A quick gist for how you partially sign a jar

build.gradle

jar {
    from(sourceSets.main.output) {
        include 'myPackages/**'
    }

    // set temp location
    destinationDir = file("build/tmp")
    archiveName = "signed.jar"

    // sign it.
    doLast {
        // your ant info...
        //I am going to assume you already know how to get this without hardcoding it.
        ant.signjar(jar: getArchivePath(),
            alias: project.sign_alias,
            keystore: project.sign_keystore,
            storepass: project.sign_password,
            keypass: project.sign_password)
    }
}

task signedJar(type: zip, dependsOn: 'classes') {
    dependsOn project.tasks.signedJart

    extension = "jar" // cheating

    // from the signed jar
    from (zipTree(project.tasks.signedJar.getArchivePath())) {
        include "**"  // ensure this doesnt get excluded by the later include line
    }
    
    // the other stuff
    // this is task is already pulling from the classes dir, so we dont have to re-specify that..  
    from(sourceSets.main.output) {
        include 'otherPackages/**'
    }

    // ignore new duplicate files.. just in case
    duplicatesStrategy = DuplicatesStrategy.EXCLUDE
}

reobf {
    obfOutput.clear(); // clear the default jar out
    reobf tasks.signedJar {  spec ->
        spec.classpath = project.sourceSets.main.compileClasspath
    }
}