Add track line with type=wiggle_0 to coverage counter output
Add test session file for match search
Add @api annotation where necessary for SequenceMatchSource, fix possible NPE if sequence not available
Have IGVCommandBarTest use events to check for chromosome navigation, should be more resilient for testing
Update uifileset to use IGVCommandBarTest instead of CommandBarTest
Add ability to build native MacOS app using appbundler.

Note that it only works when full jar (build-all) is created, haven't resolved dependencies just yet

The appropriate build command is:
ant -Dinclude.libs="true" bundle
Improve support for loading FeatureSources to/from sessions

Somewhat hacky, but this solution should properly save and restore any FeatureSource which properly implements JAXB
Move SequenceMatchXXX classes to their own package
Have fasta files not get their chromosome names sorted when loaded as a genome
Set chromosomes as ordered whenever loading from a single fasta file
Add parsing of phase string from GFF

Move readingFrame attribute to AbstractFeature, standardize naming a bit
Add basic javadoc creation task, not even close to done
Update build.xml so we shouldn't be defining bundle task unless absolutely necessary, should still be able to build/test on Java 6
Make exome button a user preference
Change plugin ids from org.broadinstitute.... to org.broad.... to match package naming a bit better
Add very basic cufflinks plugin, not ready for full use yet.

Required some fairly major changes because cufflinks outputs to files, we just read the transcripts
Minor tweaks in error reporting
Change how SequenceMatchSource loads iupac ambiguity codes, wasn't working when loading from a jar file
Fix off-by-one in mouse-over for negative strand genes
Fix bug where we couldn't right-click on alignment track title