Fix reverting a merge commit failing (#28794) (#28825)

Backport https://github.com/go-gitea/gitea/pull/28794

Fixes #22236

---
Error occurring currently while trying to revert commit using read-tree
-m approach:
> 2022/12/26 16:04:43 ...rvices/pull/patch.go:240:AttemptThreeWayMerge()
[E] [63a9c61a] Unable to run read-tree -m! Error: exit status 128 -
fatal: this operation must be run in a work tree
> 	 - fatal: this operation must be run in a work tree

We need to clone a non-bare repository for `git read-tree -m` to work.

bb371aee6e
adds support to create a non-bare cloned temporary upload repository.

After cloning a non-bare temporary upload repository, we [set default
index](https://github.com/go-gitea/gitea/blob/main/services/repository/files/cherry_pick.go#L37)
(`git read-tree HEAD`).
This operation ends up resetting the git index file (see investigation
details below), due to which, we need to call `git update-index
--refresh` afterward.

Here's the diff of the index file before and after we execute
SetDefaultIndex: https://www.diffchecker.com/hyOP3eJy/

Notice the **ctime**, **mtime** are set to 0 after SetDefaultIndex.

You can reproduce the same behavior using these steps:
```bash
$ git clone https://try.gitea.io/me-heer/test.git -s -b main
$ cd test
$ git read-tree HEAD
$ git read-tree -m 1f085d7ed8 1f085d7ed8 9933caed00
error: Entry '1' not uptodate. Cannot merge.
```

After which, we can fix like this:
```bash
$ git update-index --refresh
$ git read-tree -m 1f085d7ed8 1f085d7ed8 9933caed00
```

(cherry picked from commit 62f2d717b7e04565c5ff260746e43ed64a87b0e0)

services/packages/cargo/index.go

@@ -267,7 +267,7 @@ func alterRepositoryContent(ctx context.Context, doer *user_model.User, repo *re
 	defer t.Close()
 
 	var lastCommitID string
-	if err := t.Clone(repo.DefaultBranch); err != nil {
+	if err := t.Clone(repo.DefaultBranch, true); err != nil {
 		if !git.IsErrBranchNotExist(err) || !repo.IsEmpty {
 			return err
 		}

services/repository/files/cherry_pick.go

@@ -31,12 +31,15 @@ func CherryPick(ctx context.Context, repo *repo_model.Repository, doer *user_mod
 		log.Error("%v", err)
 	}
 	defer t.Close()
-	if err := t.Clone(opts.OldBranch); err != nil {
+	if err := t.Clone(opts.OldBranch, false); err != nil {
 		return nil, err
 	}
 	if err := t.SetDefaultIndex(); err != nil {
 		return nil, err
 	}
+	if err := t.RefreshIndex(); err != nil {
+		return nil, err
+	}
 
 	// Get the commit of the original branch
 	commit, err := t.GetBranchCommit(opts.OldBranch)

services/repository/files/diff.go

@@ -21,7 +21,7 @@ func GetDiffPreview(ctx context.Context, repo *repo_model.Repository, branch, tr
 		return nil, err
 	}
 	defer t.Close()
-	if err := t.Clone(branch); err != nil {
+	if err := t.Clone(branch, true); err != nil {
 		return nil, err
 	}
 	if err := t.SetDefaultIndex(); err != nil {

services/repository/files/patch.go

@@ -108,7 +108,7 @@ func ApplyDiffPatch(ctx context.Context, repo *repo_model.Repository, doer *user
 		log.Error("%v", err)
 	}
 	defer t.Close()
-	if err := t.Clone(opts.OldBranch); err != nil {
+	if err := t.Clone(opts.OldBranch, true); err != nil {
 		return nil, err
 	}
 	if err := t.SetDefaultIndex(); err != nil {

services/repository/files/temp_repo.go

@@ -51,8 +51,13 @@ func (t *TemporaryUploadRepository) Close() {
 }
 
 // Clone the base repository to our path and set branch as the HEAD
-func (t *TemporaryUploadRepository) Clone(branch string) error {
-	if _, _, err := git.NewCommand(t.ctx, "clone", "-s", "--bare", "-b").AddDynamicArguments(branch, t.repo.RepoPath(), t.basePath).RunStdString(nil); err != nil {
+func (t *TemporaryUploadRepository) Clone(branch string, bare bool) error {
+	cmd := git.NewCommand(t.ctx, "clone", "-s", "-b").AddDynamicArguments(branch, t.repo.RepoPath(), t.basePath)
+	if bare {
+		cmd.AddArguments("--bare")
+	}
+
+	if _, _, err := cmd.RunStdString(nil); err != nil {
 		stderr := err.Error()
 		if matched, _ := regexp.MatchString(".*Remote branch .* not found in upstream origin.*", stderr); matched {
 			return git.ErrBranchNotExist{
@@ -98,6 +103,14 @@ func (t *TemporaryUploadRepository) SetDefaultIndex() error {
 	return nil
 }
 
+// RefreshIndex looks at the current index and checks to see if merges or updates are needed by checking stat() information.
+func (t *TemporaryUploadRepository) RefreshIndex() error {
+	if _, _, err := git.NewCommand(t.ctx, "update-index", "--refresh").RunStdString(&git.RunOpts{Dir: t.basePath}); err != nil {
+		return fmt.Errorf("RefreshIndex: %w", err)
+	}
+	return nil
+}
+
 // LsFiles checks if the given filename arguments are in the index
 func (t *TemporaryUploadRepository) LsFiles(filenames ...string) ([]string, error) {
 	stdOut := new(bytes.Buffer)

services/repository/files/update.go

@@ -141,7 +141,7 @@ func ChangeRepoFiles(ctx context.Context, repo *repo_model.Repository, doer *use
 	}
 	defer t.Close()
 	hasOldBranch := true
-	if err := t.Clone(opts.OldBranch); err != nil {
+	if err := t.Clone(opts.OldBranch, true); err != nil {
 		for _, file := range opts.Files {
 			if file.Operation == "delete" {
 				return nil, err

services/repository/files/upload.go

@@ -87,7 +87,7 @@ func UploadRepoFiles(ctx context.Context, repo *repo_model.Repository, doer *use
 	defer t.Close()
 
 	hasOldBranch := true
-	if err = t.Clone(opts.OldBranch); err != nil {
+	if err = t.Clone(opts.OldBranch, true); err != nil {
 		if !git.IsErrBranchNotExist(err) || !repo.IsEmpty {
 			return err
 		}