Patch Set 11:

I made some of the suggested changes, added to the JavaDoc comments. Test coverage is at 98% of ignore classes. I am unable to reproduce test errors on a fresh clone on my machine, it may be related to the way the tests handled file paths, made some fixes in this patch.

Now looking at using TreeWalk and WorkingTreeIterator, looking at NameConflictTreeWalk as a way to get started.

Thanks for the comments and suggestions. :)