Fixes go-gitea#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.

go-gitea@bb371ae
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:
```
$ git update-index --refresh
$ git read-tree -m 1f085d7ed8 1f085d7ed8 9933caed00
```