JAL-1803 first pass at updatePDBEntry

JAL-1803 first pass at updatePDBEntry
* merge PDBEntry if same ID, existing is null or identical filename, and chaincode is unspecified or identical to new one.
* merge propagates type, chainCode, filename, and all properties to parent.

Note TODOs: we don’t recognise and merge 1QIPA onto 1QIP (yet)