Take advantage of per-class logging for iRODS publish/update scripts

[iainrb]

• Remove placeholder logger category
• Works with changes to srpipe logconf files to produce more informative log output
• Also fix duplication/formatting in changelog

[keithj]

A couple of final cases:

vcf_from_plex.pl has an old log setup remaining and passes the logger into WTSI::NPG::iRODS

update_expression_metadata.pl also passes a logger into various objects.

[iainrb]

Commit https://github.com/wtsi-npg/genotyping/pull/420/commits/99eb61332a11a4e4e87b3f33dfdb996e142a2404 fixes remaining cases of old-style logging.