KumuluzEE (since version 2.4.0) provides support for packing and running microservices as uber JARs. It also includes a Gradle task that correctly packages the microservice.
To package a KumuluzEE microservice into an uber JAR, you need to add the following task declarations into your REST module build.gradle:
dependencies {
kumuluzeeLoader 'com.kumuluz.ee:kumuluzee-loader:3.1.0'