documentation and API improvements

8 files changed, 262 insertions, 593 deletions

diff --git a/plumbing/difftree/difftree.go b/plumbing/difftree/difftree.go
index 869f496..76c5f27 100644
--- a/plumbing/difftree/difftree.go
+++ b/plumbing/difftree/difftree.go
@@ -2,252 +2,24 @@ package difftree
 
 import (
 	"bytes"
-	"fmt"
-	"io"
-	"sort"
-	"strings"
 
-	"srcd.works/go-git.v4/plumbing"
 	"srcd.works/go-git.v4/plumbing/object"
+	"srcd.works/go-git.v4/utils/merkletrie"
+	"srcd.works/go-git.v4/utils/merkletrie/noder"
 )
 
-type Action int
-
-func (a Action) String() string {
-	switch a {
-	case Insert:
-		return "Insert"
-	case Delete:
-		return "Delete"
-	case Modify:
-		return "Modify"
-	default:
-		panic(fmt.Sprintf("unsupported action: %d", a))
-	}
-}
-
-const (
-	Insert Action = iota
-	Delete
-	Modify
-)
-
-type Change struct {
-	Action
-	From ChangeEntry
-	To   ChangeEntry
-}
-
-type ChangeEntry struct {
-	Name      string
-	Tree      *object.Tree
-	TreeEntry object.TreeEntry
-}
-
-func (c *Change) Files() (from, to *object.File, err error) {
-	if c.Action == Insert || c.Action == Modify {
-		to, err = c.To.Tree.TreeEntryFile(&c.To.TreeEntry)
-		if err != nil {
-			return
-		}
-
-	}
-
-	if c.Action == Delete || c.Action == Modify {
-		from, err = c.From.Tree.TreeEntryFile(&c.From.TreeEntry)
-		if err != nil {
-			return
-		}
-	}
-
-	return
-}
-
-func (c *Change) String() string {
-	return fmt.Sprintf("<Action: %s, Path: %s>", c.Action, c.name())
-}
-
-func (c *Change) name() string {
-	if c.From.Name != "" {
-		return c.From.Name
-	}
-
-	return c.To.Name
-}
-
-type Changes []*Change
-
-func newEmpty() Changes {
-	return make([]*Change, 0, 0)
-}
-
 func DiffTree(a, b *object.Tree) ([]*Change, error) {
-	if a == b {
-		return newEmpty(), nil
-	}
-
-	if a == nil || b == nil {
-		return newWithEmpty(a, b)
-	}
-
-	return newDiffTree(a, b)
-}
-
-func (c Changes) Len() int {
-	return len(c)
-}
-
-func (c Changes) Swap(i, j int) {
-	c[i], c[j] = c[j], c[i]
-}
-
-func (c Changes) Less(i, j int) bool {
-	return strings.Compare(c[i].name(), c[j].name()) < 0
-}
-
-func (c Changes) String() string {
-	var buffer bytes.Buffer
-	buffer.WriteString("[")
-	comma := ""
-	for _, v := range c {
-		buffer.WriteString(comma)
-		buffer.WriteString(v.String())
-		comma = ", "
-	}
-	buffer.WriteString("]")
-
-	return buffer.String()
-}
-
-func newWithEmpty(a, b *object.Tree) (Changes, error) {
-	changes := newEmpty()
-
-	var action Action
-	var tree *object.Tree
-	if a == nil {
-		action = Insert
-		tree = b
-	} else {
-		action = Delete
-		tree = a
-	}
-
-	w := object.NewTreeWalker(tree, true)
-	defer w.Close()
-
-	for {
-		path, entry, err := w.Next()
-		if err == io.EOF {
-			break
-		} else if err != nil {
-			return nil, fmt.Errorf("cannot get next file: %s", err)
-		}
-
-		if entry.Mode.IsDir() {
-			continue
-		}
-
-		c := &Change{Action: action}
-
-		if action == Insert {
-			c.To.Name = path
-			c.To.TreeEntry = entry
-			c.To.Tree = tree
-		} else {
-			c.From.Name = path
-			c.From.TreeEntry = entry
-			c.From.Tree = tree
-		}
-
-		changes = append(changes, c)
-	}
-
-	return changes, nil
-}
-
-// FIXME: this is very inefficient, but correct.
-// The proper way to do this is to implement a diff-tree algorithm,
-// while taking advantage of the tree hashes to avoid traversing
-// subtrees when the hash is equal in both inputs.
-func newDiffTree(a, b *object.Tree) ([]*Change, error) {
-	var result []*Change
-
-	aChanges, err := newWithEmpty(a, nil)
-	if err != nil {
-		return nil, fmt.Errorf("cannot create nil-diff of source tree: %s", err)
-	}
-	sort.Sort(aChanges)
+	from := newTreeNoder(a)
+	to := newTreeNoder(b)
 
-	bChanges, err := newWithEmpty(nil, b)
-	if err != nil {
-		return nil, fmt.Errorf("cannot create nil-diff of destination tree: %s", err)
-	}
-	sort.Sort(bChanges)
-
-	for len(aChanges) > 0 && len(bChanges) > 0 {
-		switch comp := strings.Compare(aChanges[0].name(), bChanges[0].name()); {
-		case comp == 0: // append as "Modify" or ignore if not changed
-			modified, err := hasChange(a, b, aChanges[0].name())
-			if err != nil {
-				return nil, err
-			}
-
-			if modified {
-				c := mergeInsertAndDeleteIntoModify(aChanges[0], bChanges[0])
-				result = append(result, c)
-			}
-
-			aChanges = aChanges[1:]
-			bChanges = bChanges[1:]
-		case comp < 0: // delete first a change
-			result = append(result, aChanges[0])
-			aChanges = aChanges[1:]
-		case comp > 0: // insert first b change
-			result = append(result, bChanges[0])
-			bChanges = bChanges[1:]
-		}
+	hashEqual := func(a, b noder.Hasher) bool {
+		return bytes.Equal(a.Hash(), b.Hash())
 	}
 
-	// append all remaining changes in aChanges, if any, as deletes
-	// append all remaining changes in bChanges, if any, as inserts
-	result = append(result, aChanges...)
-	result = append(result, bChanges...)
-
-	return result, nil
-}
-
-func mergeInsertAndDeleteIntoModify(a, b *Change) *Change {
-	c := &Change{Action: Modify}
-	c.From.Name = a.From.Name
-	c.From.Tree = a.From.Tree
-	c.From.TreeEntry = a.From.TreeEntry
-	c.To.Name = b.To.Name
-	c.To.Tree = b.To.Tree
-	c.To.TreeEntry = b.To.TreeEntry
-
-	return c
-}
-
-func hasChange(a, b *object.Tree, path string) (bool, error) {
-	ha, err := hash(a, path)
-	if err != nil {
-		return false, err
-	}
-
-	hb, err := hash(b, path)
-	if err != nil {
-		return false, err
-	}
-
-	return ha != hb, nil
-}
-
-func hash(tree *object.Tree, path string) (plumbing.Hash, error) {
-	file, err := tree.File(path)
+	merkletrieChanges, err := merkletrie.DiffTree(from, to, hashEqual)
 	if err != nil {
-		var empty plumbing.Hash
-		return empty, fmt.Errorf("cannot find file %s in tree: %s", path, err)
+		return nil, err
 	}
 
-	return file.Hash, nil
+	return newChanges(merkletrieChanges)
 }
diff --git a/plumbing/difftree/difftree_test.go b/plumbing/difftree/difftree_test.go
index 7679d0f..e2519b3 100644
--- a/plumbing/difftree/difftree_test.go
+++ b/plumbing/difftree/difftree_test.go
@@ -4,14 +4,15 @@ import (
 	"sort"
 	"testing"
 
-	"github.com/src-d/go-git-fixtures"
 	"srcd.works/go-git.v4/plumbing"
 	"srcd.works/go-git.v4/plumbing/format/packfile"
 	"srcd.works/go-git.v4/plumbing/object"
 	"srcd.works/go-git.v4/plumbing/storer"
 	"srcd.works/go-git.v4/storage/filesystem"
 	"srcd.works/go-git.v4/storage/memory"
+	"srcd.works/go-git.v4/utils/merkletrie"
 
+	"github.com/src-d/go-git-fixtures"
 	. "gopkg.in/check.v1"
 )
 
@@ -33,12 +34,6 @@ func (s *DiffTreeSuite) SetUpSuite(c *C) {
 	s.cache = make(map[string]storer.EncodedObjectStorer)
 }
 
-func (s *DiffTreeSuite) tree(c *C, h plumbing.Hash) *object.Tree {
-	t, err := object.GetTree(s.Storer, h)
-	c.Assert(err, IsNil)
-	return t
-}
-
 func (s *DiffTreeSuite) commitFromStorer(c *C, sto storer.EncodedObjectStorer,
 	h plumbing.Hash) *object.Commit {
 
@@ -76,108 +71,48 @@ func (s *DiffTreeSuite) storageFromPackfile(f *fixtures.Fixture) storer.EncodedO
 
 var _ = Suite(&DiffTreeSuite{})
 
-func (s *DiffTreeSuite) TestActionString(c *C) {
-	expected := "Insert"
-	action := Insert
-	obtained := action.String()
-	c.Assert(obtained, Equals, expected)
-
-	expected = "Delete"
-	action = Delete
-	obtained = action.String()
-	c.Assert(obtained, Equals, expected)
-
-	expected = "Modify"
-	action = Modify
-	obtained = action.String()
-	c.Assert(obtained, Equals, expected)
-
-	action = 37
-	c.Assert(func() { _ = action.String() },
-		PanicMatches, "unsupported action: 37")
-}
-
-func (s *DiffTreeSuite) TestChangeFilesInsert(c *C) {
-	tree := s.tree(c, plumbing.NewHash("a8d315b2b1c615d43042c3a62402b8a54288cf5c"))
-
-	change := &Change{Action: Insert}
-	change.To.Name = "json/long.json"
-	change.To.Tree = tree
-	change.To.TreeEntry.Hash = plumbing.NewHash("49c6bb89b17060d7b4deacb7b338fcc6ea2352a9")
-
-	from, to, err := change.Files()
-	c.Assert(err, IsNil)
-	c.Assert(from, IsNil)
-	c.Assert(to.ID(), Equals, change.To.TreeEntry.Hash)
-}
-
-func (s *DiffTreeSuite) TestChangeFilesDelete(c *C) {
-	tree := s.tree(c, plumbing.NewHash("a8d315b2b1c615d43042c3a62402b8a54288cf5c"))
-
-	change := &Change{Action: Delete}
-	change.From.Name = "json/long.json"
-	change.From.Tree = tree
-	change.From.TreeEntry.Hash = plumbing.NewHash("49c6bb89b17060d7b4deacb7b338fcc6ea2352a9")
-
-	from, to, err := change.Files()
-	c.Assert(err, IsNil)
-	c.Assert(to, IsNil)
-	c.Assert(from.ID(), Equals, change.From.TreeEntry.Hash)
-}
-
-func (s *DiffTreeSuite) TestChangeFilesModify(c *C) {
-	tree := s.tree(c, plumbing.NewHash("a8d315b2b1c615d43042c3a62402b8a54288cf5c"))
-
-	change := &Change{Action: Modify}
-	change.To.Name = "json/long.json"
-	change.To.Tree = tree
-	change.To.TreeEntry.Hash = plumbing.NewHash("49c6bb89b17060d7b4deacb7b338fcc6ea2352a9")
-	change.From.Name = "json/long.json"
-	change.From.Tree = tree
-	change.From.TreeEntry.Hash = plumbing.NewHash("9a48f23120e880dfbe41f7c9b7b708e9ee62a492")
-
-	from, to, err := change.Files()
-	c.Assert(err, IsNil)
-	c.Assert(to.ID(), Equals, change.To.TreeEntry.Hash)
-	c.Assert(from.ID(), Equals, change.From.TreeEntry.Hash)
+type expectChange struct {
+	Action merkletrie.Action
+	Name   string
 }
 
-func (s *DiffTreeSuite) TestChangeString(c *C) {
-	expected := "<Action: Insert, Path: foo>"
-	change := &Change{Action: Insert}
-	change.From.Name = "foo"
-
-	obtained := change.String()
-	c.Assert(obtained, Equals, expected)
+func assertChanges(a Changes, c *C) {
+	for _, changes := range a {
+		action, err := changes.Action()
+		c.Assert(err, IsNil)
+		switch action {
+		case merkletrie.Insert:
+			c.Assert(changes.From.Tree, IsNil)
+			c.Assert(changes.To.Tree, NotNil)
+		case merkletrie.Delete:
+			c.Assert(changes.From.Tree, NotNil)
+			c.Assert(changes.To.Tree, IsNil)
+		case merkletrie.Modify:
+			c.Assert(changes.From.Tree, NotNil)
+			c.Assert(changes.To.Tree, NotNil)
+		default:
+			c.Fatalf("unknown action: %d", action)
+		}
+	}
 }
 
-func (s *DiffTreeSuite) TestChangesString(c *C) {
-	expected := "[]"
-	changes := newEmpty()
-	obtained := changes.String()
-	c.Assert(obtained, Equals, expected)
-
-	expected = "[<Action: Modify, Path: bla>]"
-	changes = make([]*Change, 1)
-	changes[0] = &Change{Action: Modify}
-	changes[0].From.Name = "bla"
+func equalChanges(a Changes, b []expectChange, c *C) bool {
+	if len(a) != len(b) {
+		return false
+	}
 
-	obtained = changes.String()
-	c.Assert(obtained, Equals, expected)
+	sort.Sort(a)
 
-	expected = "[<Action: Modify, Path: bla>, <Action: Insert, Path: foo/bar>]"
-	changes = make([]*Change, 2)
-	changes[0] = &Change{Action: Modify}
-	changes[0].From.Name = "bla"
-	changes[1] = &Change{Action: Insert}
-	changes[1].From.Name = "foo/bar"
-	obtained = changes.String()
-	c.Assert(obtained, Equals, expected)
-}
+	for i, va := range a {
+		vb := b[i]
+		action, err := va.Action()
+		c.Assert(err, IsNil)
+		if action != vb.Action || va.name() != vb.Name {
+			return false
+		}
+	}
 
-type expectChange struct {
-	Action Action
-	Name   string
+	return true
 }
 
 func (s *DiffTreeSuite) TestDiffTree(c *C) {
@@ -186,186 +121,209 @@ func (s *DiffTreeSuite) TestDiffTree(c *C) {
 		commit1    string         // the commit of the first tree
 		commit2    string         // the commit of the second tree
 		expected   []expectChange // the expected list of []changeExpect
-	}{{
-		"https://github.com/dezfowler/LiteMock.git",
-		"",
-		"",
-		[]expectChange{},
-	}, {
-		"https://github.com/dezfowler/LiteMock.git",
-		"b7965eaa2c4f245d07191fe0bcfe86da032d672a",
-		"b7965eaa2c4f245d07191fe0bcfe86da032d672a",
-		[]expectChange{},
-	}, {
-		"https://github.com/dezfowler/LiteMock.git",
-		"",
-		"b7965eaa2c4f245d07191fe0bcfe86da032d672a",
-		[]expectChange{
-			{Action: Insert, Name: "README"},
+	}{
+		{
+			"https://github.com/dezfowler/LiteMock.git",
+			"",
+			"",
+			[]expectChange{},
+		},
+		{
+			"https://github.com/dezfowler/LiteMock.git",
+			"b7965eaa2c4f245d07191fe0bcfe86da032d672a",
+			"b7965eaa2c4f245d07191fe0bcfe86da032d672a",
+			[]expectChange{},
+		},
+		{
+			"https://github.com/dezfowler/LiteMock.git",
+			"",
+			"b7965eaa2c4f245d07191fe0bcfe86da032d672a",
+			[]expectChange{
+				{Action: merkletrie.Insert, Name: "README"},
+			},
 		},
-	}, {
-		"https://github.com/dezfowler/LiteMock.git",
-		"b7965eaa2c4f245d07191fe0bcfe86da032d672a",
-		"",
-		[]expectChange{
-			{Action: Delete, Name: "README"},
+		{
+			"https://github.com/dezfowler/LiteMock.git",
+			"b7965eaa2c4f245d07191fe0bcfe86da032d672a",
+			"",
+			[]expectChange{
+				{Action: merkletrie.Delete, Name: "README"},
+			},
 		},
-	}, {
-		"https://github.com/githubtraining/example-branches.git",
-		"",
-		"f0eb272cc8f77803478c6748103a1450aa1abd37",
-		[]expectChange{
-			{Action: Insert, Name: "README.md"},
+		{
+			"https://github.com/githubtraining/example-branches.git",
+			"",
+			"f0eb272cc8f77803478c6748103a1450aa1abd37",
+			[]expectChange{
+				{Action: merkletrie.Insert, Name: "README.md"},
+			},
 		},
-	}, {
-		"https://github.com/githubtraining/example-branches.git",
-		"f0eb272cc8f77803478c6748103a1450aa1abd37",
-		"",
-		[]expectChange{
-			{Action: Delete, Name: "README.md"},
+		{
+			"https://github.com/githubtraining/example-branches.git",
+			"f0eb272cc8f77803478c6748103a1450aa1abd37",
+			"",
+			[]expectChange{
+				{Action: merkletrie.Delete, Name: "README.md"},
+			},
 		},
-	}, {
-		"https://github.com/githubtraining/example-branches.git",
-		"f0eb272cc8f77803478c6748103a1450aa1abd37",
-		"f0eb272cc8f77803478c6748103a1450aa1abd37",
-		[]expectChange{},
-	}, {
-		"https://github.com/github/gem-builder.git",
-		"",
-		"9608eed92b3839b06ebf72d5043da547de10ce85",
-		[]expectChange{
-			{Action: Insert, Name: "README"},
-			{Action: Insert, Name: "gem_builder.rb"},
-			{Action: Insert, Name: "gem_eval.rb"},
+		{
+			"https://github.com/githubtraining/example-branches.git",
+			"f0eb272cc8f77803478c6748103a1450aa1abd37",
+			"f0eb272cc8f77803478c6748103a1450aa1abd37",
+			[]expectChange{},
 		},
-	}, {
-		"https://github.com/github/gem-builder.git",
-		"9608eed92b3839b06ebf72d5043da547de10ce85",
-		"",
-		[]expectChange{
-			{Action: Delete, Name: "README"},
-			{Action: Delete, Name: "gem_builder.rb"},
-			{Action: Delete, Name: "gem_eval.rb"},
+		{
+			"https://github.com/github/gem-builder.git",
+			"",
+			"9608eed92b3839b06ebf72d5043da547de10ce85",
+			[]expectChange{
+				{Action: merkletrie.Insert, Name: "README"},
+				{Action: merkletrie.Insert, Name: "gem_builder.rb"},
+				{Action: merkletrie.Insert, Name: "gem_eval.rb"},
+			},
 		},
-	}, {
-		"https://github.com/github/gem-builder.git",
-		"9608eed92b3839b06ebf72d5043da547de10ce85",
-		"9608eed92b3839b06ebf72d5043da547de10ce85",
-		[]expectChange{},
-	}, {
-		"https://github.com/toqueteos/ts3.git",
-		"",
-		"764e914b75d6d6df1fc5d832aa9840f590abf1bb",
-		[]expectChange{
-			{Action: Insert, Name: "README.markdown"},
-			{Action: Insert, Name: "examples/bot.go"},
-			{Action: Insert, Name: "examples/raw_shell.go"},
-			{Action: Insert, Name: "helpers.go"},
-			{Action: Insert, Name: "ts3.go"},
+		{
+			"https://github.com/github/gem-builder.git",
+			"9608eed92b3839b06ebf72d5043da547de10ce85",
+			"",
+			[]expectChange{
+				{Action: merkletrie.Delete, Name: "README"},
+				{Action: merkletrie.Delete, Name: "gem_builder.rb"},
+				{Action: merkletrie.Delete, Name: "gem_eval.rb"},
+			},
 		},
-	}, {
-		"https://github.com/toqueteos/ts3.git",
-		"764e914b75d6d6df1fc5d832aa9840f590abf1bb",
-		"",
-		[]expectChange{
-			{Action: Delete, Name: "README.markdown"},
-			{Action: Delete, Name: "examples/bot.go"},
-			{Action: Delete, Name: "examples/raw_shell.go"},
-			{Action: Delete, Name: "helpers.go"},
-			{Action: Delete, Name: "ts3.go"},
+		{
+			"https://github.com/github/gem-builder.git",
+			"9608eed92b3839b06ebf72d5043da547de10ce85",
+			"9608eed92b3839b06ebf72d5043da547de10ce85",
+			[]expectChange{},
 		},
-	}, {
-		"https://github.com/toqueteos/ts3.git",
-		"764e914b75d6d6df1fc5d832aa9840f590abf1bb",
-		"764e914b75d6d6df1fc5d832aa9840f590abf1bb",
-		[]expectChange{},
-	}, {
-		"https://github.com/github/gem-builder.git",
-		"9608eed92b3839b06ebf72d5043da547de10ce85",
-		"6c41e05a17e19805879689414026eb4e279f7de0",
-		[]expectChange{
-			{Action: Modify, Name: "gem_eval.rb"},
+		{
+			"https://github.com/toqueteos/ts3.git",
+			"",
+			"764e914b75d6d6df1fc5d832aa9840f590abf1bb",
+			[]expectChange{
+				{Action: merkletrie.Insert, Name: "README.markdown"},
+				{Action: merkletrie.Insert, Name: "examples/bot.go"},
+				{Action: merkletrie.Insert, Name: "examples/raw_shell.go"},
+				{Action: merkletrie.Insert, Name: "helpers.go"},
+				{Action: merkletrie.Insert, Name: "ts3.go"},
+			},
 		},
-	}, {
-		"https://github.com/github/gem-builder.git",
-		"6c41e05a17e19805879689414026eb4e279f7de0",
-		"89be3aac2f178719c12953cc9eaa23441f8d9371",
-		[]expectChange{
-			{Action: Modify, Name: "gem_eval.rb"},
-			{Action: Insert, Name: "gem_eval_test.rb"},
-			{Action: Insert, Name: "security.rb"},
-			{Action: Insert, Name: "security_test.rb"},
+		{
+			"https://github.com/toqueteos/ts3.git",
+			"764e914b75d6d6df1fc5d832aa9840f590abf1bb",
+			"",
+			[]expectChange{
+				{Action: merkletrie.Delete, Name: "README.markdown"},
+				{Action: merkletrie.Delete, Name: "examples/bot.go"},
+				{Action: merkletrie.Delete, Name: "examples/raw_shell.go"},
+				{Action: merkletrie.Delete, Name: "helpers.go"},
+				{Action: merkletrie.Delete, Name: "ts3.go"},
+			},
 		},
-	}, {
-		"https://github.com/github/gem-builder.git",
-		"89be3aac2f178719c12953cc9eaa23441f8d9371",
-		"597240b7da22d03ad555328f15abc480b820acc0",
-		[]expectChange{
-			{Action: Modify, Name: "gem_eval.rb"},
+		{
+			"https://github.com/toqueteos/ts3.git",
+			"764e914b75d6d6df1fc5d832aa9840f590abf1bb",
+			"764e914b75d6d6df1fc5d832aa9840f590abf1bb",
+			[]expectChange{},
 		},
-	}, {
-		"https://github.com/github/gem-builder.git",
-		"597240b7da22d03ad555328f15abc480b820acc0",
-		"0260380e375d2dd0e1a8fcab15f91ce56dbe778e",
-		[]expectChange{
-			{Action: Modify, Name: "gem_eval.rb"},
-			{Action: Modify, Name: "gem_eval_test.rb"},
-			{Action: Insert, Name: "lazy_dir.rb"},
-			{Action: Insert, Name: "lazy_dir_test.rb"},
-			{Action: Modify, Name: "security.rb"},
-			{Action: Modify, Name: "security_test.rb"},
+		{
+			"https://github.com/github/gem-builder.git",
+			"9608eed92b3839b06ebf72d5043da547de10ce85",
+			"6c41e05a17e19805879689414026eb4e279f7de0",
+			[]expectChange{
+				{Action: merkletrie.Modify, Name: "gem_eval.rb"},
+			},
 		},
-	}, {
-		"https://github.com/github/gem-builder.git",
-		"0260380e375d2dd0e1a8fcab15f91ce56dbe778e",
-		"597240b7da22d03ad555328f15abc480b820acc0",
-		[]expectChange{
-			{Action: Modify, Name: "gem_eval.rb"},
-			{Action: Modify, Name: "gem_eval_test.rb"},
-			{Action: Delete, Name: "lazy_dir.rb"},
-			{Action: Delete, Name: "lazy_dir_test.rb"},
-			{Action: Modify, Name: "security.rb"},
-			{Action: Modify, Name: "security_test.rb"},
+		{
+			"https://github.com/github/gem-builder.git",
+			"6c41e05a17e19805879689414026eb4e279f7de0",
+			"89be3aac2f178719c12953cc9eaa23441f8d9371",
+			[]expectChange{
+				{Action: merkletrie.Modify, Name: "gem_eval.rb"},
+				{Action: merkletrie.Insert, Name: "gem_eval_test.rb"},
+				{Action: merkletrie.Insert, Name: "security.rb"},
+				{Action: merkletrie.Insert, Name: "security_test.rb"},
+			},
 		},
-	}, {
-		"https://github.com/github/gem-builder.git",
-		"0260380e375d2dd0e1a8fcab15f91ce56dbe778e",
-		"ca9fd470bacb6262eb4ca23ee48bb2f43711c1ff",
-		[]expectChange{
-			{Action: Modify, Name: "gem_eval.rb"},
-			{Action: Modify, Name: "security.rb"},
-			{Action: Modify, Name: "security_test.rb"},
+		{
+			"https://github.com/github/gem-builder.git",
+			"89be3aac2f178719c12953cc9eaa23441f8d9371",
+			"597240b7da22d03ad555328f15abc480b820acc0",
+			[]expectChange{
+				{Action: merkletrie.Modify, Name: "gem_eval.rb"},
+			},
 		},
-	}, {
-		"https://github.com/github/gem-builder.git",
-		"fe3c86745f887c23a0d38c85cfd87ca957312f86",
-		"b7e3f636febf7a0cd3ab473b6d30081786d2c5b6",
-		[]expectChange{
-			{Action: Modify, Name: "gem_eval.rb"},
-			{Action: Modify, Name: "gem_eval_test.rb"},
-			{Action: Insert, Name: "git_mock"},
-			{Action: Modify, Name: "lazy_dir.rb"},
-			{Action: Modify, Name: "lazy_dir_test.rb"},
-			{Action: Modify, Name: "security.rb"},
+		{
+			"https://github.com/github/gem-builder.git",
+			"597240b7da22d03ad555328f15abc480b820acc0",
+			"0260380e375d2dd0e1a8fcab15f91ce56dbe778e",
+			[]expectChange{
+				{Action: merkletrie.Modify, Name: "gem_eval.rb"},
+				{Action: merkletrie.Modify, Name: "gem_eval_test.rb"},
+				{Action: merkletrie.Insert, Name: "lazy_dir.rb"},
+				{Action: merkletrie.Insert, Name: "lazy_dir_test.rb"},
+				{Action: merkletrie.Modify, Name: "security.rb"},
+				{Action: merkletrie.Modify, Name: "security_test.rb"},
+			},
 		},
-	}, {
-		"https://github.com/rumpkernel/rumprun-xen.git",
-		"1831e47b0c6db750714cd0e4be97b5af17fb1eb0",
-		"51d8515578ea0c88cc8fc1a057903675cf1fc16c",
-		[]expectChange{
-			{Action: Modify, Name: "Makefile"},
-			{Action: Modify, Name: "netbsd_init.c"},
-			{Action: Modify, Name: "rumphyper_stubs.c"},
-			{Action: Delete, Name: "sysproxy.c"},
+		{
+			"https://github.com/github/gem-builder.git",
+			"0260380e375d2dd0e1a8fcab15f91ce56dbe778e",
+			"597240b7da22d03ad555328f15abc480b820acc0",
+			[]expectChange{
+				{Action: merkletrie.Modify, Name: "gem_eval.rb"},
+				{Action: merkletrie.Modify, Name: "gem_eval_test.rb"},
+				{Action: merkletrie.Delete, Name: "lazy_dir.rb"},
+				{Action: merkletrie.Delete, Name: "lazy_dir_test.rb"},
+				{Action: merkletrie.Modify, Name: "security.rb"},
+				{Action: merkletrie.Modify, Name: "security_test.rb"},
+			},
 		},
-	}, {
-		"https://github.com/rumpkernel/rumprun-xen.git",
-		"1831e47b0c6db750714cd0e4be97b5af17fb1eb0",
-		"e13e678f7ee9badd01b120889e0ec5fdc8ae3802",
-		[]expectChange{
-			{Action: Modify, Name: "app-tools/rumprun"},
+		{
+			"https://github.com/github/gem-builder.git",
+			"0260380e375d2dd0e1a8fcab15f91ce56dbe778e",
+			"ca9fd470bacb6262eb4ca23ee48bb2f43711c1ff",
+			[]expectChange{
+				{Action: merkletrie.Modify, Name: "gem_eval.rb"},
+				{Action: merkletrie.Modify, Name: "security.rb"},
+				{Action: merkletrie.Modify, Name: "security_test.rb"},
+			},
 		},
-	}} {
+		{
+			"https://github.com/github/gem-builder.git",
+			"fe3c86745f887c23a0d38c85cfd87ca957312f86",
+			"b7e3f636febf7a0cd3ab473b6d30081786d2c5b6",
+			[]expectChange{
+				{Action: merkletrie.Modify, Name: "gem_eval.rb"},
+				{Action: merkletrie.Modify, Name: "gem_eval_test.rb"},
+				{Action: merkletrie.Insert, Name: "git_mock"},
+				{Action: merkletrie.Modify, Name: "lazy_dir.rb"},
+				{Action: merkletrie.Modify, Name: "lazy_dir_test.rb"},
+				{Action: merkletrie.Modify, Name: "security.rb"},
+			},
+		},
+		{
+			"https://github.com/rumpkernel/rumprun-xen.git",
+			"1831e47b0c6db750714cd0e4be97b5af17fb1eb0",
+			"51d8515578ea0c88cc8fc1a057903675cf1fc16c",
+			[]expectChange{
+				{Action: merkletrie.Modify, Name: "Makefile"},
+				{Action: merkletrie.Modify, Name: "netbsd_init.c"},
+				{Action: merkletrie.Modify, Name: "rumphyper_stubs.c"},
+				{Action: merkletrie.Delete, Name: "sysproxy.c"},
+			},
+		},
+		{
+			"https://github.com/rumpkernel/rumprun-xen.git",
+			"1831e47b0c6db750714cd0e4be97b5af17fb1eb0",
+			"e13e678f7ee9badd01b120889e0ec5fdc8ae3802",
+			[]expectChange{
+				{Action: merkletrie.Modify, Name: "app-tools/rumprun"},
+			},
+		},
+	} {
 		f := fixtures.ByURL(t.repository).One()
 		sto := s.storageFromPackfile(f)
 
@@ -388,43 +346,10 @@ func (s *DiffTreeSuite) TestDiffTree(c *C) {
 		obtained, err := DiffTree(tree1, tree2)
 		c.Assert(err, IsNil,
 			Commentf("subtest %d: unable to calculate difftree: %s", i, err))
-		c.Assert(equalChanges(obtained, t.expected), Equals, true,
+		c.Assert(equalChanges(obtained, t.expected, c), Equals, true,
 			Commentf("subtest:%d\nrepo=%s\ncommit1=%s\ncommit2=%s\nexpected=%s\nobtained=%s",
 				i, t.repository, t.commit1, t.commit2, t.expected, obtained))
 
 		assertChanges(obtained, c)
 	}
 }
-
-func assertChanges(a Changes, c *C) {
-	for _, changes := range a {
-		switch changes.Action {
-		case Insert:
-			c.Assert(changes.From.Tree, IsNil)
-			c.Assert(changes.To.Tree, NotNil)
-		case Delete:
-			c.Assert(changes.From.Tree, NotNil)
-			c.Assert(changes.To.Tree, IsNil)
-		case Modify:
-			c.Assert(changes.From.Tree, NotNil)
-			c.Assert(changes.To.Tree, NotNil)
-		}
-	}
-}
-
-func equalChanges(a Changes, b []expectChange) bool {
-	if len(a) != len(b) {
-		return false
-	}
-
-	sort.Sort(a)
-
-	for i, va := range a {
-		vb := b[i]
-		if va.Action != vb.Action || va.name() != vb.Name {
-			return false
-		}
-	}
-
-	return true
-}
diff --git a/plumbing/format/index/encoder.go b/plumbing/format/index/encoder.go
index 4699d43..bdb10c1 100644
--- a/plumbing/format/index/encoder.go
+++ b/plumbing/format/index/encoder.go
@@ -62,7 +62,7 @@ func (e *Encoder) encodeHeader(idx *Index) error {
 }
 
 func (e *Encoder) encodeEntries(idx *Index) error {
-	sort.Sort(ByName(idx.Entries))
+	sort.Sort(byName(idx.Entries))
 
 	for _, entry := range idx.Entries {
 		if err := e.encodeEntry(&entry); err != nil {
@@ -143,8 +143,8 @@ func (e *Encoder) encodeFooter() error {
 	return binary.Write(e.w, e.hash.Sum(nil))
 }
 
-type ByName []Entry
+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 }
+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/object/file_test.go b/plumbing/object/file_test.go
index 426fa8f..ff01c9f 100644
--- a/plumbing/object/file_test.go
+++ b/plumbing/object/file_test.go
@@ -249,7 +249,9 @@ func (s *FileSuite) TestFileIter(c *C) {
 }
 
 func (s *FileSuite) TestFileIterSubmodule(c *C) {
-	st, err := filesystem.NewStorage(fixtures.ByTag("submodule").One().DotGit())
+	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")
diff --git a/plumbing/object/tree_test.go b/plumbing/object/tree_test.go
index 0ddf391..8ea31bb 100644
--- a/plumbing/object/tree_test.go
+++ b/plumbing/object/tree_test.go
@@ -266,7 +266,8 @@ func (s *TreeSuite) TestTreeWalkerNextNonRecursive(c *C) {
 }
 
 func (s *TreeSuite) TestTreeWalkerNextSubmodule(c *C) {
-	st, err := filesystem.NewStorage(fixtures.ByTag("submodule").One().DotGit())
+	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")
@@ -284,6 +285,8 @@ func (s *TreeSuite) TestTreeWalkerNextSubmodule(c *C) {
 
 	var count int
 	walker := NewTreeWalker(tree, true)
+	defer walker.Close()
+
 	for {
 		name, entry, err := walker.Next()
 		if err == io.EOF {
diff --git a/plumbing/storer/reference.go b/plumbing/storer/reference.go
index 40474f9..692fe88 100644
--- a/plumbing/storer/reference.go
+++ b/plumbing/storer/reference.go
@@ -18,6 +18,7 @@ type ReferenceStorer interface {
 	SetReference(*plumbing.Reference) error
 	Reference(plumbing.ReferenceName) (*plumbing.Reference, error)
 	IterReferences() (ReferenceIter, error)
+	RemoveReference(plumbing.ReferenceName) error
 }
 
 // ReferenceIter is a generic closable interface for iterating over references
diff --git a/plumbing/transport/file/common_test.go b/plumbing/transport/file/common_test.go
index 3dc4500..4f3ae8f 100644
--- a/plumbing/transport/file/common_test.go
+++ b/plumbing/transport/file/common_test.go
@@ -1,6 +1,7 @@
 package file
 
 import (
+	"io/ioutil"
 	"os"
 	"os/exec"
 	"path/filepath"
@@ -8,13 +9,13 @@ import (
 	"github.com/src-d/go-git-fixtures"
 
 	. "gopkg.in/check.v1"
-	"io/ioutil"
 )
 
 type CommonSuite struct {
 	fixtures.Suite
 	ReceivePackBin string
 	UploadPackBin  string
+	tmpDir         string // to be removed at teardown
 }
 
 var _ = Suite(&CommonSuite{})
@@ -26,14 +27,20 @@ func (s *CommonSuite) SetUpSuite(c *C) {
 		c.Skip("git command not found")
 	}
 
-	binDir, err := ioutil.TempDir(os.TempDir(), "")
+	var err error
+	s.tmpDir, err = ioutil.TempDir("", "")
 	c.Assert(err, IsNil)
-	s.ReceivePackBin = filepath.Join(binDir, "git-receive-pack")
-	s.UploadPackBin = filepath.Join(binDir, "git-upload-pack")
-	bin := filepath.Join(binDir, "go-git")
+	s.ReceivePackBin = filepath.Join(s.tmpDir, "git-receive-pack")
+	s.UploadPackBin = filepath.Join(s.tmpDir, "git-upload-pack")
+	bin := filepath.Join(s.tmpDir, "go-git")
 	cmd := exec.Command("go", "build", "-o", bin,
 		"../../../cli/go-git/...")
 	c.Assert(cmd.Run(), IsNil)
 	c.Assert(os.Symlink(bin, s.ReceivePackBin), IsNil)
 	c.Assert(os.Symlink(bin, s.UploadPackBin), IsNil)
 }
+
+func (s *CommonSuite) TearDownSuite(c *C) {
+	defer s.Suite.TearDownSuite(c)
+	c.Assert(os.RemoveAll(s.tmpDir), IsNil)
+}
diff --git a/plumbing/transport/file/server_test.go b/plumbing/transport/file/server_test.go
index 775b031..a7b4e34 100644
--- a/plumbing/transport/file/server_test.go
+++ b/plumbing/transport/file/server_test.go
@@ -2,8 +2,6 @@ package file
 
 import (
 	"fmt"
-	"io"
-	"io/ioutil"
 	"os"
 	"os/exec"
 
@@ -48,8 +46,8 @@ func (s *ServerSuite) TestPush(c *C) {
 	cmd.Dir = s.SrcPath
 	cmd.Env = os.Environ()
 	cmd.Env = append(cmd.Env, "GIT_TRACE=true", "GIT_TRACE_PACKET=true")
-	stdout, stderr, err := execAndGetOutput(c, cmd)
-	c.Assert(err, IsNil, Commentf("STDOUT:\n%s\nSTDERR:\n%s\n", stdout, stderr))
+	out, err := cmd.CombinedOutput()
+	c.Assert(err, IsNil, Commentf("combined stdout and stderr:\n%s\n", out))
 }
 
 func (s *ServerSuite) TestClone(c *C) {
@@ -61,45 +59,6 @@ func (s *ServerSuite) TestClone(c *C) {
 	)
 	cmd.Env = os.Environ()
 	cmd.Env = append(cmd.Env, "GIT_TRACE=true", "GIT_TRACE_PACKET=true")
-	stdout, stderr, err := execAndGetOutput(c, cmd)
-	c.Assert(err, IsNil, Commentf("STDOUT:\n%s\nSTDERR:\n%s\n", stdout, stderr))
-}
-
-func execAndGetOutput(c *C, cmd *exec.Cmd) (stdout, stderr string, err error) {
-	sout, err := cmd.StdoutPipe()
-	c.Assert(err, IsNil)
-	serr, err := cmd.StderrPipe()
-	c.Assert(err, IsNil)
-
-	outChan, outErr := readAllAsync(sout)
-	errChan, errErr := readAllAsync(serr)
-
-	c.Assert(cmd.Start(), IsNil)
-
-	if err = cmd.Wait(); err != nil {
-		return <-outChan, <-errChan, err
-	}
-
-	if err := <-outErr; err != nil {
-		return <-outChan, <-errChan, err
-	}
-
-	return <-outChan, <-errChan, <-errErr
-}
-
-func readAllAsync(r io.Reader) (out chan string, err chan error) {
-	out = make(chan string, 1)
-	err = make(chan error, 1)
-	go func() {
-		b, e := ioutil.ReadAll(r)
-		if e != nil {
-			err <- e
-		} else {
-			err <- nil
-		}
-
-		out <- string(b)
-	}()
-
-	return out, err
+	out, err := cmd.CombinedOutput()
+	c.Assert(err, IsNil, Commentf("combined stdout and stderr:\n%s\n", out))
 }