Debug JMOL parser so it can replace legacy Jalview PDB parser for normal use

The Jmol parser introduced in 2.9.1 generates sequence/structure mappings that are (in some way?!) not backwardly compatible when importing Jalview project files, and for various other tests.

We could have Jalview2XML detect files generated by versions prior to 2.9.1, and explicitly invoke the MCView pdb parser when importing structure data embedded in these files. Patches on this task concern making the various broken Jalview2xmlTests pass when the Jmol parser is used in place of Jalview's legacy parser.