Merge resources and classes for "run" task

How can I merge the resources and the classes for the classpath of the “run” task?

I am reworking the build.gradle of the open source game “Terasology”.

It defines an own “run” task but I try to use the gradle “run” task. Both variants have a problem with the resource files. The program needs the resource files at the same folder like the classes. Running from a JAR file or from an IDE (eclipse) works fine, because the resource files are copied to the class files.

The current (and working) solution changes the output.

sourceSets {
  main {
    output.resourcesDir = 'target/classes/main'

But this solution needs an ugly fix for the JAR task, because the resource files are twice.

jar.doFirst {
  // Work around for duplicate entries in jar bug
  sourceSets.main.output.resourcesDir = '/dev/null'
jar.doLast {
  sourceSets.main.output.resourcesDir = 'target/classes/main'

Is it possible (and wise) to copy the classes and resources to a new “run” folder and use this as the classpath for the “run” task?