diff --git a/archive/changes.go b/archive/changes.go
index d94d8bc33c..9305fe2311 100644
--- a/archive/changes.go
+++ b/archive/changes.go
@@ -280,11 +280,7 @@ func ChangesDirs(newDir, oldDir string) ([]Change, error) {
 	return newRoot.Changes(oldRoot), nil
 }
 
-func ExportChanges(root, rw string) (Archive, error) {
-	changes, err := ChangesDirs(root, rw)
-	if err != nil {
-		return nil, err
-	}
+func ExportChanges(dir string, changes []Change) (Archive, error) {
 	files := make([]string, 0)
 	deletions := make([]string, 0)
 	for _, change := range changes {
@@ -297,5 +293,11 @@ func ExportChanges(root, rw string) (Archive, error) {
 			deletions = append(deletions, filepath.Join(dir, ".wh."+base))
 		}
 	}
-	return TarFilter(root, &TarOptions{Compression: Uncompressed, Recursive: false, Includes: files, CreateFiles: deletions})
+	// FIXME: Why do we create whiteout files inside Tar code ?
+	return TarFilter(dir, &TarOptions{
+		Compression: Uncompressed,
+		Includes:    files,
+		Recursive:   false,
+		CreateFiles: deletions,
+	})
 }
diff --git a/archive/changes_test.go b/archive/changes_test.go
new file mode 100644
index 0000000000..37a3869e96
--- /dev/null
+++ b/archive/changes_test.go
@@ -0,0 +1,297 @@
+package archive
+
+import (
+	"io/ioutil"
+	"os"
+	"os/exec"
+	"path"
+	"sort"
+	"testing"
+	"time"
+)
+
+func max(x, y int) int {
+	if x >= y {
+		return x
+	}
+	return y
+}
+
+func copyDir(src, dst string) error {
+	cmd := exec.Command("cp", "-a", src, dst)
+	if err := cmd.Run(); err != nil {
+		return err
+	}
+	return nil
+}
+
+// Helper to sort []Change by path
+type byPath struct{ changes []Change }
+
+func (b byPath) Less(i, j int) bool { return b.changes[i].Path < b.changes[j].Path }
+func (b byPath) Len() int           { return len(b.changes) }
+func (b byPath) Swap(i, j int)      { b.changes[i], b.changes[j] = b.changes[j], b.changes[i] }
+
+type FileType uint32
+
+const (
+	Regular FileType = iota
+	Dir
+	Symlink
+)
+
+type FileData struct {
+	filetype    FileType
+	path        string
+	contents    string
+	permissions os.FileMode
+}
+
+func createSampleDir(t *testing.T, root string) {
+	files := []FileData{
+		{Regular, "file1", "file1\n", 0600},
+		{Regular, "file2", "file2\n", 0666},
+		{Regular, "file3", "file3\n", 0404},
+		{Regular, "file4", "file4\n", 0600},
+		{Regular, "file5", "file5\n", 0600},
+		{Regular, "file6", "file6\n", 0600},
+		{Regular, "file7", "file7\n", 0600},
+		{Dir, "dir1", "", 0740},
+		{Regular, "dir1/file1-1", "file1-1\n", 01444},
+		{Regular, "dir1/file1-2", "file1-2\n", 0666},
+		{Dir, "dir2", "", 0700},
+		{Regular, "dir2/file2-1", "file2-1\n", 0666},
+		{Regular, "dir2/file2-2", "file2-2\n", 0666},
+		{Dir, "dir3", "", 0700},
+		{Regular, "dir3/file3-1", "file3-1\n", 0666},
+		{Regular, "dir3/file3-2", "file3-2\n", 0666},
+		{Dir, "dir4", "", 0700},
+		{Regular, "dir4/file3-1", "file4-1\n", 0666},
+		{Regular, "dir4/file3-2", "file4-2\n", 0666},
+		{Symlink, "symlink1", "target1", 0666},
+		{Symlink, "symlink2", "target2", 0666},
+	}
+	for _, info := range files {
+		if info.filetype == Dir {
+			if err := os.MkdirAll(path.Join(root, info.path), info.permissions); err != nil {
+				t.Fatal(err)
+			}
+		} else if info.filetype == Regular {
+			if err := ioutil.WriteFile(path.Join(root, info.path), []byte(info.contents), info.permissions); err != nil {
+				t.Fatal(err)
+			}
+		} else if info.filetype == Symlink {
+			if err := os.Symlink(info.contents, path.Join(root, info.path)); err != nil {
+				t.Fatal(err)
+			}
+		}
+	}
+}
+
+// Create an directory, copy it, make sure we report no changes between the two
+func TestChangesDirsEmpty(t *testing.T) {
+	src, err := ioutil.TempDir("", "docker-changes-test")
+	if err != nil {
+		t.Fatal(err)
+	}
+	createSampleDir(t, src)
+	dst := src + "-copy"
+	if err := copyDir(src, dst); err != nil {
+		t.Fatal(err)
+	}
+	changes, err := ChangesDirs(dst, src)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	if len(changes) != 0 {
+		t.Fatalf("Reported changes for identical dirs: %v", changes)
+	}
+	os.RemoveAll(src)
+	os.RemoveAll(dst)
+}
+
+func mutateSampleDir(t *testing.T, root string) {
+	// Remove a regular file
+	if err := os.RemoveAll(path.Join(root, "file1")); err != nil {
+		t.Fatal(err)
+	}
+
+	// Remove a directory
+	if err := os.RemoveAll(path.Join(root, "dir1")); err != nil {
+		t.Fatal(err)
+	}
+
+	// Remove a symlink
+	if err := os.RemoveAll(path.Join(root, "symlink1")); err != nil {
+		t.Fatal(err)
+	}
+
+	// Rewrite a file
+	if err := ioutil.WriteFile(path.Join(root, "file2"), []byte("fileN\n"), 0777); err != nil {
+		t.Fatal(err)
+	}
+
+	// Replace a file
+	if err := os.RemoveAll(path.Join(root, "file3")); err != nil {
+		t.Fatal(err)
+	}
+	if err := ioutil.WriteFile(path.Join(root, "file3"), []byte("fileM\n"), 0404); err != nil {
+		t.Fatal(err)
+	}
+
+	// Touch file
+	if err := os.Chtimes(path.Join(root, "file4"), time.Now(), time.Now()); err != nil {
+		t.Fatal(err)
+	}
+
+	// Replace file with dir
+	if err := os.RemoveAll(path.Join(root, "file5")); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.MkdirAll(path.Join(root, "file5"), 0666); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create new file
+	if err := ioutil.WriteFile(path.Join(root, "filenew"), []byte("filenew\n"), 0777); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create new dir
+	if err := os.MkdirAll(path.Join(root, "dirnew"), 0766); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create a new symlink
+	if err := os.Symlink("targetnew", path.Join(root, "symlinknew")); err != nil {
+		t.Fatal(err)
+	}
+
+	// Change a symlink
+	if err := os.RemoveAll(path.Join(root, "symlink2")); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.Symlink("target2change", path.Join(root, "symlink2")); err != nil {
+		t.Fatal(err)
+	}
+
+	// Replace dir with file
+	if err := os.RemoveAll(path.Join(root, "dir2")); err != nil {
+		t.Fatal(err)
+	}
+	if err := ioutil.WriteFile(path.Join(root, "dir2"), []byte("dir2\n"), 0777); err != nil {
+		t.Fatal(err)
+	}
+
+	// Touch dir
+	if err := os.Chtimes(path.Join(root, "dir3"), time.Now(), time.Now()); err != nil {
+		t.Fatal(err)
+	}
+}
+
+func TestChangesDirsMutated(t *testing.T) {
+	src, err := ioutil.TempDir("", "docker-changes-test")
+	if err != nil {
+		t.Fatal(err)
+	}
+	createSampleDir(t, src)
+	dst := src + "-copy"
+	if err := copyDir(src, dst); err != nil {
+		t.Fatal(err)
+	}
+	mutateSampleDir(t, dst)
+
+	changes, err := ChangesDirs(dst, src)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	sort.Sort(byPath{changes})
+
+	expectedChanges := []Change{
+		{"/dir1", ChangeDelete},
+		{"/dir2", ChangeModify},
+		{"/dir3", ChangeModify},
+		{"/dirnew", ChangeAdd},
+		{"/file1", ChangeDelete},
+		{"/file2", ChangeModify},
+		{"/file3", ChangeModify},
+		{"/file4", ChangeModify},
+		{"/file5", ChangeModify},
+		{"/filenew", ChangeAdd},
+		{"/symlink1", ChangeDelete},
+		{"/symlink2", ChangeModify},
+		{"/symlinknew", ChangeAdd},
+	}
+
+	i := 0
+	for ; i < max(len(changes), len(expectedChanges)); i++ {
+		if i >= len(expectedChanges) {
+			t.Fatalf("unexpected change %s\n", changes[i].String())
+		}
+		if i >= len(changes) {
+			t.Fatalf("no change for expected change %s\n", expectedChanges[i].String())
+		}
+		if changes[i].Path == expectedChanges[i].Path {
+			if changes[i] != expectedChanges[i] {
+				t.Fatalf("Wrong change for %s, expected %s, got %d\n", changes[i].Path, changes[i].String(), expectedChanges[i].String())
+			}
+		} else if changes[i].Path < expectedChanges[i].Path {
+			t.Fatalf("unexpected change %s\n", changes[i].String())
+		} else {
+			t.Fatalf("no change for expected change %s\n", expectedChanges[i].String())
+		}
+	}
+	for ; i < len(expectedChanges); i++ {
+	}
+
+	os.RemoveAll(src)
+	os.RemoveAll(dst)
+}
+
+func TestApplyLayer(t *testing.T) {
+	return // Disable this for now as it is broken
+
+	src, err := ioutil.TempDir("", "docker-changes-test")
+	if err != nil {
+		t.Fatal(err)
+	}
+	createSampleDir(t, src)
+	dst := src + "-copy"
+	if err := copyDir(src, dst); err != nil {
+		t.Fatal(err)
+	}
+	mutateSampleDir(t, dst)
+
+	changes, err := ChangesDirs(dst, src)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	layer, err := ExportChanges(dst, changes)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	layerCopy, err := NewTempArchive(layer, "")
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	if err := ApplyLayer(src, layerCopy); err != nil {
+		t.Fatal(err)
+	}
+
+	changes2, err := ChangesDirs(src, dst)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	if len(changes2) != 0 {
+		t.Fatalf("Unexpected differences after re applying mutation: %v", changes)
+	}
+
+	os.RemoveAll(src)
+	os.RemoveAll(dst)
+}
diff --git a/archive/diff.go b/archive/diff.go
index 0e4fe3fcc2..877d076c8b 100644
--- a/archive/diff.go
+++ b/archive/diff.go
@@ -49,7 +49,7 @@ func ApplyLayer(dest string, layer Archive) error {
 			rmTargetPath := filepath.Join(filepath.Dir(fullPath), rmTargetName)
 			// Remove the file targeted by the whiteout
 			log.Printf("Removing whiteout target %s", rmTargetPath)
-			_ = os.Remove(rmTargetPath)
+			_ = os.RemoveAll(rmTargetPath)
 			// Remove the whiteout itself
 			log.Printf("Removing whiteout %s", fullPath)
 			_ = os.RemoveAll(fullPath)
diff --git a/runtime.go b/runtime.go
index 5072a00fdd..bfe1aee5a7 100644
--- a/runtime.go
+++ b/runtime.go
@@ -18,7 +18,6 @@ import (
 	"os"
 	"os/exec"
 	"path"
-	"path/filepath"
 	"sort"
 	"strings"
 	"time"
@@ -739,25 +738,7 @@ func (runtime *Runtime) Diff(container *Container) (archive.Archive, error) {
 		return nil, fmt.Errorf("Error getting container rootfs %s from driver %s: %s", container.ID, container.runtime.driver, err)
 	}
 
-	files := make([]string, 0)
-	deletions := make([]string, 0)
-	for _, change := range changes {
-		if change.Kind == archive.ChangeModify || change.Kind == archive.ChangeAdd {
-			files = append(files, change.Path)
-		}
-		if change.Kind == archive.ChangeDelete {
-			base := filepath.Base(change.Path)
-			dir := filepath.Dir(change.Path)
-			deletions = append(deletions, filepath.Join(dir, ".wh."+base))
-		}
-	}
-	// FIXME: Why do we create whiteout files inside Tar code ?
-	return archive.TarFilter(cDir, &archive.TarOptions{
-		Compression: archive.Uncompressed,
-		Includes:    files,
-		Recursive:   false,
-		CreateFiles: deletions,
-	})
+	return archive.ExportChanges(cDir, changes)
 }
 
 func linkLxcStart(root string) error {