[Docs] Add a note about subdirectories+per-file directives

I tripped over this, causing presubmit breakages:
https://crrev.com/c/884981. In retrospect, this is sort of obvious (and
would be if I looked at the comments in the source), but...

Bug: None
Test: Looked at the new file in gitiles
Change-Id: I5aac9a0da52b34b15d8947062811779bfeeb070f
Reviewed-on: https://chromium-review.googlesource.com/884988
Reviewed-by: Lei Zhang <thestig@chromium.org>
Commit-Queue: George Burgess <gbiv@chromium.org>
Cr-Commit-Position: refs/heads/master@{#532174}
1 file changed