python3: Ensure stale empty python module directories don't break the build

There are two issues inside importlib. Firstly, the modules are accessed in
on disk order. This means behaviour seen on one system might not reproduce
on another and is a real headache.

Secondly, empty directories left behind by previous modules might be looked
at. This has caused a long string of different issues for us.

As a result, patch this to a behaviour which works for us. Upstream discussion
can follow later, this is breaking builds for too many people to leave unpatched.

[YOCTO #14816]

Signed-off-by: Richard Purdie <richard.purdie@linuxfoundation.org>
(cherry picked from commit e5944a38)
Signed-off-by: Steve Sakoman <steve@sakoman.com>