Update handling of CCD residue types.

[roccomoretti]

Update the list of CCD types to the most recent version, and fix the handling for all (non-obsolete) CCDs such that they don't result in crashes when run through restype_converter.

Note that this doesn't necessarily mean that they're well typed scientifically, or that they won't crash when used, just that they don't crash when they're converted to ResidueType objects.

Other included fixes:

• Less hard-coding of atom names in the residue parameterization.
• Tracer name changes in core.chemical to better match directory hierarchy.
• Adjustment to src/core/chemical/AtomICoor.hh which speeds up (debug mode) ResidueTypeSet initialization by ~33%.
• The wwPDB has now gone to 5-character CCD codes. Update the CCD loading/updating code to better split these out. (The restype converter doesn't crash at the 5-character codes; whether they work with CIF files containing them is a yet-to-be-addressed question.)