Steps to reproduce:

On multibranch pipeline job, configure GitlabSCMSource with a clone option trait that has the shallow flag turned on.

CloneOption cloneOption = new CloneOption(true, true, "", 30);

Trigger a build of a merge request. 

Expected result:

Merge request should succeed.

Actual result:

Merge requests fails with error: 

stderr: fatal: refusing to merge unrelated histories

I believe this problem could be resolved by using

MergeWithGitSCMExtension

from the git-plugin class. The github-branch-source-plugin and the bitbucket-branch-source-plugin have both deprecated their instances of this class in order to use the one in the Git plugin. See https://github.com/jenkinsci/git-plugin/blob/5b3300dfb225927551b8b9b86efed7aa74100884/src/main/java/jenkins/plugins/git/MergeWithGitSCMExtension.java#L88

For now, our workaround is to set the shallow flag to false, which impacts all builds with Gitlab. We'd like to only set shallow to false when building MRs.