For those of you, like me, who are too impatient to wait for the official 
gradle plugin, here's a working methodology for codegen with gradle:

In your build.gradle add:

dependencies {
    <.... existing dependencies ....>
    compile 'org.jooq:jooq:3.2.2'
    compile 'org.jooq:jooq-meta:3.2.2'
    compile 'org.jooq:jooq-codegen:3.2.2'
}

ext.jooqConfigFileName = '<XML configuration file name>'
ext.jooqConfig = file jooqConfigFileName
ext.jooqGeneratedCode = file "${buildDir}/generated-sources/jooq"

task jooqCodegen (type: JavaExec) {
    inputs.files jooqConfig
    outputs.dir jooqGeneratedCode
    main = 'org.jooq.util.GenerationTool'
    classpath = sourceSets.main.compileClasspath + 
files('src/main/resources')
    args = ['/'+jooqConfigFileName]
    doFirst {
        jooqGeneratedCode.mkdirs()
    }
}

sourceSets {
    main {
        java {
            srcDir "${buildDir}/generated-sources/jooq"
        }
    }
}

compileJava.dependsOn(jooqCodegen)

Place your XML configuration file in src/main/resources and configure it as 
you would when using the CLI command.

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