refs #9842
Fix MonteCarloAbsorption for systems without emplace_back.

Refs #9842
Merge branch 'feature/9842_mc_absorb_hollow_cylinder' into develop