Copyタスクを使ってdependenciesを振り分ける場合

build.gradle

apply plugin: 'java'

repositories {
    mavenCentral()
}

dependencies {

    compile 'org.slf4j:slf4j-api:1.7.5'

    testCompile 'junit:junit:4.11'
    testCompile 'org.hamcrest:hamcrest-all:1.3'

    runtime 'org.slf4j:slf4j-simple:1.7.5'

}

def jars = configurations.testCompile - configurations.compile

defaultTasks 'cleanExtra', 'copyTestCompileJars'

task copyTestCompileJars << {
    println "copy test compile jars."
}

task cleanExtra << {
    delete "${projectDir}/extra"
}

task copyHamcrestJars(type: Copy) {
    from (jars) {
        include "hamcrest-*"
    }
    into "${projectDir}/extra/hamcrest"
}

task copyJUnitJar(type: Copy) {
    from (jars) {
        include "junit-*"
    }
    into "${projectDir}/extra/junit"
}

task copyAnotherJars(type: Copy) {
    from (configurations.testCompile) {
        exclude "hamcrest-*"
        exclude "junit-*"
    }
    into "${projectDir}/extra"
}

copyTestCompileJars.dependsOn copyHamcrestJars, copyJUnitJar, copyAnotherJars