Fix reverting a merge commit failing (#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:
```
$ git update-index --refresh
$ git read-tree -m 1f085d7ed8 1f085d7ed8 9933caed00
```

models/fixtures/repo_unit.yml

@@ -669,3 +669,10 @@
   type: 10
   config: "{}"
   created_unix: 946684810
+
+-
+  id: 101
+  repo_id: 59
+  type: 1
+  config: "{}"
+  created_unix: 946684810

models/fixtures/repository.yml

@@ -1693,3 +1693,16 @@
   size: 0
   is_fsck_enabled: true
   close_issues_via_commit_in_any_branch: false
+
+-
+  id: 59
+  owner_id: 2
+  owner_name: user2
+  lower_name: test_commit_revert
+  name: test_commit_revert
+  default_branch: main
+  is_empty: false
+  is_archived: false
+  is_private: true
+  status: 0
+  num_issues: 0

models/fixtures/user.yml

@@ -66,7 +66,7 @@
   num_followers: 2
   num_following: 1
   num_stars: 2
-  num_repos: 14
+  num_repos: 15
   num_teams: 0
   num_members: 0
   visibility: 0