Fix reverting a merge commit failing (#28794)

[me-heer]

Backport #28794

Fixes #22236

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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.

bb371ae adds support to create a non-bare cloned temporary upload repository.

After cloning a non-bare temporary upload repository, we set default index (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:

$ 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