Produce a single library for multiple file dependencies on the same file

Previously, the Gradle plugin’s ProjectLibraries produced a new library
for every file dependency, even if the dependencies where on the same
file. This would lead to a repackaging failure due to multiple
libraries having the same name.

This commit updates ProjectLibraries to treat file dependencies on the
same file as a single library, thereby resolving the name clash.

Fixes gh-1646
Merge branch '1.1.x'