Merge pull request #1491 from WormBase/staging

Staging
* WormMine integration
Merge pull request #1509 from WormBase/staging

Staging
Merge pull request #1530 from WormBase/staging

Staging
GBrowse config - indentation
#1501 - broken related papers widget
#628 - polyA sites
#1435 - legacy site moved to footer
#1141 - simplify history table
#1520 - SPELL link added to tools
logging work
Sub-issue of #1417
gbrowse links now broken for species="all" because of <all> has no
bioprojectid.  Now defaults to "c_elegans"
make gff db connection error more descriptive
* add species
Searching - cut off multiple word searches
* enable phrase searching
* #1541
new location for wormbase_user on rds; read/write access available shortly
Merge branch 'staging' of github.com:WormBase/website into staging
mysql on RDS for production
default xinetd configuration file for easy deploy
Added parametrization for the execution of individual unit tests. #1629
Removed obsolete tests that are no longer working.
Added conditional to string substitution, since Perl's strict rule enforcement would (wrongly) complain about a possibly uninitialized variable.
Removed quotation marks that would have prevended the return of "hits" in the case when no "id" could be determined. Showed up as a warning via Perl's strict rule enforcement. #1006
Phrase search only with double quotations
Natural isolates - Strain summary pages
* filter for species
* fix #1694
Added RServe client that can talk to an RServe server via STDIN/STDOUT. #885
Release version number - get from symlink
* not acedb
Update search results to return proper label for Protein objects
* related to #1383
Only reveal WBProtein ID when there are multiple genes associated
* #1383