To get full gradle support in eclipse you should install the buildship plugin. Configuring the Javascript side you can follow the instructions for maven.
File -> Import
Gradle Project
Next
When using buildship gradles default outputfolder is filtered and not visible in your workspace. Therefore you need to remove it from eclipse’s resource filter setting.
Properties
Resources
build
Java Build Path
Add Folder...
build/generated/source/apt/main
Make sure the new source folder contains the correctly generated mapper implementations when running JHipster via eclipse.