Merge pull request #1905 from WormBase/hotfix-location

Hotfix for location widget - return arrayref
hotfix substitution summary for reverse strand substitutions #662
Merge pull request #2074 from WormBase/hotfix-dbconnect

remove freshen ace code from gff.pm
extraneous gbrowse files, commiting before merge
another file to eventually remove
Merge branch 'staging' of github.com:WormBase/website into staging

Deleted files in one repo, modified in another. Removing.

Conflicts:
	conf/gbrowse/pop_demo.conf.new
	conf/gbrowse/slave_preload.conf.new
	conf/gbrowse/yeast_chr1+2.conf.new
	conf/gbrowse/yeast_renderfarm.conf.new
	conf/gbrowse/yeast_simple.conf.new
Merge pull request #2120 from WormBase/staging

WS240
Beginning work on WS240

Major features:

* GFF3 support
* R data visualization
Fixing merge conflict from variation hotfix
updates for GFF3; 70% complete
Merge pull request #2140 from WormBase/staging

Staging - WS240 work
Merge pull request #2141 from WormBase/master

WS240 work
flattening the coding transcripts / gene models tracks together
Merge branch 'staging' of github.com:WormBase/website into staging
1st iteration flattening gene models tracks
breaking out soem shared configuration
new config for D. immitis and P. redivivus
final commit of manually generated configuration files; to be replaced by programmatically generated variants
getting the manually generated conf files out of the way
deprecated file
removed old configuration and saved it in its own directory