flatten-maven-plugin - patches for the flatten all mode

[Ray Tsang]

Hi all!

Stephanie, an engineer on GCP client library, and I have been applying Maven Flatten plugin to solve some of our dependency management issues.  We discovered a couple of bugs that are fixed by Stephanie's PR: https://github.com/mojohaus/flatten-maven-plugin/pull/134

It'd be great if someone can take a look.

Thanks!