Build.gradle for eclipse project with multiple source folders

I have a eclipse project with source folders like:

/src/main/java/module1
    /src/main/java/module2
    /src/main/java/module3

inside these src folders i have packages like:

com.example.module1.xxx
    com.example.module2.yyy
    com.example.module3.zzz

I have made a gradle build using java and eclipse plugin with sourcesets like:

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'
    }

The problem is when i generate eclipse project using ‘gradle eclipse’ 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:

module1.com.exaple.module1.xxx
    module2.com.exaple.module2.yyy
    module3.com.exaple.module3.zzz

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’”

How do i modify my tasks/sourcesets to get the right project structure?

Well finally figured out that the build.gradle is fine… what i was doing wrong is i was executing command

gradle eclipse

which was just appending entries into the existing .classpath file, To generate a fresh copy i had to execute

gradle cleanEclipseClasspath eclipse

which produced the correct .classpath file.