* Added optimization package with linear assignment class.
* Improved robustness of StructureMatcher using linear assignment.
* Improved primitive cell search (faster and more robust).
* Cleanup of deprecated methods, including
pymatgen.alchemy.materials.TransformedMaterial.undo/redo_last_transformation,
pymatgen.core.site.Site.distance_and_image_old, Poscar.struct,
StructureFitter and tests.
* Miscellaneous bug fixes and speedups.