This question is already answered, but i also got same issue to debug Springboot + gradle + jHipster,
Mostly Spring boot application can debug by right click and debug, but when you use gradle, having some additional environment parameter setup then it is not possible to debug directly.
To resolve this, Eclipse provided one additional features as Remote Java Application
by using this features you can debug your application.
Follow below step:
run your gradle application with
./gradlew bootRun --debug-jvm
command
Now go to eclipse --> right click project and Debug configuration --> Remote Java Application.
add you host and port as localhost and port as 5005 (default for gradle debug, you can change it)
Refer for more detail and step.