Fixes #1634. Adds inconsistent duplicate warning

#1634 is about a library getting wiped out of deps graph when it’s
included twice in ascending order of version.
I’d say that’s a logically inconsistent state, and we should just issue
warning instead of trying to fix it.
Merge pull request #1634 from sbt/fix/1634

A library is missing from dependencyClasspath if it's added to libraryDependencies twice in ascending order