1. Added optimization package with linear assignment class. 2. Improved robustness of StructureMatcher using linear assignment. 3. Improved primitive cell search (faster and more robust). 4. 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. 5. Miscellaneous bug fixes and speedups.