Update DMUtilsTest

Finish some of the TODOs, add some delete functionality (for testing the upload/creating of files/directories, want to tear down after).
Add checking of WebToolDescriptor to ATMUtilsTests
Remove org.json, per GH #38

Migrate all json parsing to gson library

We aren't using the full serialiazation potential of gson everywhere, only in ATMUtils
Update Alignment tests

Update AlignmentPackerTest to use local file instead of remote.
Ignore BAMHttpQueryReaderTest while we settle on appropriate remote file
Update CoverageCounterTest to use local file
Merge pull request #39 from broadinstitute/JSON

Remove org.json, per GH #38
Update GenomeImpl.getLongChromosomeNames

There were some cases where no chromosomes would be considered "long". This should provide a fallback method which always finds at least 1, checking against maxChromoLength instead of genomeSize
Add test for getting 'Long' chromosome names

Testing pathological case where we have many small ones
Keep gene track when resetting session from CommandExecutor
Change DMUtilsTest to use test2.bed, instead of test.bed
Add strand parameter to MotifFinder

Not used yet, just set it to positive
Adjust logging

Add 2 more config files with logging levels debug and all, intended so we can give users different jnlps/command lines and get more info.
Change some log statements to trace from debug, mostly layout ones
Add many log.debug statements

IGV-1904
Update picard, sam, and tribble jars

Class conflicts existed due to us using old version of separate tribble, as well as newer picard version. We resolve these conflicts and change to picard package names (org.broad.tribble.util.SeekableStream -> net.sf.samtools.seekablestream.SeekableStream).

IGV-1904
Change vcf library to that in picard, variant-1.88.jar

The vcf library we were using was binary incompatible with the updated tribble library. Currently the na12878kb functionality is disabled, as that library needs to be updated as well
Add SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT)

This is standard IGV practice (apparently), and with the update more header checking of SAM files appears to be done.
Update na12878kb.jar

Was built on this developers home machine, Linux, version info below. Based on gsa-unstable tag 2.4. This version appears binary compatible with our tribble version and variant-1.88.jar

java version "1.6.0_27"
OpenJDK Runtime Environment (IcedTea6 1.12.3) (6b27-1.12.3-0ubuntu1~12.04.1)
OpenJDK Server VM (build 20.0-b12, mixed mode)

Apache Ant(TM) version 1.8.2 compiled on December 3 2011