Summary

Merging a pull request with 'rebase and fast-forward' strategy gives merge conflict error in Bitbucket server. However, there is no actual conflict within commits as they are empty. The pull request can be merged with a different merge strategy without issues. 
On the UI, it errors with 

The merge could not be completed automatically. Please clone 'project/repo, checkout 'branch_1' and merge 'branch_2' (or commit 'commit_hash_2') manually, resolving any conflicts, and push the result.

Environment

Bitbucket server / Datacenter 6.10.0

Git on the server was built from the source

Diagnosis

From Bitbucket logs, we see the merge operation fails with 

com.atlassian.bitbucket.scm.MergeException: The merge could not be completed automatically. Please clone '<PROJ/REPOSITORY>', checkout '<BRANCH1>' and merge '<BRANCH2>' (or commit '<commit-hash>') manually, resolving any conflicts, and push the result.
.
Caused by: com.atlassian.bitbucket.scm.CommandFailedException: '/opt/git/git_current/bin/git rebase -q --no-verify commit_hash_1 commit_hash_2' exited with code 1 saying: /opt/git/git_current/libexec/git-core/git-sh-setup: line 46: /opt/tmp/git/libexec/git-core/git-sh-i18n: No such file or directory

Cause

Git couldn't find the file /opt/tmp/git/libexec/git-core/git-sh-i18n

Solution

Confirm if the file /opt/tmp/git/libexec/git-core/git-sh-i18n exists and is being used by the git that Bitbucket Server is using.

In this case, the file that git couldn't find is git-core/git-sh-i18n

• As this is a core git file, this error might indicate that the git binary being used is incomplete and git should be reinstalled.
• If the file is present, it can be pointed to using environment variables. Using Git Internals - Environment Variables as a guide, GIT_EXEC_PATH can be set for the Bitbucket Server user (atlbitbucket) so that it points to the correct git path.