fix: address outdated dependencies for go-git CVE upgrade (#3440)

2026-10-19 11:10:45 +02:00 · 2025-04-11 13:24:05 -04:00
parent 16c43bb973
commit 3cf227e8af
251 changed files with 34439 additions and 5582 deletions
@@ -1,6 +1,7 @@
 # Go parameters
 GOCMD = go
 GOTEST = $(GOCMD) test 
+WASIRUN_WRAPPER := $(CURDIR)/scripts/wasirun-wrapper

 .PHONY: test
 test:
@@ -9,3 +10,9 @@ test:
 test-coverage:
 	echo "" > $(COVERAGE_REPORT); \
 	$(GOTEST) -coverprofile=$(COVERAGE_REPORT) -coverpkg=./... -covermode=$(COVERAGE_MODE) ./...
+
+.PHONY: wasitest
+wasitest: export GOARCH=wasm
+wasitest: export GOOS=wasip1
+wasitest:
+	$(GOTEST) -exec $(WASIRUN_WRAPPER) ./...
@@ -164,6 +164,8 @@ type File interface {
 	// Name returns the name of the file as presented to Open.
 	Name() string
 	io.Writer
+	// TODO: Add io.WriterAt for v6  
+	// io.WriterAt
 	io.Reader
 	io.ReaderAt
 	io.Seeker
@@ -9,6 +9,7 @@ import (
 	"path/filepath"
 	"sort"
 	"strings"
+	"syscall"
 	"time"

 	"github.com/go-git/go-billy/v5"
@@ -18,16 +19,19 @@ import (

 const separator = filepath.Separator

-// Memory a very convenient filesystem based on memory files
+var errNotLink = errors.New("not a link")
+
+// Memory a very convenient filesystem based on memory files.
 type Memory struct {
 	s *storage

 	tempCount int
 }

-//New returns a new Memory filesystem.
+// New returns a new Memory filesystem.
 func New() billy.Filesystem {
 	fs := &Memory{s: newStorage()}
+	fs.s.New("/", 0755|os.ModeDir, 0)
 	return chroot.New(fs, string(separator))
 }

@@ -57,7 +61,9 @@ func (fs *Memory) OpenFile(filename string, flag int, perm os.FileMode) (billy.F
 		}

 		if target, isLink := fs.resolveLink(filename, f); isLink {
-			return fs.OpenFile(target, flag, perm)
+			if target != filename {
+				return fs.OpenFile(target, flag, perm)
+			}
 		}
 	}

@@ -68,8 +74,6 @@ func (fs *Memory) OpenFile(filename string, flag int, perm os.FileMode) (billy.F
 	return f.Duplicate(filename, perm, flag), nil
 }

-var errNotLink = errors.New("not a link")
-
 func (fs *Memory) resolveLink(fullpath string, f *file) (target string, isLink bool) {
 	if !isSymlink(f.mode) {
 		return fullpath, false
@@ -131,8 +135,12 @@ func (a ByName) Swap(i, j int)      { a[i], a[j] = a[j], a[i] }
 func (fs *Memory) ReadDir(path string) ([]os.FileInfo, error) {
 	if f, has := fs.s.Get(path); has {
 		if target, isLink := fs.resolveLink(path, f); isLink {
-			return fs.ReadDir(target)
+			if target != path {
+				return fs.ReadDir(target)
+			}
 		}
+	} else {
+		return nil, &os.PathError{Op: "open", Path: path, Err: syscall.ENOENT}
 	}

 	var entries []os.FileInfo
@@ -169,17 +177,19 @@ func (fs *Memory) Remove(filename string) error {
 	return fs.s.Remove(filename)
 }

+// Falls back to Go's filepath.Join, which works differently depending on the
+// OS where the code is being executed.
 func (fs *Memory) Join(elem ...string) string {
 	return filepath.Join(elem...)
 }

 func (fs *Memory) Symlink(target, link string) error {
-	_, err := fs.Stat(link)
+	_, err := fs.Lstat(link)
 	if err == nil {
 		return os.ErrExist
 	}

-	if !os.IsNotExist(err) {
+	if !errors.Is(err, os.ErrNotExist) {
 		return err
 	}

@@ -230,7 +240,7 @@ func (f *file) Read(b []byte) (int, error) {
 	n, err := f.ReadAt(b, f.position)
 	f.position += int64(n)

-	if err == io.EOF && n != 0 {
+	if errors.Is(err, io.EOF) && n != 0 {
 		err = nil
 	}

@@ -269,6 +279,10 @@ func (f *file) Seek(offset int64, whence int) (int64, error) {
 }

 func (f *file) Write(p []byte) (int, error) {
+	return f.WriteAt(p, f.position)
+}
+
+func (f *file) WriteAt(p []byte, off int64) (int, error) {
 	if f.isClosed {
 		return 0, os.ErrClosed
 	}
@@ -277,8 +291,8 @@ func (f *file) Write(p []byte) (int, error) {
 		return 0, errors.New("write not supported")
 	}

-	n, err := f.content.WriteAt(p, f.position)
-	f.position += int64(n)
+	n, err := f.content.WriteAt(p, off)
+	f.position = off + int64(n)

 	return n, err
 }
@@ -6,6 +6,7 @@ import (
 	"io"
 	"os"
 	"path/filepath"
+	"strings"
 	"sync"
 )

@@ -112,7 +113,7 @@ func (s *storage) Rename(from, to string) error {
 	move := [][2]string{{from, to}}

 	for pathFrom := range s.files {
-		if pathFrom == from || !filepath.HasPrefix(pathFrom, from) {
+		if pathFrom == from || !strings.HasPrefix(pathFrom, from) {
 			continue
 		}

@@ -246,6 +246,10 @@ func (fs *BoundOS) insideBaseDir(filename string) (bool, error) {
 // a dir that is within the fs.baseDir, by first evaluating any symlinks
 // that either filename or fs.baseDir may contain.
 func (fs *BoundOS) insideBaseDirEval(filename string) (bool, error) {
+	// "/" contains all others.
+	if fs.baseDir == "/" {
+		return true, nil
+	}
 	dir, err := filepath.EvalSymlinks(filepath.Dir(filename))
 	if dir == "" || os.IsNotExist(err) {
 		dir = filepath.Dir(filename)
@@ -255,7 +259,7 @@ func (fs *BoundOS) insideBaseDirEval(filename string) (bool, error) {
 		wd = fs.baseDir
 	}
 	if filename != wd && dir != wd && !strings.HasPrefix(dir, wd+string(filepath.Separator)) {
-		return false, fmt.Errorf("path outside base dir")
+		return false, fmt.Errorf("%q: path outside base dir %q: %w", filename, fs.baseDir, os.ErrNotExist)
 	}
 	return true, nil
 }
@@ -1,5 +1,5 @@
-//go:build !plan9 && !windows && !js
-// +build !plan9,!windows,!js
+//go:build !plan9 && !windows && !wasm
+// +build !plan9,!windows,!wasm

 package osfs

@@ -0,0 +1,34 @@
+//go:build wasip1
+// +build wasip1
+
+package osfs
+
+import (
+	"os"
+	"syscall"
+)
+
+func (f *file) Lock() error {
+	f.m.Lock()
+	defer f.m.Unlock()
+	return nil
+}
+
+func (f *file) Unlock() error {
+	f.m.Lock()
+	defer f.m.Unlock()
+	return nil
+}
+
+func rename(from, to string) error {
+	return os.Rename(from, to)
+}
+
+// umask sets umask to a new value, and returns a func which allows the
+// caller to reset it back to what it was originally.
+func umask(new int) func() {
+	old := syscall.Umask(new)
+	return func() {
+		syscall.Umask(old)
+	}
+}
@@ -1,6 +1,7 @@
 package util

 import (
+	"errors"
 	"io"
 	"os"
 	"path/filepath"
@@ -33,14 +34,14 @@ func removeAll(fs billy.Basic, path string) error {

 	// Simple case: if Remove works, we're done.
 	err := fs.Remove(path)
-	if err == nil || os.IsNotExist(err) {
+	if err == nil || errors.Is(err, os.ErrNotExist) {
 		return nil
 	}

 	// Otherwise, is this a directory we need to recurse into?
 	dir, serr := fs.Stat(path)
 	if serr != nil {
-		if os.IsNotExist(serr) {
+		if errors.Is(serr, os.ErrNotExist) {
 			return nil
 		}

@@ -60,7 +61,7 @@ func removeAll(fs billy.Basic, path string) error {
 	// Directory.
 	fis, err := dirfs.ReadDir(path)
 	if err != nil {
-		if os.IsNotExist(err) {
+		if errors.Is(err, os.ErrNotExist) {
 			// Race. It was deleted between the Lstat and Open.
 			// Return nil per RemoveAll's docs.
 			return nil
@@ -81,7 +82,7 @@ func removeAll(fs billy.Basic, path string) error {

 	// Remove directory.
 	err1 := fs.Remove(path)
-	if err1 == nil || os.IsNotExist(err1) {
+	if err1 == nil || errors.Is(err1, os.ErrNotExist) {
 		return nil
 	}

@@ -96,22 +97,26 @@ func removeAll(fs billy.Basic, path string) error {
 // WriteFile writes data to a file named by filename in the given filesystem.
 // If the file does not exist, WriteFile creates it with permissions perm;
 // otherwise WriteFile truncates it before writing.
-func WriteFile(fs billy.Basic, filename string, data []byte, perm os.FileMode) error {
+func WriteFile(fs billy.Basic, filename string, data []byte, perm os.FileMode) (err error) {
 	f, err := fs.OpenFile(filename, os.O_WRONLY|os.O_CREATE|os.O_TRUNC, perm)
 	if err != nil {
 		return err
 	}
+	defer func() {
+		if f != nil {
+			err1 := f.Close()
+			if err == nil {
+				err = err1
+			}
+		}
+	}()

 	n, err := f.Write(data)
 	if err == nil && n < len(data) {
 		err = io.ErrShortWrite
 	}

-	if err1 := f.Close(); err == nil {
-		err = err1
-	}
-
-	return err
+	return nil
 }

 // Random number state.
@@ -154,7 +159,7 @@ func TempFile(fs billy.Basic, dir, prefix string) (f billy.File, err error) {
 	for i := 0; i < 10000; i++ {
 		name := filepath.Join(dir, prefix+nextSuffix())
 		f, err = fs.OpenFile(name, os.O_RDWR|os.O_CREATE|os.O_EXCL, 0600)
-		if os.IsExist(err) {
+		if errors.Is(err, os.ErrExist) {
 			if nconflict++; nconflict > 10 {
 				randmu.Lock()
 				rand = reseed()
@@ -185,7 +190,7 @@ func TempDir(fs billy.Dir, dir, prefix string) (name string, err error) {
 	for i := 0; i < 10000; i++ {
 		try := filepath.Join(dir, prefix+nextSuffix())
 		err = fs.MkdirAll(try, 0700)
-		if os.IsExist(err) {
+		if errors.Is(err, os.ErrExist) {
 			if nconflict++; nconflict > 10 {
 				randmu.Lock()
 				rand = reseed()
@@ -193,8 +198,8 @@ func TempDir(fs billy.Dir, dir, prefix string) (name string, err error) {
 			}
 			continue
 		}
-		if os.IsNotExist(err) {
-			if _, err := os.Stat(dir); os.IsNotExist(err) {
+		if errors.Is(err, os.ErrNotExist) {
+			if _, err := os.Stat(dir); errors.Is(err, os.ErrNotExist) {
 				return "", err
 			}
 		}
@@ -272,7 +277,7 @@ func ReadFile(fs billy.Basic, name string) ([]byte, error) {
 		data = data[:len(data)+n]

 		if err != nil {
-			if err == io.EOF {
+			if errors.Is(err, io.EOF) {
 				err = nil
 			}

@@ -11,7 +11,7 @@ compatibility status with go-git.
 | `init`  | `--bare`                                                                                                           | ✅     |       |                                                                                                                                                                                                                     |
 | `init`  | `--template` <br/> `--separate-git-dir` <br/> `--shared`                                                           | ❌     |       |                                                                                                                                                                                                                     |
 | `clone` |                                                                                                                    | ✅     |       | - [PlainClone](_examples/clone/main.go)                                                                                                                                                                             |
-| `clone` | Authentication: <br/> - none <br/> - access token <br/> - username + password <br/> - ssh                          | ✅     |       | - [clone ssh](_examples/clone/auth/ssh/main.go) <br/> - [clone access token](_examples/clone/auth/basic/access_token/main.go) <br/> - [clone user + password](_examples/clone/auth/basic/username_password/main.go) |
+| `clone` | Authentication: <br/> - none <br/> - access token <br/> - username + password <br/> - ssh                          | ✅     |       | - [clone ssh (private_key)](_examples/clone/auth/ssh/private_key/main.go) <br/> - [clone ssh (ssh_agent)](_examples/clone/auth/ssh/ssh_agent/main.go) <br/> - [clone access token](_examples/clone/auth/basic/access_token/main.go) <br/> - [clone user + password](_examples/clone/auth/basic/username_password/main.go) |
 | `clone` | `--progress` <br/> `--single-branch` <br/> `--depth` <br/> `--origin` <br/> `--recurse-submodules` <br/>`--shared` | ✅     |       | - [recurse submodules](_examples/clone/main.go) <br/> - [progress](_examples/progress/main.go)                                                                                                                      |

 ## Basic snapshotting
@@ -34,6 +34,7 @@ compatibility status with go-git.
 | `merge`     |             | ⚠️ (partial) | Fast-forward only                       |                                                                                                 |
 | `mergetool` |             | ❌           |                                         |                                                                                                 |
 | `stash`     |             | ❌           |                                         |                                                                                                 |
+| `sparse-checkout`     |             | ✅           |                                         | - [sparse-checkout](_examples/sparse-checkout/main.go)                                                                                               |
 | `tag`       |             | ✅           |                                         | - [tag](_examples/tag/main.go) <br/> - [tag create and push](_examples/tag-create-push/main.go) |

 ## Sharing and updating projects
@@ -31,6 +31,13 @@ In order for a PR to be accepted it needs to pass a list of requirements:
 - If the PR is a new feature, it has to come with a suite of unit tests, that tests the new functionality.
 - In any case, all the PRs have to pass the personal evaluation of at least one of the maintainers of go-git.

+### Branches
+
+The `master` branch is currently used for maintaining the `v5` major release only. The accepted changes would
+be dependency bumps, bug fixes and small changes that aren't needed for `v6`. New development should target the
+`v6-exp` branch, and if agreed with at least one go-git maintainer, it can be back ported to `v5` by creating 
+a new PR that targets `master`.
+
 ### Format of the commit message

 Every commit message should describe what was changed, under which context and, if applicable, the GitHub issue it relates to:
@@ -97,13 +97,10 @@ func Blame(c *object.Commit, path string) (*BlameResult, error) {
 		if err != nil {
 			return nil, err
 		}
-		if finished == true {
+		if finished {
 			break
 		}
 	}
-	if err != nil {
-		return nil, err
-	}

 	b.lineToCommit = make([]*object.Commit, finalLength)
 	for i := range needsMap {
@@ -309,8 +306,8 @@ func (b *blame) addBlames(curItems []*queueItem) (bool, error) {
 		for h := range hunks {
 			hLines := countLines(hunks[h].Text)
 			for hl := 0; hl < hLines; hl++ {
-				switch {
-				case hunks[h].Type == diffmatchpatch.DiffEqual:
+				switch hunks[h].Type {
+				case diffmatchpatch.DiffEqual:
 					prevl++
 					curl++
 					if curl == curItem.NeedsMap[need].Cur {
@@ -322,7 +319,7 @@ func (b *blame) addBlames(curItems []*queueItem) (bool, error) {
 							break out
 						}
 					}
-				case hunks[h].Type == diffmatchpatch.DiffInsert:
+				case diffmatchpatch.DiffInsert:
 					curl++
 					if curl == curItem.NeedsMap[need].Cur {
 						// the line we want is added, it may have been added here (or by another parent), skip it for now
@@ -331,7 +328,7 @@ func (b *blame) addBlames(curItems []*queueItem) (bool, error) {
 							break out
 						}
 					}
-				case hunks[h].Type == diffmatchpatch.DiffDelete:
+				case diffmatchpatch.DiffDelete:
 					prevl += hLines
 					continue out
 				default:
@@ -252,6 +252,7 @@ const (
 	extensionsSection          = "extensions"
 	fetchKey                   = "fetch"
 	urlKey                     = "url"
+	pushurlKey                 = "pushurl"
 	bareKey                    = "bare"
 	worktreeKey                = "worktree"
 	commentCharKey             = "commentChar"
@@ -633,6 +634,7 @@ func (c *RemoteConfig) unmarshal(s *format.Subsection) error {

 	c.Name = c.raw.Name
 	c.URLs = append([]string(nil), c.raw.Options.GetAll(urlKey)...)
+	c.URLs = append(c.URLs, c.raw.Options.GetAll(pushurlKey)...)
 	c.Fetch = fetch
 	c.Mirror = c.raw.Options.Get(mirrorKey) == "true"

@@ -43,6 +43,11 @@ func tokenizeExpression(ch rune, tokenType token, check runeCategoryValidator, r
 	return tokenType, string(data), nil
 }

+// maxRevisionLength holds the maximum length that will be parsed for a
+// revision. Git itself doesn't enforce a max length, but rather leans on
+// the OS to enforce it via its ARG_MAX.
+const maxRevisionLength = 128 * 1024 // 128kb
+
 var zeroRune = rune(0)

 // scanner represents a lexical scanner.
@@ -52,7 +57,7 @@ type scanner struct {

 // newScanner returns a new instance of scanner.
 func newScanner(r io.Reader) *scanner {
-	return &scanner{r: bufio.NewReader(r)}
+	return &scanner{r: bufio.NewReader(io.LimitReader(r, maxRevisionLength))}
 }

 // Scan extracts tokens and their strings counterpart
@@ -416,6 +416,9 @@ type ResetOptions struct {
 	// the index (resetting it to the tree of Commit) and the working tree
 	// depending on Mode. If empty MixedReset is used.
 	Mode ResetMode
+	// Files, if not empty will constrain the reseting the index to only files
+	// specified in this list.
+	Files []string
 }

 // Validate validates the fields and sets the default values.
@@ -790,3 +793,26 @@ type PlainInitOptions struct {

 // Validate validates the fields and sets the default values.
 func (o *PlainInitOptions) Validate() error { return nil }
+
+var (
+	ErrNoRestorePaths = errors.New("you must specify path(s) to restore")
+)
+
+// RestoreOptions describes how a restore should be performed.
+type RestoreOptions struct {
+	// Marks to restore the content in the index
+	Staged bool
+	// Marks to restore the content of the working tree
+	Worktree bool
+	// List of file paths that will be restored
+	Files []string
+}
+
+// Validate validates the fields and sets the default values.
+func (o *RestoreOptions) Validate() error {
+	if len(o.Files) == 0 {
+		return ErrNoRestorePaths
+	}
+
+	return nil
+}
@@ -64,6 +64,10 @@ func ReadPatterns(fs billy.Filesystem, path []string) (ps []Pattern, err error)

 	for _, fi := range fis {
 		if fi.IsDir() && fi.Name() != gitDir {
+			if NewMatcher(ps).Match(append(path, fi.Name()), true) {
+				continue
+			}
+
 			var subps []Pattern
 			subps, err = ReadPatterns(fs, append(path, fi.Name()))
 			if err != nil {
@@ -24,8 +24,8 @@ var (
 	// ErrInvalidChecksum is returned by Decode if the SHA1 hash mismatch with
 	// the read content
 	ErrInvalidChecksum = errors.New("invalid checksum")
-
-	errUnknownExtension = errors.New("unknown extension")
+	// ErrUnknownExtension is returned when an index extension is encountered that is considered mandatory
+	ErrUnknownExtension = errors.New("unknown extension")
 )

 const (
@@ -39,6 +39,7 @@ const (

 // A Decoder reads and decodes index files from an input stream.
 type Decoder struct {
+	buf       *bufio.Reader
 	r         io.Reader
 	hash      hash.Hash
 	lastEntry *Entry
@@ -49,8 +50,10 @@ type Decoder struct {
 // NewDecoder returns a new decoder that reads from r.
 func NewDecoder(r io.Reader) *Decoder {
 	h := hash.New(hash.CryptoType)
+	buf := bufio.NewReader(r)
 	return &Decoder{
-		r:         io.TeeReader(r, h),
+		buf:       buf,
+		r:         io.TeeReader(buf, h),
 		hash:      h,
 		extReader: bufio.NewReader(nil),
 	}
@@ -210,71 +213,75 @@ func (d *Decoder) readExtensions(idx *Index) error {
 	// count that they are not supported by jgit or libgit

 	var expected []byte
+	var peeked []byte
 	var err error

-	var header [4]byte
+	// we should always be able to peek for 4 bytes (header) + 4 bytes (extlen) + final hash
+	// if this fails, we know that we're at the end of the index
+	peekLen := 4 + 4 + d.hash.Size()
+
 	for {
 		expected = d.hash.Sum(nil)
-
-		var n int
-		if n, err = io.ReadFull(d.r, header[:]); err != nil {
-			if n == 0 {
-				err = io.EOF
-			}
-
+		peeked, err = d.buf.Peek(peekLen)
+		if len(peeked) < peekLen {
+			// there can't be an extension at this point, so let's bail out
 			break
 		}
-
-		err = d.readExtension(idx, header[:])
-		if err != nil {
-			break
-		}
-	}
-
-	if err != errUnknownExtension {
-		return err
-	}
-
-	return d.readChecksum(expected, header)
-}
-
-func (d *Decoder) readExtension(idx *Index, header []byte) error {
-	switch {
-	case bytes.Equal(header, treeExtSignature):
-		r, err := d.getExtensionReader()
 		if err != nil {
 			return err
 		}

+		err = d.readExtension(idx)
+		if err != nil {
+			return err
+		}
+	}
+
+	return d.readChecksum(expected)
+}
+
+func (d *Decoder) readExtension(idx *Index) error {
+	var header [4]byte
+
+	if _, err := io.ReadFull(d.r, header[:]); err != nil {
+		return err
+	}
+
+	r, err := d.getExtensionReader()
+	if err != nil {
+		return err
+	}
+
+	switch {
+	case bytes.Equal(header[:], treeExtSignature):
 		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
-		}
-
+	case bytes.Equal(header[:], resolveUndoExtSignature):
 		idx.ResolveUndo = &ResolveUndo{}
 		d := &resolveUndoDecoder{r}
 		if err := d.Decode(idx.ResolveUndo); err != nil {
 			return err
 		}
-	case bytes.Equal(header, endOfIndexEntryExtSignature):
-		r, err := d.getExtensionReader()
-		if err != nil {
-			return err
-		}
-
+	case bytes.Equal(header[:], endOfIndexEntryExtSignature):
 		idx.EndOfIndexEntry = &EndOfIndexEntry{}
 		d := &endOfIndexEntryDecoder{r}
 		if err := d.Decode(idx.EndOfIndexEntry); err != nil {
 			return err
 		}
 	default:
-		return errUnknownExtension
+		// See https://git-scm.com/docs/index-format, which says:
+		// If the first byte is 'A'..'Z' the extension is optional and can be ignored.
+		if header[0] < 'A' || header[0] > 'Z' {
+			return ErrUnknownExtension
+		}
+
+		d := &unknownExtensionDecoder{r}
+		if err := d.Decode(); err != nil {
+			return err
+		}
 	}

 	return nil
@@ -290,11 +297,10 @@ func (d *Decoder) getExtensionReader() (*bufio.Reader, error) {
 	return d.extReader, nil
 }

-func (d *Decoder) readChecksum(expected []byte, alreadyRead [4]byte) error {
+func (d *Decoder) readChecksum(expected []byte) error {
 	var h plumbing.Hash
-	copy(h[:4], alreadyRead[:])

-	if _, err := io.ReadFull(d.r, h[4:]); err != nil {
+	if _, err := io.ReadFull(d.r, h[:]); err != nil {
 		return err
 	}

@@ -476,3 +482,22 @@ func (d *endOfIndexEntryDecoder) Decode(e *EndOfIndexEntry) error {
 	_, err = io.ReadFull(d.r, e.Hash[:])
 	return err
 }
+
+type unknownExtensionDecoder struct {
+	r *bufio.Reader
+}
+
+func (d *unknownExtensionDecoder) Decode() error {
+	var buf [1024]byte
+
+	for {
+		_, err := d.r.Read(buf[:])
+		if err == io.EOF {
+			break
+		}
+		if err != nil {
+			return err
+		}
+	}
+	return nil
+}
@@ -3,8 +3,11 @@ package index
 import (
 	"bytes"
 	"errors"
+	"fmt"
 	"io"
+	"path"
 	"sort"
+	"strings"
 	"time"

 	"github.com/go-git/go-git/v5/plumbing/hash"
@@ -13,7 +16,7 @@ import (

 var (
 	// EncodeVersionSupported is the range of supported index versions
-	EncodeVersionSupported uint32 = 3
+	EncodeVersionSupported uint32 = 4

 	// ErrInvalidTimestamp is returned by Encode if a Index with a Entry with
 	// negative timestamp values
@@ -22,20 +25,25 @@ var (

 // An Encoder writes an Index to an output stream.
 type Encoder struct {
-	w    io.Writer
-	hash hash.Hash
+	w         io.Writer
+	hash      hash.Hash
+	lastEntry *Entry
 }

 // NewEncoder returns a new encoder that writes to w.
 func NewEncoder(w io.Writer) *Encoder {
 	h := hash.New(hash.CryptoType)
 	mw := io.MultiWriter(w, h)
-	return &Encoder{mw, h}
+	return &Encoder{mw, h, nil}
 }

 // Encode writes the Index to the stream of the encoder.
 func (e *Encoder) Encode(idx *Index) error {
-	// TODO: support v4
+	return e.encode(idx, true)
+}
+
+func (e *Encoder) encode(idx *Index, footer bool) error {
+
 	// TODO: support extensions
 	if idx.Version > EncodeVersionSupported {
 		return ErrUnsupportedVersion
@@ -49,7 +57,10 @@ func (e *Encoder) Encode(idx *Index) error {
 		return err
 	}

-	return e.encodeFooter()
+	if footer {
+		return e.encodeFooter()
+	}
+	return nil
 }

 func (e *Encoder) encodeHeader(idx *Index) error {
@@ -64,7 +75,7 @@ func (e *Encoder) encodeEntries(idx *Index) error {
 	sort.Sort(byName(idx.Entries))

 	for _, entry := range idx.Entries {
-		if err := e.encodeEntry(entry); err != nil {
+		if err := e.encodeEntry(idx, entry); err != nil {
 			return err
 		}
 		entryLength := entryHeaderLength
@@ -73,7 +84,7 @@ func (e *Encoder) encodeEntries(idx *Index) error {
 		}

 		wrote := entryLength + len(entry.Name)
-		if err := e.padEntry(wrote); err != nil {
+		if err := e.padEntry(idx, wrote); err != nil {
 			return err
 		}
 	}
@@ -81,7 +92,7 @@ func (e *Encoder) encodeEntries(idx *Index) error {
 	return nil
 }

-func (e *Encoder) encodeEntry(entry *Entry) error {
+func (e *Encoder) encodeEntry(idx *Index, entry *Entry) error {
 	sec, nsec, err := e.timeToUint32(&entry.CreatedAt)
 	if err != nil {
 		return err
@@ -132,9 +143,68 @@ func (e *Encoder) encodeEntry(entry *Entry) error {
 		return err
 	}

+	switch idx.Version {
+	case 2, 3:
+		err = e.encodeEntryName(entry)
+	case 4:
+		err = e.encodeEntryNameV4(entry)
+	default:
+		err = ErrUnsupportedVersion
+	}
+
+	return err
+}
+
+func (e *Encoder) encodeEntryName(entry *Entry) error {
 	return binary.Write(e.w, []byte(entry.Name))
 }

+func (e *Encoder) encodeEntryNameV4(entry *Entry) error {
+	name := entry.Name
+	l := 0
+	if e.lastEntry != nil {
+		dir := path.Dir(e.lastEntry.Name) + "/"
+		if strings.HasPrefix(entry.Name, dir) {
+			l = len(e.lastEntry.Name) - len(dir)
+			name = strings.TrimPrefix(entry.Name, dir)
+		} else {
+			l = len(e.lastEntry.Name)
+		}
+	}
+
+	e.lastEntry = entry
+
+	err := binary.WriteVariableWidthInt(e.w, int64(l))
+	if err != nil {
+		return err
+	}
+
+	return binary.Write(e.w, []byte(name+string('\x00')))
+}
+
+func (e *Encoder) encodeRawExtension(signature string, data []byte) error {
+	if len(signature) != 4 {
+		return fmt.Errorf("invalid signature length")
+	}
+
+	_, err := e.w.Write([]byte(signature))
+	if err != nil {
+		return err
+	}
+
+	err = binary.WriteUint32(e.w, uint32(len(data)))
+	if err != nil {
+		return err
+	}
+
+	_, err = e.w.Write(data)
+	if err != nil {
+		return err
+	}
+
+	return nil
+}
+
 func (e *Encoder) timeToUint32(t *time.Time) (uint32, uint32, error) {
 	if t.IsZero() {
 		return 0, 0, nil
@@ -147,7 +217,11 @@ func (e *Encoder) timeToUint32(t *time.Time) (uint32, uint32, error) {
 	return uint32(t.Unix()), uint32(t.Nanosecond()), nil
 }

-func (e *Encoder) padEntry(wrote int) error {
+func (e *Encoder) padEntry(idx *Index, wrote int) error {
+	if idx.Version == 4 {
+		return nil
+	}
+
 	padLen := 8 - wrote%8

 	_, err := e.w.Write(bytes.Repeat([]byte{'\x00'}, padLen))
@@ -32,19 +32,17 @@ func (idx *deltaIndex) findMatch(src, tgt []byte, tgtOffset int) (srcOffset, l i
 		return 0, -1
 	}

-	if len(tgt) >= tgtOffset+s && len(src) >= blksz {
-		h := hashBlock(tgt, tgtOffset)
-		tIdx := h & idx.mask
-		eIdx := idx.table[tIdx]
-		if eIdx != 0 {
-			srcOffset = idx.entries[eIdx]
-		} else {
-			return
-		}
-
-		l = matchLength(src, tgt, tgtOffset, srcOffset)
+	h := hashBlock(tgt, tgtOffset)
+	tIdx := h & idx.mask
+	eIdx := idx.table[tIdx]
+	if eIdx == 0 {
+		return
 	}

+	srcOffset = idx.entries[eIdx]
+
+	l = matchLength(src, tgt, tgtOffset, srcOffset)
+
 	return
 }

@@ -26,6 +26,13 @@ var (
 const (
 	payload      = 0x7f // 0111 1111
 	continuation = 0x80 // 1000 0000
+
+	// maxPatchPreemptionSize defines what is the max size of bytes to be
+	// premptively made available for a patch operation.
+	maxPatchPreemptionSize uint = 65536
+
+	// minDeltaSize defines the smallest size for a delta.
+	minDeltaSize = 4
 )

 type offset struct {
@@ -86,9 +93,13 @@ func ApplyDelta(target, base plumbing.EncodedObject, delta []byte) (err error) {
 }

 // PatchDelta returns the result of applying the modification deltas in delta to src.
-// An error will be returned if delta is corrupted (ErrDeltaLen) or an action command
+// An error will be returned if delta is corrupted (ErrInvalidDelta) or an action command
 // is not copy from source or copy from delta (ErrDeltaCmd).
 func PatchDelta(src, delta []byte) ([]byte, error) {
+	if len(src) == 0 || len(delta) < minDeltaSize {
+		return nil, ErrInvalidDelta
+	}
+
 	b := &bytes.Buffer{}
 	if err := patchDelta(b, src, delta); err != nil {
 		return nil, err
@@ -239,7 +250,9 @@ func patchDelta(dst *bytes.Buffer, src, delta []byte) error {
 	remainingTargetSz := targetSz

 	var cmd byte
-	dst.Grow(int(targetSz))
+
+	growSz := min(targetSz, maxPatchPreemptionSize)
+	dst.Grow(int(growSz))
 	for {
 		if len(delta) == 0 {
 			return ErrInvalidDelta
@@ -403,6 +416,10 @@ func patchDeltaWriter(dst io.Writer, base io.ReaderAt, delta io.Reader,
 // This must be called twice on the delta data buffer, first to get the
 // expected source buffer size, and again to get the target buffer size.
 func decodeLEB128(input []byte) (uint, []byte) {
+	if len(input) == 0 {
+		return 0, input
+	}
+
 	var num, sz uint
 	var b byte
 	for {
@@ -140,6 +140,8 @@ func asciiHexToByte(b byte) (byte, error) {
 		return b - '0', nil
 	case b >= 'a' && b <= 'f':
 		return b - 'a' + 10, nil
+	case b >= 'A' && b <= 'F':
+		return b - 'A' + 10, nil
 	default:
 		return 0, ErrInvalidPktLen
 	}
@@ -19,6 +19,7 @@ var (
 	// a PKCS#7 (S/MIME) signature.
 	x509SignatureFormat = signatureFormat{
 		[]byte("-----BEGIN CERTIFICATE-----"),
+		[]byte("-----BEGIN SIGNED MESSAGE-----"),
 	}

 	// sshSignatureFormat is the format of an SSH signature.
@@ -295,6 +295,7 @@ func (s TreeEntrySorter) Swap(i, j int) {
 }

 // Encode transforms a Tree into a plumbing.EncodedObject.
+// The tree entries must be sorted by name.
 func (t *Tree) Encode(o plumbing.EncodedObject) (err error) {
 	o.SetType(plumbing.TreeObject)
 	w, err := o.Writer()
@@ -0,0 +1,76 @@
+package packp
+
+import (
+	"errors"
+	"fmt"
+	"github.com/go-git/go-git/v5/plumbing"
+	"net/url"
+	"strings"
+)
+
+var ErrUnsupportedObjectFilterType = errors.New("unsupported object filter type")
+
+// Filter values enable the partial clone capability which causes
+// the server to omit objects that match the filter.
+//
+// See [Git's documentation] for more details.
+//
+// [Git's documentation]: https://github.com/git/git/blob/e02ecfcc534e2021aae29077a958dd11c3897e4c/Documentation/rev-list-options.txt#L948
+type Filter string
+
+type BlobLimitPrefix string
+
+const (
+	BlobLimitPrefixNone BlobLimitPrefix = ""
+	BlobLimitPrefixKibi BlobLimitPrefix = "k"
+	BlobLimitPrefixMebi BlobLimitPrefix = "m"
+	BlobLimitPrefixGibi BlobLimitPrefix = "g"
+)
+
+// FilterBlobNone omits all blobs.
+func FilterBlobNone() Filter {
+	return "blob:none"
+}
+
+// FilterBlobLimit omits blobs of size at least n bytes (when prefix is
+// BlobLimitPrefixNone), n kibibytes (when prefix is BlobLimitPrefixKibi),
+// n mebibytes (when prefix is BlobLimitPrefixMebi) or n gibibytes (when
+// prefix is BlobLimitPrefixGibi). n can be zero, in which case all blobs
+// will be omitted.
+func FilterBlobLimit(n uint64, prefix BlobLimitPrefix) Filter {
+	return Filter(fmt.Sprintf("blob:limit=%d%s", n, prefix))
+}
+
+// FilterTreeDepth omits all blobs and trees whose depth from the root tree
+// is larger or equal to depth.
+func FilterTreeDepth(depth uint64) Filter {
+	return Filter(fmt.Sprintf("tree:%d", depth))
+}
+
+// FilterObjectType omits all objects which are not of the requested type t.
+// Supported types are TagObject, CommitObject, TreeObject and BlobObject.
+func FilterObjectType(t plumbing.ObjectType) (Filter, error) {
+	switch t {
+	case plumbing.TagObject:
+		fallthrough
+	case plumbing.CommitObject:
+		fallthrough
+	case plumbing.TreeObject:
+		fallthrough
+	case plumbing.BlobObject:
+		return Filter(fmt.Sprintf("object:type=%s", t.String())), nil
+	default:
+		return "", fmt.Errorf("%w: %s", ErrUnsupportedObjectFilterType, t.String())
+	}
+}
+
+// FilterCombine combines multiple Filter values together.
+func FilterCombine(filters ...Filter) Filter {
+	var escapedFilters []string
+
+	for _, filter := range filters {
+		escapedFilters = append(escapedFilters, url.QueryEscape(string(filter)))
+	}
+
+	return Filter(fmt.Sprintf("combine:%s", strings.Join(escapedFilters, "+")))
+}
@@ -114,7 +114,7 @@ func (d *Demuxer) nextPackData() ([]byte, error) {

 	size := len(content)
 	if size == 0 {
-		return nil, nil
+		return nil, io.EOF
 	} else if size > d.max {
 		return nil, ErrMaxPackedExceeded
 	}
@@ -120,6 +120,9 @@ func (r *ServerResponse) decodeACKLine(line []byte) error {
 	}

 	sp := bytes.Index(line, []byte(" "))
+	if sp+41 > len(line) {
+		return fmt.Errorf("malformed ACK %q", line)
+	}
 	h := plumbing.NewHash(string(line[sp+1 : sp+41]))
 	r.ACKs = append(r.ACKs, h)
 	return nil
@@ -17,6 +17,7 @@ type UploadRequest struct {
 	Wants        []plumbing.Hash
 	Shallows     []plumbing.Hash
 	Depth        Depth
+	Filter       Filter
 }

 // Depth values stores the desired depth of the requested packfile: see
@@ -132,6 +132,17 @@ func (e *ulReqEncoder) encodeDepth() stateFn {
 		return nil
 	}

+	return e.encodeFilter
+}
+
+func (e *ulReqEncoder) encodeFilter() stateFn {
+	if filter := e.data.Filter; filter != "" {
+		if err := e.pe.Encodef("filter %s\n", filter); err != nil {
+			e.err = fmt.Errorf("encoding filter %s: %s", filter, err)
+			return nil
+		}
+	}
+
 	return e.encodeFlush
 }

@@ -188,7 +188,7 @@ func (r ReferenceName) Validate() error {

 	isBranch := r.IsBranch()
 	isTag := r.IsTag()
-	for _, part := range parts {
+	for i, part := range parts {
 		// rule 6
 		if len(part) == 0 {
 			return ErrInvalidReferenceName
@@ -205,7 +205,7 @@ func (r ReferenceName) Validate() error {
 			return ErrInvalidReferenceName
 		}

-		if (isBranch || isTag) && strings.HasPrefix(part, "-") { // branches & tags can't start with -
+		if (isBranch || isTag) && strings.HasPrefix(part, "-") && (i == 2) { // branches & tags can't start with -
 			return ErrInvalidReferenceName
 		}
 	}
@@ -19,6 +19,7 @@ import (
 	"fmt"
 	"io"
 	"net/url"
+	"path/filepath"
 	"strconv"
 	"strings"

@@ -295,7 +296,11 @@ func parseFile(endpoint string) (*Endpoint, bool) {
 		return nil, false
 	}

-	path := endpoint
+	path, err := filepath.Abs(endpoint)
+	if err != nil {
+		return nil, false
+	}
+
 	return &Endpoint{
 		Protocol: "file",
 		Path:     path,
@@ -7,6 +7,7 @@ import (
 	"io"
 	"os"
 	"path/filepath"
+	"runtime"
 	"strings"

 	"github.com/go-git/go-git/v5/plumbing/transport"
@@ -95,7 +96,23 @@ func (r *runner) Command(cmd string, ep *transport.Endpoint, auth transport.Auth
 		}
 	}

-	return &command{cmd: execabs.Command(cmd, ep.Path)}, nil
+	return &command{cmd: execabs.Command(cmd, adjustPathForWindows(ep.Path))}, nil
+}
+
+func isDriveLetter(c byte) bool {
+	return (c >= 'a' && c <= 'z') || (c >= 'A' && c <= 'Z')
+}
+
+// On Windows, the path that results from a file: URL has a leading slash. This
+// has to be removed if there's a drive letter
+func adjustPathForWindows(p string) string {
+	if runtime.GOOS != "windows" {
+		return p
+	}
+	if len(p) >= 3 && p[0] == '/' && isDriveLetter(p[1]) && p[2] == ':' {
+		return p[1:]
+	}
+	return p
 }

 type command struct {
@@ -430,11 +430,11 @@ func NewErr(r *http.Response) error {

 	switch r.StatusCode {
 	case http.StatusUnauthorized:
-		return transport.ErrAuthenticationRequired
+		return fmt.Errorf("%w: %s", transport.ErrAuthenticationRequired, reason)
 	case http.StatusForbidden:
-		return transport.ErrAuthorizationFailed
+		return fmt.Errorf("%w: %s", transport.ErrAuthorizationFailed, reason)
 	case http.StatusNotFound:
-		return transport.ErrRepositoryNotFound
+		return fmt.Errorf("%w: %s", transport.ErrRepositoryNotFound, reason)
 	}

 	return plumbing.NewUnexpectedError(&Err{r, reason})
@@ -40,8 +40,16 @@ func (l *fsLoader) Load(ep *transport.Endpoint) (storer.Storer, error) {
 		return nil, err
 	}

-	if _, err := fs.Stat("config"); err != nil {
-		return nil, transport.ErrRepositoryNotFound
+	var bare bool
+	if _, err := fs.Stat("config"); err == nil {
+		bare = true
+	}
+
+	if !bare {
+		// do not use git.GitDirName due to import cycle
+		if _, err := fs.Stat(".git"); err != nil {
+			return nil, transport.ErrRepositoryNotFound
+		}
 	}

 	return filesystem.NewStorage(fs, cache.NewObjectLRUDefault()), nil
@@ -9,6 +9,7 @@ import (
 	"time"

 	"github.com/go-git/go-billy/v5/osfs"
+
 	"github.com/go-git/go-git/v5/config"
 	"github.com/go-git/go-git/v5/internal/url"
 	"github.com/go-git/go-git/v5/plumbing"
@@ -82,7 +83,7 @@ func (r *Remote) String() string {
 	var fetch, push string
 	if len(r.c.URLs) > 0 {
 		fetch = r.c.URLs[0]
-		push = r.c.URLs[0]
+		push = r.c.URLs[len(r.c.URLs)-1]
 	}

 	return fmt.Sprintf("%s\t%s (fetch)\n%[1]s\t%[3]s (push)", r.c.Name, fetch, push)
@@ -109,8 +110,8 @@ func (r *Remote) PushContext(ctx context.Context, o *PushOptions) (err error) {
 		return fmt.Errorf("remote names don't match: %s != %s", o.RemoteName, r.c.Name)
 	}

-	if o.RemoteURL == "" {
-		o.RemoteURL = r.c.URLs[0]
+	if o.RemoteURL == "" && len(r.c.URLs) > 0 {
+		o.RemoteURL = r.c.URLs[len(r.c.URLs)-1]
 	}

 	s, err := newSendPackSession(o.RemoteURL, o.Auth, o.InsecureSkipTLS, o.CABundle, o.ProxyOptions)
@@ -491,7 +492,18 @@ func (r *Remote) fetch(ctx context.Context, o *FetchOptions) (sto storer.Referen
 	}

 	if !updated && !updatedPrune {
-		return remoteRefs, NoErrAlreadyUpToDate
+		// No references updated, but may have fetched new objects, check if we now have any of our wants
+		for _, hash := range req.Wants {
+			exists, _ := objectExists(r.s, hash)
+			if exists {
+				updated = true
+				break
+			}
+		}
+
+		if !updated {
+			return remoteRefs, NoErrAlreadyUpToDate
+		}
 	}

 	return remoteRefs, nil
@@ -878,17 +890,12 @@ func getHavesFromRef(
 		return nil
 	}

-	// No need to load the commit if we know the remote already
-	// has this hash.
-	if remoteRefs[h] {
-		haves[h] = true
-		return nil
-	}
-
 	commit, err := object.GetCommit(s, h)
 	if err != nil {
-		// Ignore the error if this isn't a commit.
-		haves[ref.Hash()] = true
+		if !errors.Is(err, plumbing.ErrObjectNotFound) {
+			// Ignore the error if this isn't a commit.
+			haves[ref.Hash()] = true
+		}
 		return nil
 	}

@@ -956,7 +956,7 @@ func (r *Repository) clone(ctx context.Context, o *CloneOptions) error {
 		}

 		if o.RecurseSubmodules != NoRecurseSubmodules {
-			if err := w.updateSubmodules(&SubmoduleUpdateOptions{
+			if err := w.updateSubmodules(ctx, &SubmoduleUpdateOptions{
 				RecurseSubmodules: o.RecurseSubmodules,
 				Depth: func() int {
 					if o.ShallowSubmodules {
@@ -1037,7 +1037,7 @@ func (r *Repository) setIsBare(isBare bool) error {
 	return r.Storer.SetConfig(cfg)
 }

-func (r *Repository) updateRemoteConfigIfNeeded(o *CloneOptions, c *config.RemoteConfig, head *plumbing.Reference) error {
+func (r *Repository) updateRemoteConfigIfNeeded(o *CloneOptions, c *config.RemoteConfig, _ *plumbing.Reference) error {
 	if !o.SingleBranch {
 		return nil
 	}
@@ -4,6 +4,9 @@ import (
 	"bytes"
 	"fmt"
 	"path/filepath"
+
+	mindex "github.com/go-git/go-git/v5/utils/merkletrie/index"
+	"github.com/go-git/go-git/v5/utils/merkletrie/noder"
 )

 // Status represents the current status of a Worktree.
@@ -77,3 +80,69 @@ const (
 	Copied             StatusCode = 'C'
 	UpdatedButUnmerged StatusCode = 'U'
 )
+
+// StatusStrategy defines the different types of strategies when processing
+// the worktree status.
+type StatusStrategy int
+
+const (
+	// TODO: (V6) Review the default status strategy.
+	// TODO: (V6) Review the type used to represent Status, to enable lazy
+	// processing of statuses going direct to the backing filesystem.
+	defaultStatusStrategy = Empty
+
+	// Empty starts its status map from empty. Missing entries for a given
+	// path means that the file is untracked. This causes a known issue (#119)
+	// whereby unmodified files can be incorrectly reported as untracked.
+	//
+	// This can be used when returning the changed state within a modified Worktree.
+	// For example, to check whether the current worktree is clean.
+	Empty StatusStrategy = 0
+	// Preload goes through all existing nodes from the index and add them to the
+	// status map as unmodified. This is currently the most reliable strategy
+	// although it comes at a performance cost in large repositories.
+	//
+	// This method is recommended when fetching the status of unmodified files.
+	// For example, to confirm the status of a specific file that is either
+	// untracked or unmodified.
+	Preload StatusStrategy = 1
+)
+
+func (s StatusStrategy) new(w *Worktree) (Status, error) {
+	switch s {
+	case Preload:
+		return preloadStatus(w)
+	case Empty:
+		return make(Status), nil
+	}
+	return nil, fmt.Errorf("%w: %+v", ErrUnsupportedStatusStrategy, s)
+}
+
+func preloadStatus(w *Worktree) (Status, error) {
+	idx, err := w.r.Storer.Index()
+	if err != nil {
+		return nil, err
+	}
+
+	idxRoot := mindex.NewRootNode(idx)
+	nodes := []noder.Noder{idxRoot}
+
+	status := make(Status)
+	for len(nodes) > 0 {
+		var node noder.Noder
+		node, nodes = nodes[0], nodes[1:]
+		if node.IsDir() {
+			children, err := node.Children()
+			if err != nil {
+				return nil, err
+			}
+			nodes = append(nodes, children...)
+			continue
+		}
+		fs := status.File(node.Name())
+		fs.Worktree = Unmodified
+		fs.Staging = Unmodified
+	}
+
+	return status, nil
+}
@@ -72,6 +72,9 @@ var (
 	// ErrIsDir is returned when a reference file is attempting to be read,
 	// but the path specified is a directory.
 	ErrIsDir = errors.New("reference path is a directory")
+	// ErrEmptyRefFile is returned when a reference file is attempted to be read,
+	// but the file is empty
+	ErrEmptyRefFile = errors.New("ref file is empty")
 )

 // Options holds configuration for the storage.
@@ -249,7 +252,7 @@ func (d *DotGit) objectPacks() ([]plumbing.Hash, error) {
 			continue
 		}

-		h := plumbing.NewHash(n[5 : len(n)-5]) //pack-(hash).pack
+		h := plumbing.NewHash(n[5 : len(n)-5]) // pack-(hash).pack
 		if h.IsZero() {
 			// Ignore files with badly-formatted names.
 			continue
@@ -661,18 +664,33 @@ func (d *DotGit) readReferenceFrom(rd io.Reader, name string) (ref *plumbing.Ref
 		return nil, err
 	}

+	if len(b) == 0 {
+		return nil, ErrEmptyRefFile
+	}
+
 	line := strings.TrimSpace(string(b))
 	return plumbing.NewReferenceFromStrings(name, line), nil
 }

+// checkReferenceAndTruncate reads the reference from the given file, or the `pack-refs` file if
+// the file was empty. Then it checks that the old reference matches the stored reference and
+// truncates the file.
 func (d *DotGit) checkReferenceAndTruncate(f billy.File, old *plumbing.Reference) error {
 	if old == nil {
 		return nil
 	}
+
 	ref, err := d.readReferenceFrom(f, old.Name().String())
+	if errors.Is(err, ErrEmptyRefFile) {
+		// This may happen if the reference is being read from a newly created file.
+		// In that case, try getting the reference from the packed refs file.
+		ref, err = d.packedRef(old.Name())
+	}
+
 	if err != nil {
 		return err
 	}
+
 	if ref.Hash() != old.Hash() {
 		return storage.ErrReferenceHasChanged
 	}
@@ -701,7 +719,11 @@ func (d *DotGit) SetRef(r, old *plumbing.Reference) error {
 // Symbolic references are resolved and included in the output.
 func (d *DotGit) Refs() ([]*plumbing.Reference, error) {
 	var refs []*plumbing.Reference
-	var seen = make(map[plumbing.ReferenceName]bool)
+	seen := make(map[plumbing.ReferenceName]bool)
+	if err := d.addRefFromHEAD(&refs); err != nil {
+		return nil, err
+	}
+
 	if err := d.addRefsFromRefDir(&refs, seen); err != nil {
 		return nil, err
 	}
@@ -710,10 +732,6 @@ func (d *DotGit) Refs() ([]*plumbing.Reference, error) {
 		return nil, err
 	}

-	if err := d.addRefFromHEAD(&refs); err != nil {
-		return nil, err
-	}
-
 	return refs, nil
 }

@@ -815,7 +833,8 @@ func (d *DotGit) addRefsFromPackedRefsFile(refs *[]*plumbing.Reference, f billy.
 }

 func (d *DotGit) openAndLockPackedRefs(doCreate bool) (
-	pr billy.File, err error) {
+	pr billy.File, err error,
+) {
 	var f billy.File
 	defer func() {
 		if err != nil && f != nil {
@@ -1020,7 +1039,7 @@ func (d *DotGit) readReferenceFile(path, name string) (ref *plumbing.Reference,

 func (d *DotGit) CountLooseRefs() (int, error) {
 	var refs []*plumbing.Reference
-	var seen = make(map[plumbing.ReferenceName]bool)
+	seen := make(map[plumbing.ReferenceName]bool)
 	if err := d.addRefsFromRefDir(&refs, seen); err != nil {
 		return 0, err
 	}
@@ -48,7 +48,7 @@ func (s *IndexStorage) Index() (i *index.Index, err error) {

 	defer ioutil.CheckClose(f, &err)

-	d := index.NewDecoder(bufio.NewReader(f))
+	d := index.NewDecoder(f)
 	err = d.Decode(idx)
 	return idx, err
 }
@@ -431,13 +431,13 @@ func (s *ObjectStorage) getFromUnpacked(h plumbing.Hash) (obj plumbing.EncodedOb

 	defer ioutil.CheckClose(w, &err)

-	s.objectCache.Put(obj)
-
 	bufp := copyBufferPool.Get().(*[]byte)
 	buf := *bufp
 	_, err = io.CopyBuffer(w, r, buf)
 	copyBufferPool.Put(bufp)

+	s.objectCache.Put(obj)
+
 	return obj, err
 }

@@ -214,10 +214,10 @@ func (s *Submodule) update(ctx context.Context, o *SubmoduleUpdateOptions, force
 		return err
 	}

-	return s.doRecursiveUpdate(r, o)
+	return s.doRecursiveUpdate(ctx, r, o)
 }

-func (s *Submodule) doRecursiveUpdate(r *Repository, o *SubmoduleUpdateOptions) error {
+func (s *Submodule) doRecursiveUpdate(ctx context.Context, r *Repository, o *SubmoduleUpdateOptions) error {
 	if o.RecurseSubmodules == NoRecurseSubmodules {
 		return nil
 	}
@@ -236,7 +236,7 @@ func (s *Submodule) doRecursiveUpdate(r *Repository, o *SubmoduleUpdateOptions)
 	*new = *o

 	new.RecurseSubmodules--
-	return l.Update(new)
+	return l.UpdateContext(ctx, new)
 }

 func (s *Submodule) fetchAndCheckout(
@@ -1,12 +1,17 @@
 package merkletrie

 import (
+	"errors"
 	"fmt"
 	"io"

 	"github.com/go-git/go-git/v5/utils/merkletrie/noder"
 )

+var (
+	ErrEmptyFileName = errors.New("empty filename in tree entry")
+)
+
 // Action values represent the kind of things a Change can represent:
 // insertion, deletions or modifications of files.
 type Action int
@@ -121,6 +126,10 @@ func (l *Changes) AddRecursiveDelete(root noder.Path) error {
 type noderToChangeFn func(noder.Path) Change // NewInsert or NewDelete

 func (l *Changes) addRecursive(root noder.Path, ctor noderToChangeFn) error {
+	if root.String() == "" {
+		return ErrEmptyFileName
+	}
+
 	if !root.IsDir() {
 		l.Add(ctor(root))
 		return nil
@@ -11,7 +11,7 @@ package merkletrie
 // corresponding changes and move the iterators further over both
 // trees.
 //
-// The table bellow show all the possible comparison results, along
+// The table below shows all the possible comparison results, along
 // with what changes should we produce and how to advance the
 // iterators.
 //
@@ -13,7 +13,7 @@ var bufioReader = sync.Pool{
 }

 // GetBufioReader returns a *bufio.Reader that is managed by a sync.Pool.
-// Returns a bufio.Reader that is resetted with reader and ready for use.
+// Returns a bufio.Reader that is reset with reader and ready for use.
 //
 // After use, the *bufio.Reader should be put back into the sync.Pool
 // by calling PutBufioReader.
@@ -35,7 +35,7 @@ func PutByteSlice(buf *[]byte) {
 }

 // GetBytesBuffer returns a *bytes.Buffer that is managed by a sync.Pool.
-// Returns a buffer that is resetted and ready for use.
+// Returns a buffer that is reset and ready for use.
 //
 // After use, the *bytes.Buffer should be put back into the sync.Pool
 // by calling PutBytesBuffer.
@@ -35,7 +35,7 @@ type ZLibReader struct {
 }

 // GetZlibReader returns a ZLibReader that is managed by a sync.Pool.
-// Returns a ZLibReader that is resetted using a dictionary that is
+// Returns a ZLibReader that is reset using a dictionary that is
 // also managed by a sync.Pool.
 //
 // After use, the ZLibReader should be put back into the sync.Pool
@@ -58,7 +58,7 @@ func PutZlibReader(z ZLibReader) {
 }

 // GetZlibWriter returns a *zlib.Writer that is managed by a sync.Pool.
-// Returns a writer that is resetted with w and ready for use.
+// Returns a writer that is reset with w and ready for use.
 //
 // After use, the *zlib.Writer should be put back into the sync.Pool
 // by calling PutZlibWriter.
@@ -25,11 +25,12 @@ import (
 )

 var (
-	ErrWorktreeNotClean     = errors.New("worktree is not clean")
-	ErrSubmoduleNotFound    = errors.New("submodule not found")
-	ErrUnstagedChanges      = errors.New("worktree contains unstaged changes")
-	ErrGitModulesSymlink    = errors.New(gitmodulesFile + " is a symlink")
-	ErrNonFastForwardUpdate = errors.New("non-fast-forward update")
+	ErrWorktreeNotClean                = errors.New("worktree is not clean")
+	ErrSubmoduleNotFound               = errors.New("submodule not found")
+	ErrUnstagedChanges                 = errors.New("worktree contains unstaged changes")
+	ErrGitModulesSymlink               = errors.New(gitmodulesFile + " is a symlink")
+	ErrNonFastForwardUpdate            = errors.New("non-fast-forward update")
+	ErrRestoreWorktreeOnlyNotSupported = errors.New("worktree only is not supported")
 )

 // Worktree represents a git worktree.
@@ -139,7 +140,7 @@ func (w *Worktree) PullContext(ctx context.Context, o *PullOptions) error {
 	}

 	if o.RecurseSubmodules != NoRecurseSubmodules {
-		return w.updateSubmodules(&SubmoduleUpdateOptions{
+		return w.updateSubmodules(ctx, &SubmoduleUpdateOptions{
 			RecurseSubmodules: o.RecurseSubmodules,
 			Auth:              o.Auth,
 		})
@@ -148,13 +149,13 @@ func (w *Worktree) PullContext(ctx context.Context, o *PullOptions) error {
 	return nil
 }

-func (w *Worktree) updateSubmodules(o *SubmoduleUpdateOptions) error {
+func (w *Worktree) updateSubmodules(ctx context.Context, o *SubmoduleUpdateOptions) error {
 	s, err := w.Submodules()
 	if err != nil {
 		return err
 	}
 	o.Init = true
-	return s.Update(o)
+	return s.UpdateContext(ctx, o)
 }

 // Checkout switch branches or restore working tree files.
@@ -307,13 +308,13 @@ func (w *Worktree) ResetSparsely(opts *ResetOptions, dirs []string) error {
 	}

 	if opts.Mode == MixedReset || opts.Mode == MergeReset || opts.Mode == HardReset {
-		if err := w.resetIndex(t, dirs); err != nil {
+		if err := w.resetIndex(t, dirs, opts.Files); err != nil {
 			return err
 		}
 	}

 	if opts.Mode == MergeReset || opts.Mode == HardReset {
-		if err := w.resetWorktree(t); err != nil {
+		if err := w.resetWorktree(t, opts.Files); err != nil {
 			return err
 		}
 	}
@@ -321,20 +322,52 @@ func (w *Worktree) ResetSparsely(opts *ResetOptions, dirs []string) error {
 	return nil
 }

+// Restore restores specified files in the working tree or stage with contents from
+// a restore source. If a path is tracked but does not exist in the restore,
+// source, it will be removed to match the source.
+//
+// If Staged and Worktree are true, then the restore source will be the index.
+// If only Staged is true, then the restore source will be HEAD.
+// If only Worktree is true or neither Staged nor Worktree are true, will
+// result in ErrRestoreWorktreeOnlyNotSupported because restoring the working
+// tree while leaving the stage untouched is not currently supported.
+//
+// Restore with no files specified will return ErrNoRestorePaths.
+func (w *Worktree) Restore(o *RestoreOptions) error {
+	if err := o.Validate(); err != nil {
+		return err
+	}
+
+	if o.Staged {
+		opts := &ResetOptions{
+			Files: o.Files,
+		}
+
+		if o.Worktree {
+			// If we are doing both Worktree and Staging then it is a hard reset
+			opts.Mode = HardReset
+		} else {
+			// If we are doing just staging then it is a mixed reset
+			opts.Mode = MixedReset
+		}
+
+		return w.Reset(opts)
+	}
+
+	return ErrRestoreWorktreeOnlyNotSupported
+}
+
 // Reset the worktree to a specified state.
 func (w *Worktree) Reset(opts *ResetOptions) error {
 	return w.ResetSparsely(opts, nil)
 }

-func (w *Worktree) resetIndex(t *object.Tree, dirs []string) error {
+func (w *Worktree) resetIndex(t *object.Tree, dirs []string, files []string) error {
 	idx, err := w.r.Storer.Index()
-	if len(dirs) > 0 {
-		idx.SkipUnless(dirs)
-	}
-
 	if err != nil {
 		return err
 	}
+
 	b := newIndexBuilder(idx)

 	changes, err := w.diffTreeWithStaging(t, true)
@@ -362,6 +395,13 @@ func (w *Worktree) resetIndex(t *object.Tree, dirs []string) error {
 			name = ch.From.String()
 		}

+		if len(files) > 0 {
+			contains := inFiles(files, name)
+			if !contains {
+				continue
+			}
+		}
+
 		b.Remove(name)
 		if e == nil {
 			continue
@@ -376,10 +416,25 @@ func (w *Worktree) resetIndex(t *object.Tree, dirs []string) error {
 	}

 	b.Write(idx)
+
+	if len(dirs) > 0 {
+		idx.SkipUnless(dirs)
+	}
+
 	return w.r.Storer.SetIndex(idx)
 }

-func (w *Worktree) resetWorktree(t *object.Tree) error {
+func inFiles(files []string, v string) bool {
+	for _, s := range files {
+		if s == v {
+			return true
+		}
+	}
+
+	return false
+}
+
+func (w *Worktree) resetWorktree(t *object.Tree, files []string) error {
 	changes, err := w.diffStagingWithWorktree(true, false)
 	if err != nil {
 		return err
@@ -395,6 +450,25 @@ func (w *Worktree) resetWorktree(t *object.Tree) error {
 		if err := w.validChange(ch); err != nil {
 			return err
 		}
+
+		if len(files) > 0 {
+			file := ""
+			if ch.From != nil {
+				file = ch.From.String()
+			} else if ch.To != nil {
+				file = ch.To.String()
+			}
+
+			if file == "" {
+				continue
+			}
+
+			contains := inFiles(files, file)
+			if !contains {
+				continue
+			}
+		}
+
 		if err := w.checkoutChange(ch, t, b); err != nil {
 			return err
 		}
@@ -642,7 +716,7 @@ func (w *Worktree) checkoutChangeRegularFile(name string,
 			return err
 		}

-		return w.addIndexFromFile(name, e.Hash, idx)
+		return w.addIndexFromFile(name, e.Hash, f.Mode, idx)
 	}

 	return nil
@@ -725,18 +799,13 @@ func (w *Worktree) addIndexFromTreeEntry(name string, f *object.TreeEntry, idx *
 	return nil
 }

-func (w *Worktree) addIndexFromFile(name string, h plumbing.Hash, idx *indexBuilder) error {
+func (w *Worktree) addIndexFromFile(name string, h plumbing.Hash, mode filemode.FileMode, idx *indexBuilder) error {
 	idx.Remove(name)
 	fi, err := w.Filesystem.Lstat(name)
 	if err != nil {
 		return err
 	}

-	mode, err := filemode.NewFromOSFileMode(fi.Mode())
-	if err != nil {
-		return err
-	}
-
 	e := &index.Entry{
 		Hash:       h,
 		Name:       name,
@@ -1058,7 +1127,7 @@ func rmFileAndDirsIfEmpty(fs billy.Filesystem, name string) error {
 	dir := filepath.Dir(name)
 	for {
 		removed, err := removeDirIfEmpty(fs, dir)
-		if err != nil {
+		if err != nil && !os.IsNotExist(err) {
 			return err
 		}

@@ -5,6 +5,7 @@ import (
 	"errors"
 	"io"
 	"path"
+	"regexp"
 	"sort"
 	"strings"

@@ -23,6 +24,10 @@ var (
 	// ErrEmptyCommit occurs when a commit is attempted using a clean
 	// working tree, with no changes to be committed.
 	ErrEmptyCommit = errors.New("cannot create empty commit: clean working tree")
+
+	// characters to be removed from user name and/or email before using them to build a commit object
+	// See https://git-scm.com/docs/git-commit#_commit_information
+	invalidCharactersRe = regexp.MustCompile(`[<>\n]`)
 )

 // Commit stores the current contents of the index in a new commit along with
@@ -38,8 +43,6 @@ func (w *Worktree) Commit(msg string, opts *CommitOptions) (plumbing.Hash, error
 		}
 	}

-	var treeHash plumbing.Hash
-
 	if opts.Amend {
 		head, err := w.r.Head()
 		if err != nil {
@@ -61,16 +64,34 @@ func (w *Worktree) Commit(msg string, opts *CommitOptions) (plumbing.Hash, error
 		return plumbing.ZeroHash, err
 	}

+	// First handle the case of the first commit in the repository being empty.
+	if len(opts.Parents) == 0 && len(idx.Entries) == 0 && !opts.AllowEmptyCommits {
+		return plumbing.ZeroHash, ErrEmptyCommit
+	}
+
 	h := &buildTreeHelper{
 		fs: w.Filesystem,
 		s:  w.r.Storer,
 	}

-	treeHash, err = h.BuildTree(idx, opts)
+	treeHash, err := h.BuildTree(idx, opts)
 	if err != nil {
 		return plumbing.ZeroHash, err
 	}

+	previousTree := plumbing.ZeroHash
+	if len(opts.Parents) > 0 {
+		parentCommit, err := w.r.CommitObject(opts.Parents[0])
+		if err != nil {
+			return plumbing.ZeroHash, err
+		}
+		previousTree = parentCommit.TreeHash
+	}
+
+	if treeHash == previousTree && !opts.AllowEmptyCommits {
+		return plumbing.ZeroHash, ErrEmptyCommit
+	}
+
 	commit, err := w.buildCommitObject(msg, opts, treeHash)
 	if err != nil {
 		return plumbing.ZeroHash, err
@@ -121,8 +142,8 @@ func (w *Worktree) updateHEAD(commit plumbing.Hash) error {

 func (w *Worktree) buildCommitObject(msg string, opts *CommitOptions, tree plumbing.Hash) (plumbing.Hash, error) {
 	commit := &object.Commit{
-		Author:       *opts.Author,
-		Committer:    *opts.Committer,
+		Author:       w.sanitize(*opts.Author),
+		Committer:    w.sanitize(*opts.Committer),
 		Message:      msg,
 		TreeHash:     tree,
 		ParentHashes: opts.Parents,
@@ -148,6 +169,14 @@ func (w *Worktree) buildCommitObject(msg string, opts *CommitOptions, tree plumb
 	return w.r.Storer.SetEncodedObject(obj)
 }

+func (w *Worktree) sanitize(signature object.Signature) object.Signature {
+	return object.Signature{
+		Name:  invalidCharactersRe.ReplaceAllString(signature.Name, ""),
+		Email: invalidCharactersRe.ReplaceAllString(signature.Email, ""),
+		When:  signature.When,
+	}
+}
+
 type gpgSigner struct {
 	key *openpgp.Entity
 	cfg *packet.Config
@@ -175,10 +204,6 @@ type buildTreeHelper struct {
 // BuildTree builds the tree objects and push its to the storer, the hash
 // of the root tree is returned.
 func (h *buildTreeHelper) BuildTree(idx *index.Index, opts *CommitOptions) (plumbing.Hash, error) {
-	if len(idx.Entries) == 0 && (opts == nil || !opts.AllowEmptyCommits) {
-		return plumbing.ZeroHash, ErrEmptyCommit
-	}
-
 	const rootNode = ""
 	h.trees = map[string]*object.Tree{rootNode: {}}
 	h.entries = map[string]*object.TreeEntry{}
@@ -1,3 +1,4 @@
+//go:build linux
 // +build linux

 package git
@@ -21,6 +22,6 @@ func init() {
 	}
 }

-func isSymlinkWindowsNonAdmin(err error) bool {
+func isSymlinkWindowsNonAdmin(_ error) bool {
 	return false
 }
@@ -29,10 +29,23 @@ var (
 	// ErrGlobNoMatches in an AddGlob if the glob pattern does not match any
 	// files in the worktree.
 	ErrGlobNoMatches = errors.New("glob pattern did not match any files")
+	// ErrUnsupportedStatusStrategy occurs when an invalid StatusStrategy is used
+	// when processing the Worktree status.
+	ErrUnsupportedStatusStrategy = errors.New("unsupported status strategy")
 )

 // Status returns the working tree status.
 func (w *Worktree) Status() (Status, error) {
+	return w.StatusWithOptions(StatusOptions{Strategy: defaultStatusStrategy})
+}
+
+// StatusOptions defines the options for Worktree.StatusWithOptions().
+type StatusOptions struct {
+	Strategy StatusStrategy
+}
+
+// StatusWithOptions returns the working tree status.
+func (w *Worktree) StatusWithOptions(o StatusOptions) (Status, error) {
 	var hash plumbing.Hash

 	ref, err := w.r.Head()
@@ -44,11 +57,14 @@ func (w *Worktree) Status() (Status, error) {
 		hash = ref.Hash()
 	}

-	return w.status(hash)
+	return w.status(o.Strategy, hash)
 }

-func (w *Worktree) status(commit plumbing.Hash) (Status, error) {
-	s := make(Status)
+func (w *Worktree) status(ss StatusStrategy, commit plumbing.Hash) (Status, error) {
+	s, err := ss.new(w)
+	if err != nil {
+		return nil, err
+	}

 	left, err := w.diffCommitWithStaging(commit, false)
 	if err != nil {
@@ -488,7 +504,7 @@ func (w *Worktree) copyFileToStorage(path string) (hash plumbing.Hash, err error
 	return w.r.Storer.SetEncodedObject(obj)
 }

-func (w *Worktree) fillEncodedObjectFromFile(dst io.Writer, path string, fi os.FileInfo) (err error) {
+func (w *Worktree) fillEncodedObjectFromFile(dst io.Writer, path string, _ os.FileInfo) (err error) {
 	src, err := w.Filesystem.Open(path)
 	if err != nil {
 		return err
@@ -503,7 +519,7 @@ func (w *Worktree) fillEncodedObjectFromFile(dst io.Writer, path string, fi os.F
 	return err
 }

-func (w *Worktree) fillEncodedObjectFromSymlink(dst io.Writer, path string, fi os.FileInfo) error {
+func (w *Worktree) fillEncodedObjectFromSymlink(dst io.Writer, path string, _ os.FileInfo) error {
 	target, err := w.Filesystem.Readlink(path)
 	if err != nil {
 		return err
@@ -543,9 +559,11 @@ func (w *Worktree) doUpdateFileToIndex(e *index.Entry, filename string, h plumbi
 		return err
 	}

-	if e.Mode.IsRegular() {
-		e.Size = uint32(info.Size())
-	}
+	// The entry size must always reflect the current state, otherwise
+	// it will cause go-git's Worktree.Status() to divert from "git status".
+	// The size of a symlink is the length of the path to the target.
+	// The size of Regular and Executable files is the size of the files.
+	e.Size = uint32(info.Size())

 	fillSystemInfo(e, info.Sys())
 	return nil