diff --git a/src/main/scala/com/typesafe/sbt/packager/universal/UniversalPlugin.scala b/src/main/scala/com/typesafe/sbt/packager/universal/UniversalPlugin.scala
index 5262a59ee..d4714e100 100644
--- a/src/main/scala/com/typesafe/sbt/packager/universal/UniversalPlugin.scala
+++ b/src/main/scala/com/typesafe/sbt/packager/universal/UniversalPlugin.scala
@@ -3,6 +3,7 @@ package packager
 package universal
 
 import sbt._
+import sbt.Keys.cacheDirectory
 import Keys._
 import Archives._
 import sbt.Keys.TaskStreams
@@ -36,7 +37,7 @@ trait UniversalPlugin extends Plugin {
         mappings <<= sourceDirectory map findSources,
         dist <<= (packageBin, streams) map printDist,
         stagingDirectory <<= target apply (_ / "stage"),
-        stage <<= (stagingDirectory, mappings) map stageFiles
+        stage <<= (cacheDirectory, stagingDirectory, mappings) map stageFiles(config.name)
       )) ++ Seq(
         sourceDirectory in config <<= sourceDirectory apply (_ / config.name),
         target in config <<= target apply (_ / config.name)
@@ -54,9 +55,12 @@ trait UniversalPlugin extends Plugin {
     dist
   }
 
-  private[this] def stageFiles(to: File, mappings: Seq[(File, String)]): Unit = {
-    val copies = mappings collect { case (f, p) => f -> (to / p) }
-    IO.copy(copies)
+  private[this] def stageFiles(config: String)(cacheDirectory: File, to: File, mappings: Seq[(File, String)]): Unit = {
+    val cache = cacheDirectory / ("packager-mappings-" + config)
+    val copies = mappings map {
+      case (file, path) => file -> (to / path)
+    }
+    Sync(cache)(copies)
     // Now set scripts to executable using Java's lack of understanding of permissions.
     // TODO - Config file user-readable permissions....
     for {
diff --git a/src/sbt-test/universal/clear-stage-dir/build.sbt b/src/sbt-test/universal/clear-stage-dir/build.sbt
new file mode 100644
index 000000000..8c687dea6
--- /dev/null
+++ b/src/sbt-test/universal/clear-stage-dir/build.sbt
@@ -0,0 +1,7 @@
+import NativePackagerKeys._
+
+packagerSettings
+
+name := "simple-test"
+
+version := "0.1.0"
diff --git a/src/sbt-test/universal/clear-stage-dir/project/plugins.sbt b/src/sbt-test/universal/clear-stage-dir/project/plugins.sbt
new file mode 100644
index 000000000..b53de154c
--- /dev/null
+++ b/src/sbt-test/universal/clear-stage-dir/project/plugins.sbt
@@ -0,0 +1 @@
+addSbtPlugin("com.typesafe.sbt" % "sbt-native-packager" % sys.props("project.version"))
diff --git a/src/sbt-test/universal/clear-stage-dir/src/universal/conf/test b/src/sbt-test/universal/clear-stage-dir/src/universal/conf/test
new file mode 100644
index 000000000..ab1006ffd
--- /dev/null
+++ b/src/sbt-test/universal/clear-stage-dir/src/universal/conf/test
@@ -0,0 +1 @@
+# Test configuration to include in zips.
diff --git a/src/sbt-test/universal/clear-stage-dir/src/universal/conf/test2 b/src/sbt-test/universal/clear-stage-dir/src/universal/conf/test2
new file mode 100644
index 000000000..c181ac4a0
--- /dev/null
+++ b/src/sbt-test/universal/clear-stage-dir/src/universal/conf/test2
@@ -0,0 +1 @@
+# removable file
\ No newline at end of file
diff --git a/src/sbt-test/universal/clear-stage-dir/test b/src/sbt-test/universal/clear-stage-dir/test
new file mode 100644
index 000000000..d6e088c0b
--- /dev/null
+++ b/src/sbt-test/universal/clear-stage-dir/test
@@ -0,0 +1,9 @@
+# Stage the distribution and ensure files show up.
+> universal:stage
+$ exists target/universal/stage/conf/test
+$ exists target/universal/stage/conf/test2
+$ delete src/universal/conf/test2
+> universal:stage
+$ exists target/universal/stage/conf/test
+$ absent target/universal/stage/conf/test2
+