build.gradle

apply plugin: 'java'
apply plugin: 'java-library-distribution'

repositories {
    mavenCentral()
}

dependencies {
    compile 'org.apache.commons:commons-lang3:3.3.2'
}

// Task "distZip" added by plugin "java-library-distribution":
distZip.shouldRunAfter(build)

jar {
    // Keep jar clean:
    exclude 'META-INF/*.SF', 'META-INF/*.DSA', 'META-INF/*.RSA', 'META-INF/*.MF'
    
    manifest {
        attributes 'Main-Class': 'com.somepackage.MainClass',
                   'Class-Path': configurations.runtime.files.collect { "lib/$it.name" }.join(' ')
    }
    // How-to add class path:
    //     http://stackoverflow.com/questions/22659463/add-classpath-in-manifest-using-gradle
    //     https://gist.github.com/simon04/6865179
}

A textual preview of the results can be found here.

If you use gradle 3.0 and the io.spring.gradle:dependency-management-plugin, you must delay setting the Class-Path like this:

afterEvaluate {
     jar {
        manifest {
            attributes (
                    'Class-Path': configurations.runtime.files.collect { "lib/$it.name" }.join(' ')
            )
        }
    }
}