Ignore working directory when excluding system patterns.

Fixes #1604 by removing working directory from excluded patterns.
I thought the point of `inclusion_patterns` was to provide a user-configurable list of things we always want to include and the current directory is just the default value we include in that list.  Still not clear to me why this should only apply to the current directory and not to all inclusion patterns.

If you were to apply this to all inclusion patterns, what would go wrong?  Can you provide an example that would not work correctly if we went that route?

Besides the fact that in my understanding we need to honor `inclusion_patterns` here, there's another issue: if there's any code that has changed the current directory, this would not work properly, right?  The inclusion patterns has the nice benefit of being the current directory as of when the process started, which is the correct value to continue to apply for the lifetime of the process, right?