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	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
```
			
			
This commit is contained in:
		| @@ -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) | ||||
|   | ||||
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