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
Only show consensus sites

rather than all calls
Update sam libraries to 1.89

IGV-1904 #close
Modify build.xml so we can run tests without compiling main source
Add searching of negative strand to MotifFinderSource

Both the positive and negative strand are searched. What this means is that the sequence a user enters will be searched for on the  loaded sequence, and it's reverse complement. The feature is displayed at the positive-strand coords in either case.

This is not very efficient at the moment, we reverse-complement each chunk of sequence rather than the user-entered motif. This also means the returned order is backwards, so we need to do some reversing and combining of collections to give features in the proper order. Since this developer doesn't know how to reverse-complement a regex, we went this way.

Refactored some test code as well

IGV-1905 #resolve
Set cufflinks_plugin to invisible
Adjust test target dependencies

So that our "tests" target still compiles source as necessary.
Wrap text by word in MotifFinderDialog
Ignore testSearchWholeChromo
Change test_nocompile -> tests_nocompile