Custom Project Layout

Hello, I would like to know how to define custom project Layout. Here is my situation: I have old project:

+myproject
       |-----backend
       |-----widget
       |-----web
        |-----tests
       ...other javasources

I have created new sourceSets as a solution:

sourceSets{
  myproject{
    java.srcDirs=[
      'backend',
      'shared',
      'dashboard_web',
      'gwt_common',
      'surveys-backend',
      'widgety'
     ]
    output.classesDir=file("$buildDir/bin")
     compileClasspath= sourceSets.main.output+ configurations.myproject
    runtimeClasspath= output+compileClasspath
    }

My problem is with eclipse, I don’t know why I still got errors in markers layout, also what I found crazy that I can compile successfully and gradle generate classes to the destination specified for classesDir . Thank you for your answers