Add publishedApiDoclet library, and ant task which uses it

This is a library which uses a javadoc doclet will publish only those classes/methods which contain a
particular tag in their javadoc. We've been using an annotation. Still need to modify the relevant methods.

IGV-1882 #comment
Add source for publishedApiDoclet

We add it here because it seems like the library is abandoned and we don't want to lose it. License is LGPL 2.1, compatible with ours, although since we aren't including it in the build that's not completely necessary.

IGV-1882 #comment
Change from using @api annotation to @api javadoc tag

IGV-1882 #comment
Change javadoc tags

 user: -> @author
 date: -> @date
Make sure splice junctions calculated regardless of whether downsampling is on or off
Add comment about how to specify logger
Better log errors when loading genome in HostedDataTest
Recalculate/reset track panel heights when loading session without panels element
Improve MessageUtils.confirm to be more headless friendly
Merge branch 'master' into Javadoc2

Conflicts:
	src/org/broad/igv/feature/genome/Genome.java
	src/org/broad/igv/feature/genome/GenomeManager.java
	src/org/broad/igv/ui/IGV.java
Merge pull request #41 from broadinstitute/Javadoc2

Javadoc2

Add ant task (and necessary library) for creating javadoc ONLY for those elements with an "@api" tag in the javadoc
Add ".chrom.sizes" option for defining genomes for igvtools.
Commented out copy of non-existant "services" directory in build file.
Add a few log statements
Add IGVSeekableHTTPStream which calls to IGVUrlHelper

This is largely to workaround servers crashing when caching large files. When reading large TDFs sometimes we only see the first 24 bytes (TODO we could definitely handle that failure better and more gracefully). IGVUrlHelper uses HttpUtils.getInstance.openConnection

IGV-1922
Change log.info -> log.debug in TDF reading sections

IGV-1922