Bert's blog

Resolving painful git merges

git is an amazing repository system that greatly facilitates the management of large, collaborative code projects. It can store a large number of source code files and their history, and allows separate developers to work on the same code simultaneously, without constantly causing major issues when the same file gets edited by separate developers.

The power of git is however limited, and there will always be cases where even git is not able to resolve the problems that arise when you try to join the work done by different people into a single, coherent version of the code. In this post, I will give a short overview of the possible ways to resolve these conflicts manually, and show that git has some useful tools to help out with this.

The ideal world

In an ideal world, the online repository for your code project will always contain a master branch that contains the latest working version of your code. All developers that want to make their own changes should always make these changes to the master branch. However, they should not make the changes to the branch directly, but should instead create separate branches in which the changes are made. Whenever they are happy with the changes to their branch, they should open a pull request for their branch and merge the changes they made into the master branch. The master branch hence acts as a central root for all the individual branches that contain changes that are still under development.

When multiple developers make changes to the code, they will hence all have a separate branch that branched off from the master at some point. However, as pull requests get merged back into master, the actual master branch can diverge from the original master branch that was the root of a specific development branch. When a pull request is created for such a branch, this can lead to conflicts.

In order to avoid this situation, developers should always rebase their development branch against the latest version of the master branch. During a rebase, git will rewind the development branch to the original point when the development branch branched off from the master. It will then change the master at that point to the current version of the master, and replay all the changes that were made in the development branch on top of that. This way, it will seem as if the changes made in the development branch were made directly on top of the latest master. Once this is done, their will not be any merge conflicts any more, and a pull request can be created and successfully merged.

What can go wrong?

There are many things that happen in the real world that are far removed from this ideal world. First of all, there is the premise that the master branch will always contain the latest version of the code. Personally, I have some issues with this, as the master branch is also the default branch that gets used when a user makes a fresh clone of a repository. If all changes are to end up in master, then it would be very easy to break a user’s workflow by making changes that affect the user experience. Ideally, such changes should not be rolled out as soon as they are made, but should be rolled out in a controlled way through the release of a new code version. You could of course force users to use a specific branch that contains a frozen older version of the code, or force them to use official releases instead of simply cloning the repository. But personally I prefer to use the master branch as a frozen older version, and make all changes in a specific development branch.

The second thing that could go wrong is the rebasing step required before every pull request with the master (or the dedicated development branch). git is generally quite good at figuring out what the changes are that were introduced by a specific commit, so replaying them should be straightforward. There are however cases where a commit introduces changes in a file that was also changed in the new master. To figure out where a change needs to be made, git uses a combination of line numbers (those can very easily change if another change is introduced), and unchanged code fragments surrounding the change. If an external change affects both the line numbers and the code surrounding a change, then git cannot figure out how to apply the change from the commit, and a conflict arises.

Solving these conflicts is usually easy, but requires manual intervention. Suppose for example that you are rebasing against master using the following command (issues from your local development branch):

git rebase master

If a merge conflict arises, git will always tell you about this, and cause the branch to end up in an incomplete state, i.e. you will not be able to switch branches or make any commits until the conflicts have been resolved.

The first step in resolving the conflicts is looking at the output of git status. This command will tell you that you are actively rebasing your branch, and it will also give you a full list of all the changes that it managed to automatically replay, and of all files that contain unresolved conflicts.

Unresolved conflicts can occur in various ways: both your branch and the new master can have added or removed a file with the same name, or (more likely) both your branch and the new master can have made changes to the same file. In the latter case, git will have made an attempt at merging the two files based on the limited information it has available (line numbers and surrounding code). It will have added the changes from both the branches, and will surround them with <<<<<, ====== and >>>>>> (this will very likely cause compilation errors; you really need to fix the conflicts). You will need to open the file in question in a text editor, locate these characters and decide what to do: keep both changes, choose one or the other, or create some complicated combination of both. Once you are done editing the file, you need to tell git that file is ready, by running git add <NAME OF THE FILE>.

If both branches added or removed a file (and the files that were added were the same), you probably want to keep these changes as they are. You will also need to tell this to git using git add <NAME OF THE FILE>. If both branches added a file, but that file is not the same, then things can get really complicated. By default, git will make a copy of both files, and append the branch name (or commit hash string) as a suffix to the file name. This way, you have all the necessary information to decide how to proceed. You will need to either choose one of the versions, or create your own hybrid version. Once you are done, you will again need to tell git about this using git add <NAME OF THE FILE>.

Note that you can always decide to completely ignore the changes made to a file by one of the branches and simply use the version of the other branch. To do this, you can run git checkout --ours/--theirs <NAME OF THE FILE>, where --ours means using the version of the branch against which you are rebasing (the master in our example), and --theirs means using the version contained in the branch you are rebasing. I personally find this convention quite confusing, so it is important to know what we and them means in this context.

Note that git checkout --ours/--theirs will only work for files with active conflicts. If the rebase did an automatic merge of another file and you would rather use a specific version for that file, you will need to manually undo the automatic merge. This is not very convenient, but it is unfortunately how git works in my experience.

Once all conflicts are resolved (and git added!) you can continue the rebase:

git rebase --continue

git will replay the commits made in the branch you are rebasing one by one, so you might end up having additional conflicts that need to be resolved after this. The rebase is complete when all commits have been successfully replayed.

Note that you can always opt to skip a specific commit (git rebase --skip). I have personally never done this, but I expect that this could be useful in some cases. And of course, you can also always decide to abort the rebase altogether, using git rebase --abort. This will restore the repository into its original state (but will also remove all the changes you made when you were resolving conflicts).

Merging distant branches

To minimise the pain when doing a rebase, you should try to often rebase against a central branch. In large projects, a daily rebase is common. It is also a very good idea to only branch off from that central branch, so that all changes are only made with respect to that branch.

In a non-ideal real world, rebasing does not always happen that often. And even worse: branches do not always branch off from a central branch. git is so powerful that it will allow you to branch off from any other branch, which means that you can have a branch of a branch of a branch of the central branch (and even much deeper; you get the gist). And that makes things… interesting. Suppose for example that you were to rebase the first level branch (the one that branched off from the central branch) against the new master. This will effectively create a new branch that is no longer a direct parent for the second level branch. If you then try to rebase that second level branch against the first level branch, you might end up resolving the same conflicts you already solved again, as the new first level branch will no longer match the root of the second level branch.

Even worse things happen with forks, i.e. copies of a repository that act as an independent repository. These forks do not only contain a copy of the master branch of a repository, but also of all its active branches. If changes are made in the fork to different branches (independently of the changes made to those same branches in the original repository), then it can become almost impossible to merge those changes back into the original repository, especially if you do not know through which intermediate branches the changes were made.

To deal with these issues, there are a number of options. The first one is to do an actual merge. While a rebase tries to replay the changes you made on top of the master (rewriting the git history for the branch in the process), a merge will simply figure out what the differences are between two branches, and will try to apply those differences as new changes. In a way, this is a clearer situation for you as a developer to deal with, as you will immediately see all conflicts, and you will be able to make all the changes required to resolve the entire merge. On the other hand, this will probably be a very painful step, and it will also lead to a loss of the detailed history of the branch that is merged in; all changes made in the branch will show up as a single commit in the central branch.

The second option is to try to figure out what the branch history of the two branches you want to merge is. Unless someone forcefully changed the git history, two branches from the same repository or from a repository and a fork of that repository can always be traced back to some common ancestor. Once you find that ancestor, you can figure out how they diverged from that ancestor. You can then do a step-wise rebase of one of the branches against that ancestor (subsequently rebasing each of the intermediate branches until you have a clean git history from the ancestor to your branch), and then do a step-wise rebase of that new branch against the ancestors of the other branch. If you do this well, then this should be feasible without being too painful.

If the situation is really bad and you are only interested in merging some changes from one branch into the other one, you can also consider using a patch. A patch is a textual representation of the changes introduced by a commit (or a number of commits), similar to the output you get from git diff. git has a number of commands that can generate such representations (git format-patch is the most appropriate one). Once you have a patch, you can apply that patch to any branch using git apply <NAME OF PATCH FILE>. git will then try to make the changes described in the patch to that branch, independent of the history of the branch and the history of the branch that generated the patch. While this will likely fail for branches that have drifted too far apart (and for patches that contain a lot of changes), it might work to recover small changes to files that did not change dramatically between the two branches.


git is very powerful, and so it also contains all the tools you would ever need to resolve even the most desperate merge conflicts. Some of these tools can be very tricky to use, but if used correctly, they will help you out.

So if you end up in a seemingly impossible merge chaos, remember:

  • don’t panic! You can always abort a merge or rebase.
  • a git commit is simply a list of changes to a specific state of the repository. If you know what the original state of the repository was to which those changes were applied, you can always replay those changes on top of another state that was based on that same state. The worst merge conflicts arise when you try to merge git histories that do not derive from a common ancestor; in this case you should try to find a common ancestor and make sure your git histories agree on that.
  • you can always recover specific changes using a patch, which could be a lot less painful and equally useful as doing a full merge.

And of course, as long as all your changes are stored in a repository, you can always manually copy and paste them across branches. But if you need to revert to that, you are probably not using git correctly.

Professional astronomer.