7 files changed, 98 insertions, 10 deletions
diff --git a/plumbing/format/index/encoder.go b/plumbing/format/index/encoder.go
index e5de135..bdb10c1 100644
--- a/plumbing/format/index/encoder.go
+++ b/plumbing/format/index/encoder.go
@@ -6,6 +6,7 @@ import (
 	"errors"
 	"hash"
 	"io"
+	"sort"
 	"time"
 
 	"srcd.works/go-git.v4/utils/binary"
@@ -61,6 +62,8 @@ func (e *Encoder) encodeHeader(idx *Index) error {
 }
 
 func (e *Encoder) encodeEntries(idx *Index) error {
+	sort.Sort(byName(idx.Entries))
+
 	for _, entry := range idx.Entries {
 		if err := e.encodeEntry(&entry); err != nil {
 			return err
@@ -139,3 +142,9 @@ func (e *Encoder) padEntry(wrote int) error {
 func (e *Encoder) encodeFooter() error {
 	return binary.Write(e.w, e.hash.Sum(nil))
 }
+
+type byName []Entry
+
+func (l byName) Len() int           { return len(l) }
+func (l byName) Swap(i, j int)      { l[i], l[j] = l[j], l[i] }
+func (l byName) Less(i, j int) bool { return l[i].Name < l[j].Name }
diff --git a/plumbing/format/index/encoder_test.go b/plumbing/format/index/encoder_test.go
index 914ee26..a6a0ea2 100644
--- a/plumbing/format/index/encoder_test.go
+++ b/plumbing/format/index/encoder_test.go
@@ -26,6 +26,11 @@ func (s *IndexSuite) TestEncode(c *C) {
 		}, {
 			CreatedAt:  time.Now(),
 			ModifiedAt: time.Now(),
+			Name:       "bar",
+			Size:       82,
+		}, {
+			CreatedAt:  time.Now(),
+			ModifiedAt: time.Now(),
 			Name:       strings.Repeat(" ", 20),
 			Size:       82,
 		}},
@@ -42,6 +47,11 @@ func (s *IndexSuite) TestEncode(c *C) {
 	c.Assert(err, IsNil)
 
 	c.Assert(idx, DeepEquals, output)
+
+	c.Assert(output.Entries[0].Name, Equals, strings.Repeat(" ", 20))
+	c.Assert(output.Entries[1].Name, Equals, "bar")
+	c.Assert(output.Entries[2].Name, Equals, "foo")
+
 }
 
 func (s *IndexSuite) TestEncodeUnsuportedVersion(c *C) {
diff --git a/plumbing/format/index/index.go b/plumbing/format/index/index.go
index e5dc178..a95dba2 100644
--- a/plumbing/format/index/index.go
+++ b/plumbing/format/index/index.go
@@ -36,9 +36,14 @@ const (
 // in the worktree, having information about the working files. Changes in
 // worktree are detected using this Index. The Index is also used during merges
 type Index struct {
-	Version     uint32
-	Entries     []Entry
-	Cache       *Tree
+	// Version is index version
+	Version uint32
+	// Entries collection of entries represented by this Index. The order of
+	// this collection is not guaranteed
+	Entries []Entry
+	// Cache represents the 'Cached tree' extension
+	Cache *Tree
+	// ResolveUndo represents the 'Resolve undo' extension
 	ResolveUndo *ResolveUndo
 }
 
@@ -84,7 +89,7 @@ type TreeEntry struct {
 	// Path component (relative to its parent directory)
 	Path string
 	// Entries is the number of entries in the index that is covered by the tree
-	// this entry represents
+	// this entry represents.
 	Entries int
 	// Trees is the number that represents the number of subtrees this tree has
 	Trees int
diff --git a/plumbing/object/file.go b/plumbing/object/file.go
index 35e7f24..4866777 100644
--- a/plumbing/object/file.go
+++ b/plumbing/object/file.go
@@ -81,7 +81,7 @@ func (iter *FileIter) Next() (*File, error) {
 			return nil, err
 		}
 
-		if entry.Mode.IsDir() {
+		if entry.Mode.IsDir() || entry.Mode == SubmoduleMode {
 			continue
 		}
 
diff --git a/plumbing/object/file_test.go b/plumbing/object/file_test.go
index 4c8bbb6..ff01c9f 100644
--- a/plumbing/object/file_test.go
+++ b/plumbing/object/file_test.go
@@ -247,3 +247,31 @@ func (s *FileSuite) TestFileIter(c *C) {
 
 	c.Assert(count, Equals, 1)
 }
+
+func (s *FileSuite) TestFileIterSubmodule(c *C) {
+	dotgit := fixtures.ByURL("https://github.com/git-fixtures/submodule.git").One().DotGit()
+	st, err := filesystem.NewStorage(dotgit)
+
+	c.Assert(err, IsNil)
+
+	hash := plumbing.NewHash("a692ec699bff9117c1ed91752afbb7d9d272ebef")
+	commit, err := GetCommit(st, hash)
+	c.Assert(err, IsNil)
+
+	tree, err := commit.Tree()
+	c.Assert(err, IsNil)
+
+	expected := []string{
+		".gitmodules",
+	}
+
+	var count int
+	i := tree.Files()
+	i.ForEach(func(f *File) error {
+		c.Assert(f.Name, Equals, expected[count])
+		count++
+		return nil
+	})
+
+	c.Assert(count, Equals, 1)
+}
diff --git a/plumbing/object/tree.go b/plumbing/object/tree.go
index 3bcd80a..27d8578 100644
--- a/plumbing/object/tree.go
+++ b/plumbing/object/tree.go
@@ -375,11 +375,6 @@ func (w *TreeWalker) Next() (name string, entry TreeEntry, err error) {
 			return
 		}
 
-		if entry.Mode == SubmoduleMode {
-			err = nil
-			continue
-		}
-
 		if entry.Mode.IsDir() {
 			obj, err = GetTree(w.s, entry.Hash)
 		}
diff --git a/plumbing/object/tree_test.go b/plumbing/object/tree_test.go
index be721b9..8ea31bb 100644
--- a/plumbing/object/tree_test.go
+++ b/plumbing/object/tree_test.go
@@ -4,7 +4,10 @@ import (
 	"io"
 	"os"
 
+	fixtures "github.com/src-d/go-git-fixtures"
+
 	"srcd.works/go-git.v4/plumbing"
+	"srcd.works/go-git.v4/storage/filesystem"
 
 	. "gopkg.in/check.v1"
 	"srcd.works/go-git.v4/plumbing/storer"
@@ -262,6 +265,44 @@ func (s *TreeSuite) TestTreeWalkerNextNonRecursive(c *C) {
 	c.Assert(count, Equals, 8)
 }
 
+func (s *TreeSuite) TestTreeWalkerNextSubmodule(c *C) {
+	dotgit := fixtures.ByURL("https://github.com/git-fixtures/submodule.git").One().DotGit()
+	st, err := filesystem.NewStorage(dotgit)
+	c.Assert(err, IsNil)
+
+	hash := plumbing.NewHash("a692ec699bff9117c1ed91752afbb7d9d272ebef")
+	commit, err := GetCommit(st, hash)
+	c.Assert(err, IsNil)
+
+	tree, err := commit.Tree()
+	c.Assert(err, IsNil)
+
+	expected := []string{
+		".gitmodules",
+		"basic",
+		"itself",
+	}
+
+	var count int
+	walker := NewTreeWalker(tree, true)
+	defer walker.Close()
+
+	for {
+		name, entry, err := walker.Next()
+		if err == io.EOF {
+			break
+		}
+
+		c.Assert(err, IsNil)
+		c.Assert(entry, NotNil)
+		c.Assert(name, Equals, expected[count])
+
+		count++
+	}
+
+	c.Assert(count, Equals, 3)
+}
+
 var treeWalkerExpects = []struct {
 	Path, Mode, Name, Hash, Tree string
 }{{