for method transcript_display_xref_sources, updated the ignore setup to be consistent with refactoring of DisplayXrefs.pm

Making sure multiple includes of the registry does not result in major issues with error detection (earlier work suggested a possible issue with this)

password is not always required

We can now set a reconnection timeout outside of the normal realms of MySQL disconnect/reconnect. This means we have something closer to a pooled connection which stays active for as long as people need it & dies off at the required rate

added UniParc source
added sources for ferret and platyfish

Adding a "print out what would have happened" script to the checkout; could be rolled into the main script in the future. Also extended the options for DNADB and CCDSDB. We also check if we had a DB which contained DNA as not doing so is a very very very bad thing.

Test cases now pass, we have a capture warns asserting for known bad scenarios and use the Test::Builder code to see if we want to do to screen warning for test cases. Not sure how un # lines in TAP are dealt with; we may want to substitute STDOUT/STDERR for something which can delegate to Test::Builder for note()

Trying to improve the current test cases. Accidentally caused some issues from rerunning the code multiple times as well

[ENSCORESW-238]. Highlighted by Ken Youens-Clark on dev. We call show_valid_species() without a reference to $self

Script used to decode what canonical assignment says has occured during a run. The script accounts for most issues apart from those nasty ones in which case you must firgure that out yourself.