(This is a port of sbt/sbt#2258)
sbt was reporting warning abouts inconsistent versions of dependencies
even if these dependencies didn't have the same configuration (as in
`provided` vs `compile`).
This commit fixes this problem by comparing the dependencies by
organization, artifact name and configuration.
Undeprecated `CustomPomParser` because it looks like nothing has
replaced it yet.
Removed usage of trait `scala.NotNull`, because it has been deprecated
as of Scala 2.11 and its support has never been implemented in scalac.