RAT-98: report skipped files

[Claudenw]

Fixes issues raised by report skipped processing, specifically issues with Maven not correctly skipping files that should be skipped.

In the process of working on the bugs additional testing code was implemented to allows testing on file systems that are not native. Most name based code now checks against UNIX, WINDOWS, and OSX.

Significant additional work was undertaken to ensure that the document names work as expected.

[ottlinger]

@Claudenw did you accidentally push an old branch as the build fails with spotbugs errors?

[Claudenw]

@ottlinger
Actually, it is a work in progress. I had to rework the descending exclusion processing because it was returning incorrect results. That triggered a number of changes in integration tests and the like because they were not set correctly to begin with. Net result is a large change but accurate results and more use of the assertJ package.

My next step is to see how I can split this into smaller pieces.