https://github.com/sbt/sbt-proguard/issues/28

ProguardPlugin.scala

import sbt._
import sbt.Keys._

import sbtassembly.AssemblyPlugin, AssemblyPlugin.autoImport._

object ProguardKeys {
  val proguard = taskKey[File]("builds the proguarded jar file")
  val proguardOptions = settingKey[Seq[String]]("CLI options")
  val proguardVersion = settingKey[String]("proguard's artefact version")

  val Proguard: Configuration = config("proguard").hide
}

object ProguardPlugin extends AutoPlugin {
  val autoImport = ProguardKeys
  import autoImport._

  override def requires = AssemblyPlugin
  override def trigger = noTrigger
  override def projectConfigurations = Seq(Proguard)

  override def projectSettings =
    Seq(
      proguardOptions := Nil,
      proguardVersion := "5.3.3",
      libraryDependencies += "net.sf.proguard" % "proguard-base" % proguardVersion.value % Proguard,
      proguard := {
        val app_jars = (managedClasspath in Proguard).value

        // not java 9 compatible...
        val syslib = file(scala.util.Properties.jdkHome) / "jre/lib/rt.jar"

        val options = ForkOptions(
          javaHome = javaHome.value,
          outputStrategy = outputStrategy.value,
          bootJars = Vector.empty[java.io.File],
          workingDirectory = Option(baseDirectory.value),
          runJVMOptions = (javaOptions in proguard).value.toVector,
          connectInput = connectInput.value,
          envVars = Map.empty[String, String]
        )

        FileFunction
          .cached(streams.value.cacheDirectory / "proguard") {
            (in: Set[File]) =>
              val Seq(input) = in.toSeq
              val out = target.value / s"${name.value}-proguard-${version.value}.jar"
              new ForkRun(options)
                .run(
                  "proguard.ProGuard",
                  Attributed.data(app_jars),
                  Seq("-injars", input.getCanonicalPath) ++
                    Seq("-outjars", out.getCanonicalPath) ++
                    Seq("-libraryjars", syslib.getCanonicalPath) ++
                    proguardOptions.value,
                  state.value.log
                )
                .failed
                .foreach(f => sys.error(f.getMessage))
              Set(out)
          }(Set(assembly.value))
          .head
      }
    ) ++ inConfig(Proguard)(
      managedClasspath := Classpaths
        .managedJars(configuration.value, classpathTypes.value, update.value)
    )
}