PR merge using Rebase and merge times out

Issue Summary

While trying to merge PR using Rebase and merge or Rebase and fast-forward strategy getting the message: 'git cat-file --batch' timed out; exited with code 0 on the Bitbucket UI and in the logs.

This is reproducible on Data Center: Not tried

Steps to Reproduce

1. Step 1: Create branch in repository where the first file is encountered within a subdirectory more than 1 level deep
2. Step 2: Create a PR between another branch with the same kind of directory structure (this can happen if either source or destination branch has only folders at the top-level or both the branches have only folders at the top-level)
3. Step 3: Try to merge using Rebase and Merge strategy

Expected Results

The PR will be merged successfully.

Actual Results

The PR merge will timeout after around 5 minutes
The below exception is thrown in the atlassian-bitbucket.log file:

2023-04-05 18:49:31,022 DEBUG [http-nio-6882-exec-8] ajaitly @XEBU6Fx1124x347x0 1c0nnck 0:0:0:0:0:0:0:1 "POST /rest/api/latest/projects/FIR/repos/dir-test/pull-requests/2/merge HTTP/1.1" c.a.s.i.r.e.ServiceExceptionMapper Mapping ServiceException to REST response 500
com.atlassian.bitbucket.scm.CommandTimeoutException: 'git cat-file --batch' timed out; exited with code 0
	at com.atlassian.stash.internal.scm.git.mesh.DefaultErrorTranslator.translateTimeout(DefaultErrorTranslator.java:426)
...............

can also be exited with code 15 in some cases.

• Bitbucket Profiler logs:

  2023-04-05 18:49:31,028 | http-nio-6882-exec-8 | @XEBU6Fx1124x347x0 | ajaitly | 1c0nnck
  [300082.5ms] - "POST /rest/api/latest/projects/FIR/repos/dir-test/pull-requests/2/merge HTTP/1.1"
   [300066.3ms] - PullRequest com.atlassian.bitbucket.pull.PullRequestService.merge(PullRequestMergeRequest)
    [1.6ms] - InternalPullRequest com.atlassian.stash.internal.pull.PullRequestDao.findByRepositoryScopedId(int,long)
    [1.1ms] - Object com.atlassian.stash.internal.Dao.update(Object)
    [300050.8ms] - Branch com.atlassian.stash.internal.scm.git.mesh.RpcPullRequestClient.merge(PullRequest,Builder,String)
    [2.2ms] - Object com.atlassian.stash.internal.Dao.update(Object)
  

• Bitbucket Access logs:

  0:0:0:0:0:0:0:1 | http | o@XEBU6Fx1124x347x0 | ajaitly | 2023-04-05 18:49:31,028 | "POST /rest/api/latest/projects/FIR/repos/dir-test/pull-requests/2/merge HTTP/1.1" | "http://localhost:6882/b882/projects/FIR/repos/dir-test/pull-requests/2/overview" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/111.0.0.0 Safari/537.36" | 500 | 133 | 164 | - | 300083 | 1c0nnck | 
  

• Mesh application logs

  2023-04-05 18:44:23,860 DEBUG [grpc-server:thread-19] ajaitly 4518L3RRx1124x240x2 @XEBU6Fx1124x324x0 127.0.0.1 "PullRequestService/UpdateRefs" (>1 <0) c.a.bitbucket.mesh.git.RawGitAgent afd42a5d473d451cd133-12: Could not resolve refs/pull-requests/2/from directly or from packed-refs
  2023-04-05 18:44:23,861 DEBUG [grpc-server:thread-19] ajaitly 4518L3RRx1124x240x2 @XEBU6Fx1124x324x0 127.0.0.1 "PullRequestService/UpdateRefs" (>1 <0) c.a.bitbucket.mesh.git.RawGitAgent afd42a5d473d451cd133-12: Could not resolve refs/pull-requests/2/merge directly or from packed-refs
  2023-04-05 18:44:23,862 DEBUG [grpc-server:thread-19] ajaitly 4518L3RRx1124x240x2 @XEBU6Fx1124x324x0 127.0.0.1 "PullRequestService/UpdateRefs" (>1 <0) c.a.bitbucket.mesh.git.RawGitAgent afd42a5d473d451cd133-12: Could not resolve stash-refs/pull-requests/2/from directly or from packed-refs
  2023-04-05 18:44:23,864 DEBUG [grpc-server:thread-19] ajaitly 4518L3RRx1124x240x2 @XEBU6Fx1124x324x0 127.0.0.1 "PullRequestService/UpdateRefs" (>1 <0) c.a.bitbucket.mesh.git.RawGitAgent afd42a5d473d451cd133-12: Could not resolve refs/pull-requests/2/from directly or from packed-refs
  

Workaround

• Workaround 1: Try using a different merge strategy for merging the pull request (for example "Merge commit --no-ff" or "Squash --squash")
• Workaround 2: Add a file to the top-level of the repository