Merge pull request #976 from WormBase/staging

Bring staging into master
Major changes:
* GBrowse work: b_malayi, a_suum_davis
* Auto update staging when push to staging
* remove 3rd party files
* DO_term model
* Transposon model
* port over motif details
* many small changes (person, clone, gene, etc)
added TSL sites and operons
Merge pull request #991 from epaule/master

on request of the canadian branch

fix #990
WormAtlas link fix
* wasn't showing up on 'production' sites
* #988, #811
Add ensEMBLGenomes to external_urls
* fix circular link #981
Protein - Homology
* add more descriptive homology group types
* request from @Paul-Davis, fix #981
Gene - Genetics
* Alleles tables changes:
* from @tuli
* 1) 'Other' -> 'Not curated'
* 3) fix spacing in locations
* #724
formatting Gene - Genetics
* #724
Anatomy term - Associations
Anatomy functions - always display Assay
* fix #457
Anatomy term - Associations - bugifx
* for 'production' instance types
* #457
Gene - Genetics - Allele table
* include /all/ aa positions, not just last
* include isoform position refers to
* #724
Genotype on Strain fix
* fix #993
Anatomy term - Associations
* add Assay to Anatomy function NOTs
* fix #457
Revisit genotype display
* keep markup loop for non-variation objects
* #993
Gene - Genetics, alleles tables
* filter out Natural_variant type
* move column order
* #724
Update strains venn diagram
* close #994
Revisit venn diagram
* clean up template code
* align top
* #994
Merge pull request #995 from WormBase/staging

Major changes:

Alleles table: Gene page - genetics widget
Strain venn diagram display
flanking sequence model change
Anatomy_function display
genotype printing bug fix
Update m_hapla.conf

that should make at least the CDSes reappear
Merge pull request #1000 from epaule/master

slightly fixed config for hapla