Backport https://github.com/go-gitea/gitea/pull/28794Fixes#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
```
Backport #28844 by @AdamMajer
Git 2.43.0 will not detect a git repository as valid without refs/
subdirectory present. `git gc` cleans this up and puts it in
packed-refs. We must keep refs/ non-empty.
Co-authored-by: Adam Majer <amajer@suse.de>
