Fix bug in how Exclude works

Two problems fixed:
1) We make Exclude paths absolute at one point to simplify
handling later on. This needs to be done for all Exclude
properties, not only AllCops/Exclude.
2) When checking if a file matches a pattern we must try
both the absolute and the relative path, since patterns
of both varieties exist.
Merge pull request #1498 from jonas054/fix_exclude_bug

Fix bug in how Exclude works