Merge pull request #4894 from eed3si9n/wip/zipping

Fix java.util.zip.ZipException: duplicate entry

main-actions/src/main/scala/sbt/Package.scala

@@ -104,7 +104,7 @@ object Package {
     }
 
     val inputFiles = conf.sources.map(_._1).toSet
-    val inputs = conf.sources :+: lastModified(inputFiles) :+: manifest :+: HNil
+    val inputs = conf.sources.distinct :+: lastModified(inputFiles) :+: manifest :+: HNil
     cachedMakeJar(inputs)(() => exists(conf.jar))
     ()
   }

sbt/src/sbt-test/package/mappings/build.sbt

@@ -5,6 +5,7 @@ version := "0.2"
 mappings in (Compile, packageBin) ++= {
   val test = file("test")
   Seq(
+    test -> "test1",
     test -> "test1",
     test -> "test2"
   )