Remove BondType from Bond

All Bond objects are assumed to be covalent bonds
By default, Bonds will now add themselves to their Atoms' bond lists.
For LINK records, work strictly with atoms that aren't alt locs
Use the new bond constructor in PDBFileReader
Add a test making sure ligands get bonds too
Loop through all non-water groups for intra-residue bonds, not just sequence residues
By default, keep the bond arraylist as small as possible
Trim to size all bond arraylists after creating the bonds