New PluginExecutor command

- A plugin class can be defined outside of the Adam jar, but run through
  the normal AdamMain
- An example plugin, the "Take10Plugin" is included in the test
  directory
- Adds a test suite to the cli module, which can reference the items
  available in the core module
- Adds notion of AccessControl to control the records which can be
  accessed
Build Fix & Changes for Frank's comments
Revert change
Updates for latest strand of comments

- Functional test
- More comments
Merge pull request #108 from genomebridge/plugin

Adding new PluginExecutor command
fix typo in log4j config, but junk is still spewed to stdout
Remove existing BQSR implementation
Make quality scores into ints
Scaffolding for BQSR implementation
add Util.hashCombine
add stuff to Observation
Make ObservationTable ctor private
ObservationTable fixes/changes
Empirical error probability tweaks
Don't need to broadcast SnpTable; it's only referenced once
add Recalibrator skeleton
Rename PhredQualityScore to QualityScore
ObservationTable fixes
ObservationTable doesn't need to be sorted
adjust variable naming