diff --git a/.travis.yml b/.travis.yml
index 84a1e2f13..3c1dc5097 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -12,7 +12,7 @@ env:
   matrix:
     - SBT_CMD=";mimaReportBinaryIssues ;scalafmtCheckAll ;headerCheck ;test:headerCheck ;whitesourceOnPush ;test:compile; publishLocal ;mainSettingsProj/test ;safeUnitTests ;otherUnitTests; doc"
     - SBT_CMD="scripted actions/* apiinfo/* compiler-project/* ivy-deps-management/* reporter/* tests/* watch/* classloader-cache/* package/*"
-    - SBT_CMD="scripted dependency-management/* plugins/* project-load/* java/* run/*"
+    - SBT_CMD="scripted dependency-management/* plugins/* project-load/* java/* run/* nio/*"
     - SBT_CMD="repoOverrideTest:scripted dependency-management/*; scripted source-dependencies/* project/*"
 
 matrix:
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 29f1319c0..75813a56e 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -10,7 +10,7 @@ object Dependencies {
   def nightlyVersion: Option[String] = sys.props.get("sbt.build.version")
 
   // sbt modules
-  private val ioVersion = nightlyVersion.getOrElse("1.3.0-M12")
+  private val ioVersion = nightlyVersion.getOrElse("1.3.0-M13")
   private val utilVersion = nightlyVersion.getOrElse("1.3.0-M8")
   private val lmVersion =
     sys.props.get("sbt.build.lm.version") match {
diff --git a/sbt/src/sbt-test/nio/file-hashes/build.sbt b/sbt/src/sbt-test/nio/file-hashes/build.sbt
index 637d5ae6d..eba843fca 100644
--- a/sbt/src/sbt-test/nio/file-hashes/build.sbt
+++ b/sbt/src/sbt-test/nio/file-hashes/build.sbt
@@ -32,10 +32,10 @@ val checkAdded = taskKey[Unit]("check that modified files are returned")
 checkAdded := Def.taskDyn {
   val files = (foo / allInputFiles).value
   val added = (foo / changedInputFiles).value.map(_.created).getOrElse(Nil)
-  if (added.isEmpty || files.sameElements(added)) Def.task(assert(true))
+  if (added.isEmpty || (files.toSet == added.toSet)) Def.task(assert(true))
   else Def.task {
     val base = baseDirectory.value / "base"
-    assert(files.sameElements(Seq("Bar.md", "Foo.txt").map(p => (base / p).toPath)))
+    assert(files.toSet == Set("Bar.md", "Foo.txt").map(p => (base / p).toPath))
     assert(added == Seq((baseDirectory.value / "base" / "Bar.md").toPath))
   }
 }.value
diff --git a/sbt/src/sbt-test/nio/legacy-filters/build.sbt b/sbt/src/sbt-test/nio/legacy-filters/build.sbt
new file mode 100644
index 000000000..2be01658b
--- /dev/null
+++ b/sbt/src/sbt-test/nio/legacy-filters/build.sbt
@@ -0,0 +1,8 @@
+Compile / excludeFilter := "Bar.scala" || "Baz.scala"
+
+val checkSources = inputKey[Unit]("Check that the compile sources match the input file names")
+checkSources := {
+  val sources = Def.spaceDelimited("").parsed.toSet
+  val actual = (Compile / unmanagedSources).value.map(_.getName).toSet
+  assert(sources == actual)
+}
diff --git a/sbt/src/sbt-test/nio/legacy-filters/src/main/scala/Bar.scala b/sbt/src/sbt-test/nio/legacy-filters/src/main/scala/Bar.scala
new file mode 100644
index 000000000..afa08f013
--- /dev/null
+++ b/sbt/src/sbt-test/nio/legacy-filters/src/main/scala/Bar.scala
@@ -0,0 +1 @@
+class Bar {
\ No newline at end of file
diff --git a/sbt/src/sbt-test/nio/legacy-filters/src/main/scala/Foo.scala b/sbt/src/sbt-test/nio/legacy-filters/src/main/scala/Foo.scala
new file mode 100644
index 000000000..43c42f145
--- /dev/null
+++ b/sbt/src/sbt-test/nio/legacy-filters/src/main/scala/Foo.scala
@@ -0,0 +1 @@
+class Foo
\ No newline at end of file
diff --git a/sbt/src/sbt-test/nio/legacy-filters/test b/sbt/src/sbt-test/nio/legacy-filters/test
new file mode 100644
index 000000000..ae779a65c
--- /dev/null
+++ b/sbt/src/sbt-test/nio/legacy-filters/test
@@ -0,0 +1,9 @@
+> checkSources Foo.scala
+
+> compile
+
+> set Compile / excludeFilter := HiddenFileFilter
+
+> checkSources Foo.scala Bar.scala
+
+-> compile
\ No newline at end of file
diff --git a/sbt/src/sbt-test/nio/make-clone/build.sbt b/sbt/src/sbt-test/nio/make-clone/build.sbt
index f10df2f02..8bee73e73 100644
--- a/sbt/src/sbt-test/nio/make-clone/build.sbt
+++ b/sbt/src/sbt-test/nio/make-clone/build.sbt
@@ -1,6 +1,8 @@
 import java.nio.file.{ Files, Path }
 import scala.sys.process._
 
+val compileOpts = settingKey[Seq[String]]("Extra compile options")
+compileOpts := { if (scala.util.Properties.isLinux) "-fPIC" :: "-std=gnu99" :: Nil else Nil }
 val compileLib = taskKey[Seq[Path]]("Compile the library")
 compileLib / sourceDirectory := sourceDirectory.value / "lib"
 compileLib / fileInputs := {
@@ -34,7 +36,8 @@ compileLib := {
       cFiles.map { file =>
         val outFile = objectDir.resolve(objectFileName(file))
         logger.info(s"Compiling $file to $outFile")
-        Seq("gcc", "-c", file.toString, s"-I$include", "-o", outFile.toString).!!
+        (Seq("gcc") ++ compileOpts.value ++
+          Seq("-c", file.toString, s"-I$include", "-o", outFile.toString)).!!
         outFile
       }
   }
@@ -87,15 +90,14 @@ compileMain := {
         case Seq(main) =>
           Files.createDirectories(outDir)
           logger.info(s"Building executable $outPath")
-          Seq(
-            "gcc",
+          (Seq("gcc") ++ compileOpts.value ++ Seq(
             main.toString,
             s"-I$include",
             "-o",
             outPath.toString,
             s"-L${library.getParent}",
             "-lfoo"
-          ).!!
+          )).!!
           outPath
         case main =>
           throw new IllegalStateException(s"multiple main files detected: ${main.mkString(",")}")