Can You Avoid the Git ‘Fatal: Refusing to Merge Unrelated Histories’ Error?

One of the most common Git errors, "fatal: refusing to merge histories" occurs when there is an attempt to merge unrelated projects in one branch. This happens because the pull request or clone is not compatible with the commit histories and tags of a branch. 

Resolving this error is not that difficult, though. The causes that lead to this problem and the solutions for it are presented below. The more intriguing question may be, would it be possible to stop this error from happening in the first place? 

Possible Scenarios that Produce the Error

The Git "fatal: refusing to merge histories" error is essentially an issue of incompatibility. But how does this incompatibility manifest? Described below are three common scenarios that demonstrate the occurrence of the error.

• The issue can originate from the .git directory. The directory could be corrupted or it may have been unwittingly erased. Accidental deletions and sudden corruption can take place during the cleaning process of a project. These can also occur when a project is being cloned. When Git is unable to find the information it needs about a project's history, it is bound to flag an incompatibility and yield an error.
• The error may also happen when the branches have different HEAD positions during the pulling or pushing of data from a remote repository. Since Git does not see commonality because of the different HEAD positions, data cannot be matched. It then perceives the branches as incompatible.
• Another scenario is when creating a new Git repository with some commits in it. As you attempt to pull from an existing remote repository, the "fatal: refusing to merge unrelated histories" may appear because the remote pull and branch histories are not the same. The situation is seen by Git as an attempt to bring together unrelated branches.

Is it possible to avoid these scenarios? Maybe. However, since the "fatal: refusing to merge histories" error continues to be an issue even now, it appears that developers are either not mindful of avoiding the scenarios listed above or they just forget that these can result in an error.

Resolving the Error

The "fatal: refusing to merge unrelated histories" error has two possible solutions: short and long. The shorter solution entails the granting of permission to merge unrelated histories. The longer way involves the unstaging of current commits, stashing of unsaved files, cloning, unstashing, and then committing.

Short Solution

Addressing the error with the first solution means using the --allow-unrelated-histories git flag. The flag is appended to the command git pull origin master, where "origin" is a variable that can be replaced with the remote repository you are pulling from and "master" can be replaced with the branch to which the pull request will be merged.

The command makes it possible to merge unrelated branches. It works seamlessly unless there are file conflicts. If conflicts are discovered, there is no other choice but to use the longer solution.

Long Solution 

The longer solution starts with the running of the git reset HEAD~ command to unstage all files in the last commit. This is followed by the stashing of unsaved files through the git stash command to start with a clean working tree that will be the destination when pulling a remote repository. 

After pulling a remote repository into the target branch (cloning), the stashed files can then be unstashed. There are two ways to do this. One is through the command git pop and the other is git stash apply. 

git pop has the effect of moving (popping) the changes stashed and reapplying them to the current code. git stash apply is different, as it keeps the changes in the stash and applies them to the current code.

Finally, the contents of the stashed branch are placed into the new clone. This culminates the whole process of eliminating the history conflicts that may have been encountered in the code.

Preventing the Error

As mentioned, many continue to wittingly or accidentally execute the three scenarios listed earlier, which cause the "fatal: refusing to merge histories" error to show up. If these are too many to remember and avoid, here's a simpler and more comprehensive reminder to prevent the error from occurring: avoid pulling remote repositories into branches that already bear commits on them. 

Understandably, there will be instances when branch commits are preferably kept. In such cases, the logical solution is to build an entirely new branch, then pull the code in, and merge the local branch into the main flow manually. Doing this eliminates the possibility for Git to see incompatibilities in histories or fail to find the information it needs to ascertain that the data in two merging projects are similar and not in conflict with each other.

To illustrate, if your current code is in Branch A, you have to create a completely new and separate branch (to be referred to as Branch B here). Use the command git clone -b [branch] [remote_repo] to clone the remote repository into Branch B. Then, run the command git merge A to merge the two branches together.

In Summary

Those who have been using Git for some time are likely familiar with the "fatal: refusing to merge histories" error. It is actually a minor error, but many continue to encounter it. Interestingly, even if developers are familiar with the reasons why this happens, it is not that easy to consciously avoid it.

It is ideal to be able to avoid and prevent this common Git error. However, the most that can be done is to have mastery in troubleshooting the error. It would be difficult to apply the “prevention is better than cure” adage here, even though preventing the problem is not really that difficult. Nevertheless, there are automated Kubernetes troubleshooting solutions available to make the resolution of this and other Git issues even faster and more efficient.