title: build.gradle for eclipse project with multiple source folders
body: <p>I have a eclipse project with source folders like:</p>
  
  <pre><code>/src/main/java/module1
  /src/main/java/module2
  /src/main/java/module3
  </code></pre>
  
  <p>inside these src folders i have packages like:</p>
  
  <pre><code>com.example.module1.xxx
  com.example.module2.yyy
  com.example.module3.zzz
  </code></pre>
  
  <p>I have made a gradle build using java and eclipse plugin with sourcesets like:</p>
  
  <pre><code>apply plugin: 'java'
  apply plugin: 'eclipse'
  sourceSets {
      main {
          java {
              srcDirs = ['src/main/java/module1']
              srcDir 'src/main/resources'
              srcDir 'src/main/java/module2'
              srcDir 'src/main/java/module3'
          }
      }
  }
  jar{
      manifest {
          attributes 'Implementation-Title': 'Example Project',
                     'Implementation-Version': '1.0.0'    
      }
  }
  
  repositories {
      mavenCentral()
  }
  dependencies{
      compile group: 'com.zaxxer', name: 'HikariCP', version: '2.2.5'
      compile group: 'org.apache.logging.log4j', name: 'log4j-api', version: log4j2Version
      compile group: 'org.apache.logging.log4j', name: 'log4j-core', version: log4j2Version
      compile group: 'org.apache.logging.log4j', name: 'log4j-slf4j-impl', version: log4j2Version
      compile group: 'org.apache.logging.log4j', name: 'log4j-jul', version: log4j2Version
      compile group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: log4j2Version
      compile group: 'org.slf4j', name: 'slf4j-api', version: '1.7.9'
  }
  </code></pre>
  
  <p>The problem is when i generate eclipse project using <code>gradle eclipse</code> it correctly generates the 3 module source folders, a resources source folder but it also generates the super source folder src/main/java having all the nested source folders with packages like:</p>
  
  <pre><code>module1.com.exaple.module1.xxx
  module2.com.exaple.module2.yyy
  module3.com.exaple.module3.zzz
  </code></pre>
  
  <p>Thus i get error in eclipse "Cannot nest '${projectdir}/src/main/java/module1' inside '${projectdir}/src/main/java'. To enable the nesting exclude 'module1/' from '${projectdir}/src/main/java'"</p>
  
  <p>How do i modify my tasks/sourcesets to get the right project structure?</p>