delete records from display_xref_priority and gene_desc_priority when status is reset to parsing_finished or mapping_finished

added option run_all to run even if there has been no change to the species

added tables display_xref_priority and gene_desc_priority - they are used in DisplayXrefs.pm http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-219

changes to set_display_xrefs and set_gene_descriptions http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-219

call ArrayExpressParser to create direct xrefs- this has to be done during mapping as we need current gene stable_ids to generate ArrayExpress xrefs

Correcting PubMed xref problem where xref table entries contained gene IDs not PMIDs by changing parameters in add_xref call.

replaces old method of known/novel 'coding' groups

get RefSeq_mRNA xrefs from CCDS where the xref maps to only 1 ensembl transcript http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-88

if RefSeq_protein xref was mapped to ensembl protein and it's corresponding RefSeq_mRNA was mapped to the transcript which produces the protein - this is treated as the best match http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-88

Adding the scope guard which is a way we can cause code to be executed even during a die. Very useful for non-global resource cleanup operations (finally blocks)

Delete a database with minimal lock interuptions and without having to use direct data file access and flushes.

Moved the filters around and made ensembldoxygenfilter.pl a standalone script to avoid having to edit the Doxygen PerlFilter installation which was our only original way of doing this. Namespacing also means dependency management is easier with less to level packages getting in the way