transitive_deps_set was incorrect, it was not considering the
dependencies of dependencies in some cases. I've corrected it and tidied
it up a little.

The test case from leftaroundabout, as linked to from the ticket, is
added with small modifications to flatten directory structure.

Test Plan: make test TEST=T13949

Reviewers: austin, bgamari, alexbiehl

Reviewed By: alexbiehl

Subscribers: rwbarton, thomie, alexbiehl

GHC Trac Issues: #13949

Differential Revision: https://phabricator.haskell.org/D3720