Merging throws fatal: refusing to merge unrelated histories Git error

[nelsonni]

Describe the bug
When merging linked-worktree branches within the EPICLab/ant-design, specifically task-1-base and task-1-compare, the merge is not initiated and instead throws:

fatal: refusing to merge unrelated histories

To Reproduce
Steps to reproduce the behavior:

1. Launch Synectic
2. Go to File → Open...
3. Select the root directory of a repository with a base branch that reside in a linked worktrees
4. Go to Action → Merge...
5. Select the Repository from the drop-down menu
6. Select Base that resides in the linked worktree and Compare branches from the drop-down
7. Select the Merge button
8. Wait for the merge process to complete
9. See error

Expected behavior
The merge process should complete with Resolve 1 conflict and commit resolution before continuing. being displayed on the Merge dialog.

Screenshots

Versions (please complete the following information):

• OS: MacOS
• Synectic Version: 2.3.0
• git: 2.32.1 (Apple Git-133)

Additional context
Related to merging issues in #831.

[nelsonni]

Based on the article, How to fix ‘fatal: refusing to merge unrelated histories’ Git error:

The fatal: refusing to merge histories error is a fairly common Git error. It appears when a developer tries to merge two unrelated projects into a single branch.

This error appears when the branch has its commit histories and tags incompatible with the pull request or clone.

[nelsonni]

This issue does not occur on my system, but does on @pannapat's MacOS system. After further investigation, it appears that the .git file is not created in the task-1-base linked worktree directory:

[nelsonni]

This issue appears to be related to the process of adding new linked worktrees (via git-worktree.add()) during the merge process (via merges.merge(), which calls git-porcelain.checkout().

The initial fix involves switching away from using isomorphic-git commands and directly calling git worktree add {worktreeDir} {branch} instead. However, this can still result in the fatal: refusing to merge unrelated histories error. Attempting to do these steps in the terminal (and bypassing Synectic) shows the following different error:

projects/ant-design:~ (master) $ git merge task-1-base task-1-compare
fatal: refusing to merge unrelated histories

projects/ant-design:~ (master) $ git worktree remove task-1-base

projects/ant-design:~ (master) $ git branch -d task-1-base
warning: deleting branch 'task-1-base' that has been merged to
         'refs/remotes/origin/task-1-base', but not yet merged to HEAD.
Deleted branch task-1-base (was e199a7a30).