Eliminate Gradle 1.6 deprecation warnings

Recently Spring framework build has been updated to use Gradle 1.6.
With the new version some of the Gradle APIs have been deprecated.
These deprecated APIs have been used by Spring build specific Gradle
plugins, which resulted in deprecation warnings in build output.

This patch changes Spring build specific Gradle plugins to use new
Gradle APIs instead of deprecated ones.

Even after this change build still produces warnings about Gradle
deprecated APIs being used. These come from Spring shared Gradle
plugins and other 3rd party Gradle plugins in use, like Gradle
Artifactory Plugin (GAP), which are still not updated to Gradle 1.6.
Related tickets for updating of these plugins to Gradle 1.6 are
GRADLE-53 and GAP-144, and once they get resolved Spring framework
build should further be updated.

Issue: SPR-10572
Fix MergePlugin

The submitted pull requests for SPR-10572 did not build.

This commit fixes the MergePlugin to create from configurations rather
than the project. It also removes unnecessarily added code that was
commented out.

Issue: SPR-10572