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
```

tests/gitea-repositories-meta/user2/test_commit_revert.git/HEAD

@@ -0,0 +1 @@
+ref: refs/heads/main

tests/gitea-repositories-meta/user2/test_commit_revert.git/config

@@ -0,0 +1,8 @@
+[core]
+	repositoryformatversion = 0
+	filemode = true
+	bare = true
+	ignorecase = true
+	precomposeunicode = true
+[remote "origin"]
+	url = https://try.gitea.io/me-heer/test_commit_revert.git

tests/gitea-repositories-meta/user2/test_commit_revert.git/description

@@ -0,0 +1 @@
+Unnamed repository; edit this file 'description' to name the repository.

tests/gitea-repositories-meta/user2/test_commit_revert.git/info/exclude

@@ -0,0 +1,6 @@
+# git ls-files --others --exclude-from=.git/info/exclude
+# Lines that start with '#' are comments.
+# For a project mostly in C, the following would be a good set of
+# exclude patterns (uncomment them if you want to use them):
+# *.[oa]
+# *~

tests/gitea-repositories-meta/user2/test_commit_revert.git/packed-refs

@@ -0,0 +1,3 @@
+# pack-refs with: peeled fully-peeled sorted 
+46aa6ab2c881ae90e15d9ccfc947d1625c892ce5 refs/heads/develop
+deebcbc752e540bab4ce3ee713d3fc8fdc35b2f7 refs/heads/main

tests/integration/repo_mergecommit_revert_test.go

@@ -0,0 +1,34 @@
+package integration
+
+import (
+	"net/http"
+	"testing"
+
+	"code.gitea.io/gitea/tests"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestRepoMergeCommitRevert(t *testing.T) {
+	defer tests.PrepareTestEnv(t)()
+	session := loginUser(t, "user2")
+
+	req := NewRequest(t, "GET", "/user2/test_commit_revert/_cherrypick/deebcbc752e540bab4ce3ee713d3fc8fdc35b2f7/main?ref=main&refType=branch&cherry-pick-type=revert")
+	resp := session.MakeRequest(t, req, http.StatusOK)
+
+	htmlDoc := NewHTMLParser(t, resp.Body)
+	req = NewRequestWithValues(t, "POST", "/user2/test_commit_revert/_cherrypick/deebcbc752e540bab4ce3ee713d3fc8fdc35b2f7/main", map[string]string{
+		"_csrf":           htmlDoc.GetCSRF(),
+		"last_commit":     "deebcbc752e540bab4ce3ee713d3fc8fdc35b2f7",
+		"page_has_posted": "true",
+		"revert":          "true",
+		"commit_summary":  "reverting test commit",
+		"commit_message":  "test message",
+		"commit_choice":   "direct",
+		"new_branch_name": "test-revert-branch-1",
+	})
+	resp = session.MakeRequest(t, req, http.StatusSeeOther)
+
+	// A successful revert redirects to the main branch
+	assert.EqualValues(t, "/user2/test_commit_revert/src/branch/main", resp.Header().Get("Location"))
+}