diff --git a/src/scala/org/pantsbuild/zinc/compiler/OutputUtils.scala b/src/scala/org/pantsbuild/zinc/compiler/OutputUtils.scala
index d6fa0ea94fba..bfeb8e50f8d9 100644
--- a/src/scala/org/pantsbuild/zinc/compiler/OutputUtils.scala
+++ b/src/scala/org/pantsbuild/zinc/compiler/OutputUtils.scala
@@ -19,17 +19,21 @@ object OutputUtils {
    * @param dir File handle containing the contents to sort
    * @return sorted set of all paths within the `dir`
    */
-  def sort(dir:File): mutable.TreeSet[(Path, Boolean)] = {
-    val sorted = new mutable.TreeSet[(Path, Boolean)]()
+  def sort(dir:File): mutable.TreeSet[Path] = {
+    val sorted = new mutable.TreeSet[Path]()
 
     val fileSortVisitor = new SimpleFileVisitor[Path]() {
       override def preVisitDirectory(path: Path, attrs: BasicFileAttributes): FileVisitResult = {
-        sorted.add(path, false)
+        if (!path.endsWith("/")) {
+          sorted.add(Paths.get(path.toString, "/"))
+        } else {
+          sorted.add(path)
+        }
         FileVisitResult.CONTINUE
       }
 
       override def visitFile(path: Path, attrs: BasicFileAttributes): FileVisitResult = {
-        sorted.add(path, true)
+        sorted.add(path)
         FileVisitResult.CONTINUE
       }
     }
@@ -50,25 +54,30 @@ object OutputUtils {
    * @param jarEntryTime time to be set for each JAR entry
    */
   def createJar(
-    base: String, filePaths: mutable.TreeSet[(Path, Boolean)], outputJarPath: Path, jarEntryTime: Long) {
+    base: String, filePaths: mutable.TreeSet[Path], outputJarPath: Path, jarEntryTime: Long) {
 
     val target = new JarOutputStream(Files.newOutputStream(outputJarPath))
 
-    def addToJar(source: (Path, Boolean), entryName: String): FileVisitResult = {
-      val jarEntry = new JarEntry(entryName)
+    def jarEntry(name: String): JarEntry = {
+      val jarEntry = new JarEntry(name)
       // setting jarEntry time to a fixed value for all entries within the jar so that jars are
       // byte-for-byte reproducible.
       jarEntry.setTime(jarEntryTime)
+      jarEntry
+    }
 
-      target.putNextEntry(jarEntry)
-      if (source._2) {
-        Files.copy(source._1, target)
+    def addToJar(source: Path, entryName: String): FileVisitResult = {
+      if (source.toFile.isDirectory) {
+        target.putNextEntry(jarEntry(entryName))
+      } else {
+        target.putNextEntry(jarEntry(entryName))
+        Files.copy(source, target)
       }
       target.closeEntry()
       FileVisitResult.CONTINUE
     }
 
-    val pathToName = filePaths.zipWithIndex.map{case(k, v) => (k, relativize(base, k._1))}.toMap
+    val pathToName = filePaths.zipWithIndex.map{case(k, v) => (k, relativize(base, k))}.toMap
     pathToName.map(e => addToJar(e._1, e._2))
     target.close()
   }
diff --git a/src/scala/org/pantsbuild/zinc/compiler/Settings.scala b/src/scala/org/pantsbuild/zinc/compiler/Settings.scala
index 5df34cd75638..c361d2350e88 100644
--- a/src/scala/org/pantsbuild/zinc/compiler/Settings.scala
+++ b/src/scala/org/pantsbuild/zinc/compiler/Settings.scala
@@ -50,7 +50,7 @@ case class Settings(
   sbt: SbtJars                      = SbtJars(),
   _incOptions: IncOptions           = IncOptions(),
   analysis: AnalysisOptions         = AnalysisOptions(),
-  creationTime: Long                = System.currentTimeMillis()
+  creationTime: Long                = 0
 ) {
   import Settings._
 
diff --git a/tests/scala/org/pantsbuild/zinc/compiler/JarCreationSpec.scala b/tests/scala/org/pantsbuild/zinc/compiler/JarCreationSpec.scala
index 8f5f8334af9f..96dfed959a05 100644
--- a/tests/scala/org/pantsbuild/zinc/compiler/JarCreationSpec.scala
+++ b/tests/scala/org/pantsbuild/zinc/compiler/JarCreationSpec.scala
@@ -15,7 +15,7 @@ class JarCreationSpec extends WordSpec with MustMatchers {
   "JarCreationWithoutClasses" should {
     "succeed when input classes are not provided" in {
       IO.withTemporaryDirectory { tempInputDir =>
-        val filePaths = new mutable.TreeSet[(Path, Boolean)]()
+        val filePaths = new mutable.TreeSet[Path]()
 
         IO.withTemporaryDirectory { tempOutputDir =>
           val jarOutputPath = Paths.get(tempOutputDir.toString, "spec-empty-output.jar")
@@ -26,11 +26,12 @@ class JarCreationSpec extends WordSpec with MustMatchers {
       }
     }
   }
+  
   "JarCreationWithClasses" should {
     "succeed when input classes are provided" in {
       IO.withTemporaryDirectory { tempInputDir =>
         val tempFile = File.createTempFile("Temp", ".class", tempInputDir)
-        val filePaths = mutable.TreeSet((tempFile.toPath, true))
+        val filePaths = mutable.TreeSet(tempFile.toPath)
 
         IO.withTemporaryDirectory { tempOutputDir =>
           val jarOutputPath = Paths.get(tempOutputDir.toString, "spec-valid-output.jar")
@@ -48,7 +49,7 @@ class JarCreationSpec extends WordSpec with MustMatchers {
       IO.withTemporaryDirectory { tempInputDir =>
         val nestedTempDir = Files.createTempDirectory(tempInputDir.toPath, "tmp")
         val nestedTempClass = File.createTempFile("NestedTemp", ".class", nestedTempDir.toFile)
-        val filePaths = mutable.TreeSet((nestedTempDir, false), (nestedTempClass.toPath, true))
+        val filePaths = mutable.TreeSet(nestedTempDir, nestedTempClass.toPath)
         IO.withTemporaryDirectory { tempOutputDir =>
           val jarOutputPath = Paths.get(tempOutputDir.toString, "spec-valid-output.jar")