We're experiencing the same issue, running with: Gradle 1.0-milestone-1

That said both of the gradle commands listed above work for us. I could submit a test project (if useful), but it isn't substantively different.

As mentioned in the forum thread – I'm not seeing enhanced classes ending up in the .jar, this is easily verified by using javap to inspect them.

Is there a easy workaround?

I worked around this problem by using the datanucleus ant task. Below is how I updated build.gradle from the attached example.zip. With these changes, the test passes.

apply plugin: 'java'

repositories {
	mavenCentral()
}

configurations {
 jdo {
 	extendsFrom compile
 }
}
dependencies {
   compile 'org.datanucleus:datanucleus-core:1.1.5',
           'javax.jdo:jdo2-api:2.3-eb'
	jdo 'org.datanucleus:datanucleus-enhancer:1.1.4'
   testCompile 'junit:junit:4.7'
    
}

task jdoEnhance << {
	ant.taskdef(name: 'enhancer', classname: 'org.datanucleus.enhancer.tools.EnhancerTask', classpath: configurations.jdo.asPath) 
	ant.enhancer( dir: sourceSets.main.output.classesDir.canonicalPath.toURI().toString(), verbose: 'true') {
		classpath {
			pathelement(location: sourceSets.main.output.classesDir.canonicalPath.toURI().toString())
			pathelement(path: configurations.jdo.asPath)
		}
		fileset(dir: sourceSets.main.output.classesDir.canonicalPath.toURI().toString()) {
			include(name: '**/*.class')
		}
	}
}

classes.dependsOn jdoEnhance

Quote from http://www.datanucleus.org/products/datanucleus/enhancer.html#javac on running enhancer via annotations:
"Note that this works by waiting a period of time until all classes will have been compiled before invoking the enhancement step. We advise against using it, and better to use post-compile directly"

It looks like this is a limitation of running datanucleus enhancer via annotations rather than a gradle bug.

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Thanks again for reporting this issue. We haven't heard back from you after our inquiry from November 15th. We are closing this issue now. Please create an issue on GitHub if you still feel passionate about getting it resolved.