I created a small example gradle project similar to mine which reproduces this error.

It's much more complicated, but this seems to work:

task deployJar(type: Jar, dependsOn: jar) {
  baseName = project.name + '-deploy'
  deps = configurations.runtime + configurations.archives.allArtifactFiles
  depClasses = { deps.collect { it.isDirectory() ? it : zipTree(it) } }
  from(depClasses) { 
    exclude 'META-INF/MANIFEST.MF'
  }
  manifest {
    attributes 'Main-Class': 'com.benmccann.test.frontend.server.WebServer'
  }
}

Hit this myself. Unfortunately, seems to run much much slower than the ant equivalent:

    <target name="fatJar" depends="jar">
        <jar destfile="${libs.dir}/${ant.project.name}-deploy-${version}.jar">
            <zipgroupfileset dir="lib" includes="*.jar"/>
            <fileset dir="${classes.main.dir}"/>
        </jar>
    </target>

I just fixed the cookbook example.

//incorrect:
from configurations.compile.collect { it.isDirectory() ? it : zipTree(it) }

//correct:
from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }

Since we're passing closure to the from() method it means that the it will be evaluated at execution time. At execution time, the configuration is already resolved meaning that all dependencies are downloaded, etc.