JGI_Parser: Backport further changes from ensembl-xref
JGI_Parser: Backport further changes from ensembl-xref

Summary:
 - new "please see the NOTICE file" copyright note
 - use confess() instead of croak()
 - add POD blocks for all functions
 - drop support for JGI 2.0 format, which we do not use in Ensembl
 - restructured the code responsible for extraction of data from input
   records
 - more reformatting and clean-up

Issue: ENSCORESW-3214

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Ensembl/ensembl,Ensembl/ensembl,Ensembl/ensembl,james-monkeyshines/ensembl,Ensembl/ensembl,james-monkeyshines/ensembl,james-monkeyshines/ensembl,james-monkeyshines/ensembl