Server/Config.t: &try_err: quieten "perlcritic --gentle".
bugfix 3c8e8797 ColumnChooser window now bigger

resize the window, not its contents
.gitignore update

matches f98d6444
B:O:Server::GFF::GRCIssues: use Name and Note fields in GFF.

Also changes description -> Note for Dna{Dna,Pep}AlignFeatures.
Bio::Vega::Utils::Detaint - for use in B:V:U:EnsEMBL2GFF.
B:B:O:Server::GFF::GRCIssues: add URLs.
scripts/<some> - migrate to B:O:S:Config->SpeciesDat->dataset(...)

faster script startup
fixes the rest of RT#398147

scripts/lace/save_satellite_db
  clearer output on bad key
scripts/lace/remove_duplicate_genes - delete

use scripts/loutre/repair_duplicate_names instead

this does SELECT ... FROM gene_stable_id
 and only bulk-edit changes since 2004
cope with user's config file being empty

fixes RT#400509
note use of "slow" Config::IniFiles

demonstration of O(n^2) behaviour and a bodge-fix for old 2.58 at
  https://bitbucket.org/mcast/perl-config-inifiles/branch/perf_258

part of efficiency improvements for RT#398298
configure XML::Simple to use XML::Parser (expat)

efficiency improvement for RT#398298
  XMLin using LibXML was taking ~38sec for human chr1-38
  now using Expat takes ~5.2sec

setting in multiple places each with {local $GLOBALVAR}
because global config is ugly & we have no central place for it
B:O:L:AceDatabase: ensure DNA also appears in main featursets list, RT400142.
resolve merge conflict, plus tweak to sql query used to identify number of inserted assembly entries that map to existing seq_region_ids
finish_ensembl_vega - fixed error in SQL so that x_ref.info_type is now fixed
raise Session Window after ZMap new_view

for RT#397932

tested under metacity and usually works,
 except when that refuses to allow windows to come forwards
docs/Evidence_Alignments.txt: maybe fire up blixem directly.
Test::OtterLaceOnTheFly: add 'genomic' tag where appropriate.

In preparation for 'transcript' variants.
B:O:L:OnTheFly::Transcript: basic tests.
B:O:GappedAlignment: consolidate_introns().

Consolidates 5', main intron and 3' into a single intron element.
t/etc/align: BC018923.{fwd,rev}.fa are now used directly in tests.