Fix t4094, t4095 - these shouldn't be refactor errors.

One part of refactoring may be adding/removing included tup files, so we have to be able to adjust the directory dependency links. As long as the commands end up being the same (and gitignore), it's fine.
Added t4097 - unflag directories that were refactored.

If a 'tup refactor' successfully re-parses everything, then we should unflag all those directories so they aren't re-parsed again. This also shouldn't cause an error because of database changes.
Added t4098 - account for a new directory being parsed during refactoring.

Some innocuous nodes may be created, such as environment variables, or the ghost node for a Tupfile when we are first parsing. These shouldn't cause refactoring errors.
Added t4099 - adding 'include_rules' should not cause a refactoring error.

This already works, but is a good thing to check.