WINDUP-379: Overwrite prompt is ignored in non-interactive mode, and results in automatic deletion of the output folder
WINDUP-369: Be able to focus effort on specific jars in the ear or war
WINDUP-369: Reporting of the ignored files
Merge pull request #348 from jsight/fix_for_overwrite_prompt

WINDUP-379: Overwrite prompt is ignored in non-interactive mode, and res...
Merge branch 'WINDUP-369' of https://github.com/mbriskar/windup into mbriskar-WINDUP-369
Tweaked javadoc, and made a minor change to model naming
Merge branch 'mbriskar-WINDUP-369'
Initial work on complex query support.