Added in Class Indexing.
Added in Module support.
Updated test cases for lucene search. Added group collection for improved search response.
Removed unused collector.  Leveraging the TermFirstPassGroupingCollector instead.
Moved classes to appropriate package.
Fixed bug in the joining of modules to archives.
Cleaned up sysouts from test.
Added the LuceneModuleIndex.
Merge pull request #69 from OndraZizka/master

Improve not found err msg; Javadoc; Fix indent
Merge branch 'master' of https://github.com/windup/windup
Worked around current issue of creating junk hints based on what should be candidate issues.

Also, changed log statement to debug from info.
Fixed a null pointer exception bug.
All reports to render correctly in Eclipse internal web browser on
windows. Resolves issue #73
Add new constructor to ReportEngine that will take an already created
WindupEngine. Resolves issue #75
Merge pull request #74 from itewk/master

Updates to Windup needed for windup-eclipse-plugin
Prevent NPE.
Error messages, comments, remove code duplication
Cleanup, javadoc.