Added flow signal distribution chart code

Signed-off-by: Chantal Roth <croth@nobilitas.com>
added .gitignore
Merge branch 'chantal'

Conflicts:
	.gitignore
	src/com/iontorrent/data/FlowDistribution.java
	src/com/iontorrent/utils/SimpleDialog.java
	src/com/iontorrent/views/FlowSignalDistributionPanel.form
	src/com/iontorrent/views/FlowSignalDistributionPanel.java
	src/org/broad/igv/PreferenceManager.java
	src/org/broad/igv/batch/CommandExecutor.java
	src/org/broad/igv/sam/AlignmentTrack.java
	src/org/broad/igv/ui/IGV.java
	src/org/broad/igv/ui/PreferencesEditor.java
	web/webstart.js
Merge pull request #24 from broadinstitute/master

Update v2.2 to parse plugin paths properly.
Update tribble jar to r121
Added null check
Fix problem with gene list manager (disconnected button)
Minimum width for DNA methylation heatmaps.  Impossible to see otherwise.
Mistakenly thought collections2.filter worked in place. Created wrapper, CollUtils.filter, which returns a filtered list (usually we use lists) or null if input was null
Change set -> Collection in UI
Modify pruneGraph so it only filters on genes, and thus preserves seed genes with no connections
Modify testPruneGraph so we add "Protein" attribute to nodes, so they are filtered correctly. Add additional tests
Change "path" -> "default_path" where necessary
Use pluginSpecReader.getToolPath, as we should, so we get tool path either from XML spec or from preferences.

Move some text keys to static final constants.
Add "region" parameter to "snapshot" batch command; so syntax is "snapshot <filename> [region]. If blank, behavior same as before.
Bug fix -- missing "info" links on load menu
Refine popup text for CN summary track
Refactoring, updating docs
Remove quotes from color strings -- common problem with Excel exports
Remove cmdArg text from dialog, as well as command name. Put tool name and command name in dialog title.

Have RunPlugin dialog adjust size better for long track names.
Change PEStats.insertSizes to a DoubleArrayList, from a double[].

Previously, was allocating insertSizes = new double[MAX=10000] with each instance creation of PEStats. Huge waste of memory. Using DoubleArrayList and a much smaller pre-allocation should be more efficient