Gradle Zip task to do multiple sub-trees?

Try this:

task zip(type: Zip) {
    from jar.outputs.files
    from('bar/') {
        into('bar')
    }
}

First... the jar should be in the root / of the zip (which seems to be what you want). Second, by specifying the from jar.outputs.files, there is an implicit dependsOn on the jar task, so this shows another way of accomplishing what you want. Except with this approach if the jar name changes over time it doesn't matter. Let me know if you need additional help.

Apparently the comments to an answer will not allow for a convenient way to show more code... or it isn't obvious :) I have a project which is for a client... so I can't share the full project / build file. Here is what I can share (I changed the project specific acron to XXX):

task zip(type: Zip) {

    from jar.outputs.files

    from('scripts/') {
        fileMode = 0755
        include '**/runXXX.sh'
        include '**/runXXX.bat'
    }
    from('lib/') {
        include '**/*.jar'
        into('lib')
    }
    from('.') {
        include 'xxx.config'
    }

}

This creates a zip with the project jar in the root of the zip. Copies the scripts from a directory to the root, copies the config file to the root and creates a directory in the root of the zip named /lib and copies all the jars from the project /lib to the zip/lib.