UPDATED: never mind most of that. I see that I was confused that my suggestions were completely off the mark, as I now realized that the toggles don’t mean what I think they mean. Perhaps the toggles should be changed to a labeled toggle that says “only include” and “include all except”.
@Vinadon
I was confused as well by the settings.
For example, the two verbs “Ignore or include” should never be the description of a toggle. Pick one verb and leave out the other; then the user knows that having the toggle enabled means that verb. And whichever setting makes the “File types” setting irrelevant, the textarea for “File types” should become disabled.
The term “unlinked files” should be changed to “orphaned files”. And “unresolved links” should be changed to “broken links”. That way, I wouldn’t have to think so hard.
It’s little tweaks like that would make the user experience much smoother.