6 files changed, 362 insertions, 78 deletions

diff --git a/formats/index/decoder.go b/formats/index/decoder.go
index 8e37fd1..f3d4343 100644
--- a/formats/index/decoder.go
+++ b/formats/index/decoder.go
@@ -2,7 +2,9 @@ package index
 
 import (
 	"bytes"
+	"crypto/sha1"
 	"errors"
+	"hash"
 	"io"
 	"io/ioutil"
 	"strconv"
@@ -13,38 +15,42 @@ import (
 )
 
 var (
-	// IndexVersionSupported is the range of supported index versions
-	IndexVersionSupported = struct{ Min, Max uint32 }{Min: 2, Max: 4}
+	// DecodeVersionSupported is the range of supported index versions
+	DecodeVersionSupported = struct{ Min, Max uint32 }{Min: 2, Max: 4}
 
-	// ErrUnsupportedVersion is returned by Decode when the idxindex file
-	// version is not supported.
-	ErrUnsupportedVersion = errors.New("Unsuported version")
 	// ErrMalformedSignature is returned by Decode when the index header file is
 	// malformed
-	ErrMalformedSignature = errors.New("Malformed index signature file")
+	ErrMalformedSignature = errors.New("malformed index signature file")
+	// ErrInvalidChecksum is returned by Decode if the SHA1 hash missmatch with
+	// the read content
+	ErrInvalidChecksum = errors.New("invalid checksum")
 
-	indexSignature          = []byte{'D', 'I', 'R', 'C'}
-	treeExtSignature        = []byte{'T', 'R', 'E', 'E'}
-	resolveUndoExtSignature = []byte{'R', 'E', 'U', 'C'}
+	errUnknownExtension = errors.New("unknown extension")
 )
 
 const (
-	EntryExtended = 0x4000
-	EntryValid    = 0x8000
-
-	nameMask         = 0xfff
-	intentToAddMask  = 1 << 13
-	skipWorkTreeMask = 1 << 14
+	entryHeaderLength = 62
+	entryExtended     = 0x4000
+	entryValid        = 0x8000
+	nameMask          = 0xfff
+	intentToAddMask   = 1 << 13
+	skipWorkTreeMask  = 1 << 14
 )
 
+// A Decoder reads and decodes idx files from an input stream.
 type Decoder struct {
 	r         io.Reader
+	hash      hash.Hash
 	lastEntry *Entry
 }
 
 // NewDecoder returns a new decoder that reads from r.
 func NewDecoder(r io.Reader) *Decoder {
-	return &Decoder{r: r}
+	h := sha1.New()
+	return &Decoder{
+		r:    io.TeeReader(r, h),
+		hash: h,
+	}
 }
 
 // Decode reads the whole index object from its input and stores it in the
@@ -56,20 +62,20 @@ func (d *Decoder) Decode(idx *Index) error {
 		return err
 	}
 
-	idx.EntryCount, err = binary.ReadUint32(d.r)
+	entryCount, err := binary.ReadUint32(d.r)
 	if err != nil {
 		return err
 	}
 
-	if err := d.readEntries(idx); err != nil {
+	if err := d.readEntries(idx, int(entryCount)); err != nil {
 		return err
 	}
 
 	return d.readExtensions(idx)
 }
 
-func (d *Decoder) readEntries(idx *Index) error {
-	for i := 0; i < int(idx.EntryCount); i++ {
+func (d *Decoder) readEntries(idx *Index, count int) error {
+	for i := 0; i < count; i++ {
 		e, err := d.readEntry(idx)
 		if err != nil {
 			return err
@@ -86,11 +92,11 @@ func (d *Decoder) readEntry(idx *Index) (*Entry, error) {
 	e := &Entry{}
 
 	var msec, mnsec, sec, nsec uint32
+	var flags uint16
 
-	flowSize := 62
 	flow := []interface{}{
-		&msec, &mnsec,
 		&sec, &nsec,
+		&msec, &mnsec,
 		&e.Dev,
 		&e.Inode,
 		&e.Mode,
@@ -98,19 +104,19 @@ func (d *Decoder) readEntry(idx *Index) (*Entry, error) {
 		&e.GID,
 		&e.Size,
 		&e.Hash,
-		&e.Flags,
+		&flags,
 	}
 
 	if err := binary.Read(d.r, flow...); err != nil {
 		return nil, err
 	}
 
-	read := flowSize
-	e.CreatedAt = time.Unix(int64(msec), int64(mnsec))
-	e.ModifiedAt = time.Unix(int64(sec), int64(nsec))
-	e.Stage = Stage(e.Flags>>12) & 0x3
+	read := entryHeaderLength
+	e.CreatedAt = time.Unix(int64(sec), int64(nsec))
+	e.ModifiedAt = time.Unix(int64(msec), int64(mnsec))
+	e.Stage = Stage(flags>>12) & 0x3
 
-	if e.Flags&EntryExtended != 0 {
+	if flags&entryExtended != 0 {
 		extended, err := binary.ReadUint16(d.r)
 		if err != nil {
 			return nil, err
@@ -121,20 +127,21 @@ func (d *Decoder) readEntry(idx *Index) (*Entry, error) {
 		e.SkipWorktree = extended&skipWorkTreeMask != 0
 	}
 
-	if err := d.readEntryName(idx, e); err != nil {
+	if err := d.readEntryName(idx, e, flags); err != nil {
 		return nil, err
 	}
 
 	return e, d.padEntry(idx, e, read)
 }
 
-func (d *Decoder) readEntryName(idx *Index, e *Entry) error {
+func (d *Decoder) readEntryName(idx *Index, e *Entry, flags uint16) error {
 	var name string
 	var err error
 
 	switch idx.Version {
 	case 2, 3:
-		name, err = d.doReadEntryName(e)
+		len := flags & nameMask
+		name, err = d.doReadEntryName(len)
 	case 4:
 		name, err = d.doReadEntryNameV4()
 	default:
@@ -168,10 +175,8 @@ func (d *Decoder) doReadEntryNameV4() (string, error) {
 	return base + string(name), nil
 }
 
-func (d *Decoder) doReadEntryName(e *Entry) (string, error) {
-	pLen := e.Flags & nameMask
-
-	name := make([]byte, int64(pLen))
+func (d *Decoder) doReadEntryName(len uint16) (string, error) {
+	name := make([]byte, len)
 	if err := binary.Read(d.r, &name); err != nil {
 		return "", err
 	}
@@ -195,50 +200,88 @@ func (d *Decoder) padEntry(idx *Index, e *Entry, read int) error {
 	return nil
 }
 
+// TODO: support 'Split index' and 'Untracked cache' extensions, take in count
+//       that they are not supported by jgit or libgit
 func (d *Decoder) readExtensions(idx *Index) error {
+	var expected []byte
 	var err error
+
+	var header [4]byte
 	for {
-		err = d.readExtension(idx)
+		expected = d.hash.Sum(nil)
+
+		var n int
+		if n, err = io.ReadFull(d.r, header[:]); err != nil {
+			if n == 0 {
+				err = io.EOF
+			}
+
+			break
+		}
+
+		err = d.readExtension(idx, header[:])
 		if err != nil {
 			break
 		}
 	}
 
-	if err == io.EOF {
-		return nil
+	if err != errUnknownExtension {
+		return err
 	}
 
-	return err
+	return d.readChecksum(expected, header)
 }
 
-func (d *Decoder) readExtension(idx *Index) error {
-	var s = make([]byte, 4)
-	if _, err := io.ReadFull(d.r, s); err != nil {
-		return err
+func (d *Decoder) readExtension(idx *Index, header []byte) error {
+	switch {
+	case bytes.Equal(header, treeExtSignature):
+		r, err := d.getExtensionReader()
+		if err != nil {
+			return err
+		}
+
+		idx.Cache = &Tree{}
+		d := &treeExtensionDecoder{r}
+		if err := d.Decode(idx.Cache); err != nil {
+			return err
+		}
+	case bytes.Equal(header, resolveUndoExtSignature):
+		r, err := d.getExtensionReader()
+		if err != nil {
+			return err
+		}
+
+		idx.ResolveUndo = &ResolveUndo{}
+		d := &resolveUndoDecoder{r}
+		if err := d.Decode(idx.ResolveUndo); err != nil {
+			return err
+		}
+	default:
+		return errUnknownExtension
 	}
 
+	return nil
+}
+
+func (d *Decoder) getExtensionReader() (io.Reader, error) {
 	len, err := binary.ReadUint32(d.r)
 	if err != nil {
-		return err
+		return nil, err
 	}
 
-	switch {
-	case bytes.Equal(s, treeExtSignature):
-		t := &Tree{}
-		td := &treeExtensionDecoder{&io.LimitedReader{R: d.r, N: int64(len)}}
-		if err := td.Decode(t); err != nil {
-			return err
-		}
+	return &io.LimitedReader{R: d.r, N: int64(len)}, nil
+}
 
-		idx.Cache = t
-	case bytes.Equal(s, resolveUndoExtSignature):
-		ru := &ResolveUndo{}
-		rud := &resolveUndoDecoder{&io.LimitedReader{R: d.r, N: int64(len)}}
-		if err := rud.Decode(ru); err != nil {
-			return err
-		}
+func (d *Decoder) readChecksum(expected []byte, alreadyRead [4]byte) error {
+	var h core.Hash
+	copy(h[:4], alreadyRead[:])
+
+	if err := binary.Read(d.r, h[4:]); err != nil {
+		return err
+	}
 
-		idx.ResolveUndo = ru
+	if bytes.Compare(h[:], expected) != 0 {
+		return ErrInvalidChecksum
 	}
 
 	return nil
@@ -259,7 +302,7 @@ func validateHeader(r io.Reader) (version uint32, err error) {
 		return 0, err
 	}
 
-	if version < IndexVersionSupported.Min || version > IndexVersionSupported.Max {
+	if version < DecodeVersionSupported.Min || version > DecodeVersionSupported.Max {
 		return 0, ErrUnsupportedVersion
 	}
 
diff --git a/formats/index/decoder_test.go b/formats/index/decoder_test.go
index cf4c872..a05417d 100644
--- a/formats/index/decoder_test.go
+++ b/formats/index/decoder_test.go
@@ -26,7 +26,7 @@ func (s *IdxfileSuite) TestDecode(c *C) {
 	c.Assert(err, IsNil)
 
 	c.Assert(idx.Version, Equals, uint32(2))
-	c.Assert(idx.EntryCount, Equals, uint32(9))
+	c.Assert(idx.Entries, HasLen, 9)
 }
 
 func (s *IdxfileSuite) TestDecodeEntries(c *C) {
@@ -97,7 +97,7 @@ func (s *IdxfileSuite) TestDecodeMergeConflict(c *C) {
 	c.Assert(err, IsNil)
 
 	c.Assert(idx.Version, Equals, uint32(2))
-	c.Assert(idx.EntryCount, Equals, uint32(13))
+	c.Assert(idx.Entries, HasLen, 13)
 
 	expected := []struct {
 		Stage Stage
@@ -136,7 +136,7 @@ func (s *IdxfileSuite) TestDecodeExtendedV3(c *C) {
 	c.Assert(err, IsNil)
 
 	c.Assert(idx.Version, Equals, uint32(3))
-	c.Assert(idx.EntryCount, Equals, uint32(11))
+	c.Assert(idx.Entries, HasLen, 11)
 
 	c.Assert(idx.Entries[6].Name, Equals, "intent-to-add")
 	c.Assert(idx.Entries[6].IntentToAdd, Equals, true)
@@ -153,7 +153,7 @@ func (s *IdxfileSuite) TestDecodeResolveUndo(c *C) {
 	c.Assert(err, IsNil)
 
 	c.Assert(idx.Version, Equals, uint32(2))
-	c.Assert(idx.EntryCount, Equals, uint32(8))
+	c.Assert(idx.Entries, HasLen, 8)
 
 	ru := idx.ResolveUndo
 	c.Assert(ru.Entries, HasLen, 2)
@@ -178,7 +178,7 @@ func (s *IdxfileSuite) TestDecodeV4(c *C) {
 	c.Assert(err, IsNil)
 
 	c.Assert(idx.Version, Equals, uint32(4))
-	c.Assert(idx.EntryCount, Equals, uint32(11))
+	c.Assert(idx.Entries, HasLen, 11)
 
 	names := []string{
 		".gitignore", "CHANGELOG", "LICENSE", "binary.jpg", "go/example.go",
diff --git a/formats/index/doc.go b/formats/index/doc.go
index 285eade..00466af 100644
--- a/formats/index/doc.go
+++ b/formats/index/doc.go
@@ -1,4 +1,4 @@
-// Package idxfile implements a encoder/decoder of index format files
+// Package index implements a encoder/decoder of index format files
 package index
 
 /*
diff --git a/formats/index/encoder.go b/formats/index/encoder.go
new file mode 100644
index 0000000..94fbc68
--- /dev/null
+++ b/formats/index/encoder.go
@@ -0,0 +1,141 @@
+package index
+
+import (
+	"bytes"
+	"crypto/sha1"
+	"errors"
+	"hash"
+	"io"
+	"time"
+
+	"gopkg.in/src-d/go-git.v4/utils/binary"
+)
+
+var (
+	// EncodeVersionSupported is the range of supported index versions
+	EncodeVersionSupported uint32 = 2
+
+	// ErrInvalidTimestamp is returned by Encode if a Index with a Entry with
+	// negative timestamp values
+	ErrInvalidTimestamp = errors.New("negative timestamps are not allowed")
+)
+
+// An Encoder writes an Index to an output stream.
+type Encoder struct {
+	w    io.Writer
+	hash hash.Hash
+}
+
+// NewEncoder returns a new encoder that writes to w.
+func NewEncoder(w io.Writer) *Encoder {
+	h := sha1.New()
+	mw := io.MultiWriter(w, h)
+	return &Encoder{mw, h}
+}
+
+// Encode writes the Index to the stream of the encoder.
+func (e *Encoder) Encode(idx *Index) error {
+	// TODO: support versions v3 and v4
+	// TODO: support extensions
+	if idx.Version != EncodeVersionSupported {
+		return ErrUnsupportedVersion
+	}
+
+	if err := e.encodeHeader(idx); err != nil {
+		return err
+	}
+
+	if err := e.encodeEntries(idx); err != nil {
+		return err
+	}
+
+	return e.encodeFooter()
+}
+
+func (e *Encoder) encodeHeader(idx *Index) error {
+	return binary.Write(e.w,
+		indexSignature,
+		idx.Version,
+		uint32(len(idx.Entries)),
+	)
+}
+
+func (e *Encoder) encodeEntries(idx *Index) error {
+	for _, entry := range idx.Entries {
+		if err := e.encodeEntry(&entry); err != nil {
+			return err
+		}
+
+		wrote := entryHeaderLength + len(entry.Name)
+		if err := e.padEntry(wrote); err != nil {
+			return err
+		}
+	}
+
+	return nil
+}
+
+func (e *Encoder) encodeEntry(entry *Entry) error {
+	if entry.IntentToAdd || entry.SkipWorktree {
+		return ErrUnsupportedVersion
+	}
+
+	sec, nsec, err := e.timeToUint32(&entry.CreatedAt)
+	if err != nil {
+		return err
+	}
+
+	msec, mnsec, err := e.timeToUint32(&entry.ModifiedAt)
+	if err != nil {
+		return err
+	}
+
+	flags := uint16(entry.Stage&0x3) << 12
+	if l := len(entry.Name); l < nameMask {
+		flags |= uint16(l)
+	} else {
+		flags |= nameMask
+	}
+
+	flow := []interface{}{
+		sec, nsec,
+		msec, mnsec,
+		entry.Dev,
+		entry.Inode,
+		entry.Mode,
+		entry.UID,
+		entry.GID,
+		entry.Size,
+		entry.Hash[:],
+		flags,
+	}
+
+	if err := binary.Write(e.w, flow...); err != nil {
+		return err
+	}
+
+	return binary.Write(e.w, []byte(entry.Name))
+}
+
+func (e *Encoder) timeToUint32(t *time.Time) (uint32, uint32, error) {
+	if t.IsZero() {
+		return 0, 0, nil
+	}
+
+	if t.Unix() < 0 || t.UnixNano() < 0 {
+		return 0, 0, ErrInvalidTimestamp
+	}
+
+	return uint32(t.Unix()), uint32(t.Nanosecond()), nil
+}
+
+func (e *Encoder) padEntry(wrote int) error {
+	padLen := 8 - wrote%8
+
+	_, err := e.w.Write(bytes.Repeat([]byte{'\x00'}, padLen))
+	return err
+}
+
+func (e *Encoder) encodeFooter() error {
+	return binary.Write(e.w, e.hash.Sum(nil))
+}
diff --git a/formats/index/encoder_test.go b/formats/index/encoder_test.go
new file mode 100644
index 0000000..3085988
--- /dev/null
+++ b/formats/index/encoder_test.go
@@ -0,0 +1,78 @@
+package index
+
+import (
+	"bytes"
+	"strings"
+	"time"
+
+	. "gopkg.in/check.v1"
+	"gopkg.in/src-d/go-git.v4/core"
+)
+
+func (s *IdxfileSuite) TestEncode(c *C) {
+	idx := &Index{
+		Version: 2,
+		Entries: []Entry{{
+			CreatedAt:  time.Now(),
+			ModifiedAt: time.Now(),
+			Dev:        4242,
+			Inode:      424242,
+			UID:        84,
+			GID:        8484,
+			Size:       42,
+			Stage:      TheirMode,
+			Hash:       core.NewHash("e25b29c8946e0e192fae2edc1dabf7be71e8ecf3"),
+			Name:       "foo",
+		}, {
+			CreatedAt:  time.Now(),
+			ModifiedAt: time.Now(),
+			Name:       strings.Repeat(" ", 20),
+			Size:       82,
+		}},
+	}
+
+	buf := bytes.NewBuffer(nil)
+	e := NewEncoder(buf)
+	err := e.Encode(idx)
+	c.Assert(err, IsNil)
+
+	output := &Index{}
+	d := NewDecoder(buf)
+	err = d.Decode(output)
+	c.Assert(err, IsNil)
+
+	c.Assert(idx, DeepEquals, output)
+}
+
+func (s *IdxfileSuite) TestEncodeUnsuportedVersion(c *C) {
+	idx := &Index{Version: 3}
+
+	buf := bytes.NewBuffer(nil)
+	e := NewEncoder(buf)
+	err := e.Encode(idx)
+	c.Assert(err, Equals, ErrUnsupportedVersion)
+}
+
+func (s *IdxfileSuite) TestEncodeWithIntentToAddUnsuportedVersion(c *C) {
+	idx := &Index{
+		Version: 2,
+		Entries: []Entry{{IntentToAdd: true}},
+	}
+
+	buf := bytes.NewBuffer(nil)
+	e := NewEncoder(buf)
+	err := e.Encode(idx)
+	c.Assert(err, Equals, ErrUnsupportedVersion)
+}
+
+func (s *IdxfileSuite) TestEncodeWithSkipWorktreeUnsuportedVersion(c *C) {
+	idx := &Index{
+		Version: 2,
+		Entries: []Entry{{SkipWorktree: true}},
+	}
+
+	buf := bytes.NewBuffer(nil)
+	e := NewEncoder(buf)
+	err := e.Encode(idx)
+	c.Assert(err, Equals, ErrUnsupportedVersion)
+}
diff --git a/formats/index/index.go b/formats/index/index.go
index bea199e..35a5391 100644
--- a/formats/index/index.go
+++ b/formats/index/index.go
@@ -1,12 +1,24 @@
 package index
 
 import (
+	"errors"
 	"os"
 	"time"
 
 	"gopkg.in/src-d/go-git.v4/core"
 )
 
+var (
+	// ErrUnsupportedVersion is returned by Decode when the idxindex file
+	// version is not supported.
+	ErrUnsupportedVersion = errors.New("Unsuported version")
+
+	indexSignature          = []byte{'D', 'I', 'R', 'C'}
+	treeExtSignature        = []byte{'T', 'R', 'E', 'E'}
+	resolveUndoExtSignature = []byte{'R', 'E', 'U', 'C'}
+)
+
+// Stage during merge
 type Stage int
 
 const (
@@ -25,7 +37,6 @@ const (
 // worktree are detected using this Index. The Index is also used during merges
 type Index struct {
 	Version     uint32
-	EntryCount  uint32
 	Entries     []Entry
 	Cache       *Tree
 	ResolveUndo *ResolveUndo
@@ -35,20 +46,31 @@ type Index struct {
 // represents exactly one stage of a file. If a file path is unmerged then
 // multiple Entry instances may appear for the same path name.
 type Entry struct {
-	CreatedAt  time.Time
+	// Hash is the SHA1 of the represented file
+	Hash core.Hash
+	// Name is the  Entry path name relative to top level directory
+	Name string
+	// CreatedAt time when the tracked path was created
+	CreatedAt time.Time
+	// ModifiedAt time when the tracked path was changed
 	ModifiedAt time.Time
+	// Dev and Inode of the tracked path
 	Dev, Inode uint32
-	Mode       os.FileMode
-	UID, GID   uint32
-	Size       uint32
-	Flags      uint16
-	Stage      Stage
-
+	// Mode of the path
+	Mode os.FileMode
+	// UID and GID, userid and group id of the owner
+	UID, GID uint32
+	// Size is the length in bytes for regular files
+	Size uint32
+	// Stage on a merge is defines what stage is representing this entry
+	// https://git-scm.com/book/en/v2/Git-Tools-Advanced-Merging
+	Stage Stage
+	// SkipWorktree used in sparse checkouts
+	// https://git-scm.com/docs/git-read-tree#_sparse_checkout
 	SkipWorktree bool
-	IntentToAdd  bool
-
-	Hash core.Hash
-	Name string
+	// IntentToAdd record only the fact that the path will be added later
+	// https://git-scm.com/docs/git-add ("git add -N")
+	IntentToAdd bool
 }
 
 // Tree contains pre-computed hashes for trees that can be derived from the