Boilerplate.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Annotation editor.

Launch the server and direct the browser to `/#/curate`.  Login, if need be,
and you will see the first curation task.  Hit `Done` to save the curated gene
model on the server and move to the next task.

Annotation editing functionality builds on the excellent work done by JBrowse
and WebApollo.

JBrowse / WebApollo integration
-------------------------------

JB and WA code, with several modifications, lives as a part of the source tree
in app/src/JBrowse and JBrowse/WebApollo.

JB contains upstream’s src/JBrowse, img, and all CSS (including that of WA --
just one line) compiled into one styles.css.  JB/WA contains upstream’s WA/js.
I hacked JB’s plugin system so that loading CSS for plugins is none of it’s
concern, additionally removing the dependency on lazyload.  JB/main.js loads
styles.css using require-css and WA using the reduced plugin architecture. This
combines JB & WA into one unit.

JB/main.js instantiates JB and returns a facade object.  Rest of Afra
inter-operates with JB through the facade.  At the moment we have a single API
call, `load`, to load a task into JB.  We will need another API call to access
contents of the annotations track.

JB’s dependencies are managed through Bower. I have locked to the latest
point-release of the dependencies that follow semantic versioning.  While we
track rolling updates from Github for the rest -- either Bower doesn’t support
locking to a SHA or it just didn’t work on my Mac.  It’s worth noting that
these dependencies are extremely focussed and move slow: hopefully things won’t
break for a while.  In the near future, we should be able to remove a few more
dependencies and / or lock to a working SHA using Bower.  WA depends on some
old release of jquery and jqueryui. I made it a part of the source tree
(app/src/jqueryui) to get things rolling for now.

Modified default track styles for JB so it looks quite presentable.

Perl sub-system of JB & WA is a part of the source tree as well: Perl modules
in src/perl5 and executable scripts in bin.  setup.sh lives as a part of `rake
setup` and installs dependencies to $HOME/.extlib.  Additionally, I dropped
support for the deprecated legacy wiggle format and legacy bam-to-json.pl.

Included for testing, MAKER2 generated gene prediction in GFF3 format for two
scaffolds of fire ant genome.

FIXME

* Unable to zoom out
* Make editing work fully

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

drop more than one feature

make exons resizable

trying add_exon
Mock dashboard.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
jbrowse refresh hack