After lot f google one thought came to my mind, how this is been handled in myeclipse? I have downloaded myeclipse and imported my project in myeclipse, then added maven nature to all project.
Then I have checked deployment assembly of WAR project, there base project added in deployment assembly without any value in deploy path, then i had opened .setting folder from WAR project I have checked the org.eclipse.wst.common.component file where i have found one entry which were doing overlay maven build in deployment assembly, that line is as follows,
<dependent-module deploy-path="/" handle="module:/overlay/prj/base-project?includes=**/**&excludes=META-INF/MANIFEST.MF">
<dependency-type>consumes</dependency-type>
</dependent-module>
here is a solution for overlay issue of maven build, which we need to configure in deployment assembly in component file of .setting folder of project.