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

jar.doFirst {
    for(file in configurations.compile) {
        jar.merge(file)
    }
}

configurations {
    releaseJars
}

dependencies {
    releaseJars group: 'javax.mail', name: 'mail', version: '1.4'
    //etc
}

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

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
    }
}

apply plugin: 'groovy'

repositories {
    mavenCentral()
}

configurations {
    // custom config of files we want to include in our fat jar that we send to hadoop
    includeInJar
}

dependencies {
    includeInJar 'org.codehaus.groovy:groovy:1.8.6'

    configurations.compile.extendsFrom(configurations.includeInJar)
}

jar {
    into('lib') {
        println "includeInJar: " + configurations.includeInJar.collect { File file -> file }
        from configurations.includeInJar
    }

}

%  gradle jar
includeInJar: [/Users/tnaleid/.gradle/caches/artifacts-8/filestore/org.codehaus.groovy/groovy/1.8.6/jar/553ca93e0407c94c89b058c482a404427ac7fc72/groovy-1.8.6.jar, /Users/tnaleid/.gradle/caches/artifacts-8/filestore/antlr/antlr/2.7.7/jar/83cd2cd674a217ade95a4bb83a8a14f351f48bd0/antlr-2.7.7.jar, /Users/tnaleid/.gradle/caches/artifacts-8/filestore/asm/asm/3.2/jar/9bc1511dec6adf302991ced13303e4140fdf9ab7/asm-3.2.jar, /Users/tnaleid/.gradle/caches/artifacts-8/filestore/asm/asm-tree/3.2/jar/cd792e29c79d170c5d0bdd05adf5807cf6875c90/asm-tree-3.2.jar, /Users/tnaleid/.gradle/caches/artifacts-8/filestore/asm/asm-commons/3.2/jar/e7a19b8c60589499e35f5d2068d09013030b8891/asm-commons-3.2.jar, /Users/tnaleid/.gradle/caches/artifacts-8/filestore/asm/asm-util/3.2/jar/37ebfdad34d5f1f45109981465f311bbfbe82dcf/asm-util-3.2.jar, /Users/tnaleid/.gradle/caches/artifacts-8/filestore/asm/asm-analysis/3.2/jar/c624956db93975b7197699dcd7de6145ca7cf2c8/asm-analysis-3.2.jar]
:compileJava UP-TO-DATE
:compileGroovy UP-TO-DATE
:processResources UP-TO-DATE
:classes UP-TO-DATE
:jar

BUILD SUCCESSFUL

Total time: 3.387 secs

%  jar tvf build/libs/gradletest.jar
     0 Mon Mar 12 11:40:00 CDT 2012 META-INF/
    25 Mon Mar 12 11:40:00 CDT 2012 META-INF/MANIFEST.MF
     0 Mon Mar 12 11:40:00 CDT 2012 lib/
5546084 Mon Mar 05 13:13:32 CST 2012 lib/groovy-1.8.6.jar
445288 Mon Mar 05 13:13:38 CST 2012 lib/antlr-2.7.7.jar
 43398 Mon Mar 05 13:13:40 CST 2012 lib/asm-3.2.jar
 21878 Mon Mar 05 13:13:40 CST 2012 lib/asm-tree-3.2.jar
 33094 Mon Mar 05 13:13:40 CST 2012 lib/asm-commons-3.2.jar
 36551 Mon Mar 05 13:13:40 CST 2012 lib/asm-util-3.2.jar
 17985 Mon Mar 05 13:13:40 CST 2012 lib/asm-analysis-3.2.jar

configurations{
    //declare custom config if necessary, otherwise just use compile
    myLibs
}
dependencies {
    //add lib/*.jar files to myLibs
    myLibs fileTree(dir: 'lib', include: '*.jar')
    compile {
        //set compile configuration to extend from myLibs
        extendsFrom myLibs
    }
}
// task to copy libs to output/lib dir
task copyToLib(type: Copy) {
    into "$buildDir/output/lib"
    from configurations.myLibs
}

jar {
    //include contents of output dir
    from "$buildDir/output"
    manifest {
        //...
    }
}

//set build task to depend on copyToLib
build.dependsOn(copyToLib)