gradle – how do I build a jar with a lib dir with other jars in it?

If you have all the jars inside a directory (lets call it libs) in your project, you only need this:

jar {
    into('lib') {
        from 'libs'
    }
}

I guess it is more likely that these jars are dependencies of some sort. Then you could do it like this:

configurations {
    // configuration that holds jars to copy into lib
    extraLibs
}
dependencies {
    extraLibs 'org.something:something-dep1:version'
    extraLibs 'org.something:something-dep2:version'
}

jar {
    into('lib') {
        from configurations.extraLibs
    }
}