I ran into the same problem as previously discussed on the old forum. Unfortunately, I could not find any follow up on this issue.
In my case, I have tried to include the following dependency in my build:
compile "org.scalanlp:breeze-natives_2.11:0.11.2"
When I run the Eclipse plugin, it generates a pom entry in the classpath that breaks the build in Eclipse:
<classpathentry kind="lib" path="/home/mmarcini/.gradle/caches/modules-2/files-2.1/com.github.fommil.netlib/all/1.1.2/f235011206ac009adad2d6607f222649aba5ca9e/all-1.1.2.pom" exported="true"/>
At the moment, I use a workaround from here, but it would be great to fix this in the plugin. I use Gradle 2.3
$ gradle -version
------------------------------------------------------------
Gradle 2.3
------------------------------------------------------------
Build time: 2015-02-16 05:09:33 UTC
Build number: none
Revision: 586be72bf6e3df1ee7676d1f2a3afd9157341274
Groovy: 2.3.9
Ant: Apache Ant(TM) version 1.9.3 compiled on December 23 2013
JVM: 1.8.0_45 (Oracle Corporation 25.45-b02)
OS: Linux 3.13.0-49-generic amd64
Martin