experimental code that moves the "api" subpackage into its own jar which then gets re-packaged with a jar that doesnt have said sub-package. Output is a jar with the qualifier "universal". This concept can be adapted to pacakage a Coremod-only jar into the mainmod.jar to comply to the new forge coremod policy.

build.gradle

// at the end of your build.gradle

// Create API library zip
// Warning: This jar will be reobfuscated! Its only used to package it with the universal jar
task apiJar(type: Jar) {
	from(sourceSets.main.output) {
        include "**/api/**"
    }
    classifier = 'obf-api'
    includeEmptyDirs = false
}

// task to create a jar containing all classes from the main sourceSet output and the api.jar
// also sets up the manifest attribute 'ContainedDeps' which fml uses to extract the api jar at runtime
task packedJar(type: Jar, dependsOn: 'reobfApiJar') {
    manifest {
        attributes 'FMLAT': "${modid}_at.cfg"
        attributes 'ContainedDeps': "${archivesBaseName}-${version}-api.jar"
    }
    from(sourceSets.main.output) {
        exclude('**/api/**')
    }
    from("${buildDir}/libs") {
        include("*-${version}-api.jar")
    }

    classifier = 'universal'
}

// tell gradle to reobfuscate our jars
reobf {
    // jar is done by default
    // jar { }
    apiJar { }
    packedJar { }
}