How to make git merge handle uncommitted changes to my working tree?

As far as I can tell, the best you can do is what you already have with git stash. I too find it strange that merge wants to deal only with clean trees.

• If local work is uncommitted
  • And you've introduced completely new files that don’t exist in the remote branch:
  • Or the files affected by your local work have ZERO overlap with the files affected by the changes you need to pull from the remote:
    • You're in luck: git pull will "just work"
  • Otherwise:
    • If your local changes have NO overlap with changes you are pulling:
      • git stash will work:
        • git stash save
        • git pull
        • git stash pop
    • If your local changes have SOME overlap with changes you are pulling:
      • git stash will require manual conflict resolution:
        • git stash save
        • git pull
        • git stash pop
        • resolve merge conflicts
        • git reset
        • git stash drop
• If local work is committed
  • And the files affected by your local work have ZERO overlap with the files affected by
    • You're in luck: git pull will "just work"
    • However: git pull --rebase will "work even better" because of a cleaner history
    • there is no merge commit; your changes will be committed after upstream changes
  • Otherwise:
    • git pull will require manual conflict resolution:
      • git pull
      • resolve merge conflicts
      • git add FILE for each conflicting FILE
      • git commit
    • git pull --rebase could still "work even better" because of a cleaner history
      • however, resolving merge conflicts could be much harder

For a detailed explanation, please see: https://happygitwithr.com/pull-tricky.html

Forget everything you ever learned from subversion.

Always commit before introducing external changes.

Imagine you had a mostly-working tree -- maybe not perfect, but you're making some progress. Then you go to do a merge and the code you're bringing in just wreaked havoc (was buggy itself, too many conflicts to deal with, etc...). Wouldn't it be nice if you could just undo that?

If you commit, you can. If you don't, you're just going to suffer.

Remember: What you commit doesn't have to be what you push, but what you don't commit you can easily lose.

Just do the safe and easy thing and commit early and commit often.

You cannot tell git merge to merge changes on files that have changes with respect to your local repository. This protects you from losing your changes on those times when a merge goes badly.

With the CVS and SVN approach to merging, if you did not manually copy your files before the update and it scrambled them on merge, you have to manually re-edit to get back to a good state.

If you either commit your changes or stash them before doing a merge, everything is reversible. If the merge does not go well you can try several ways of making it work out and go with the one that works best.

If you do commit experimental or debug changes, you might use git rebase to move them after the commits you get via git merge to make it easier to get rid of them or to avoid pushing them to a repository accidentally.

Note that using git rebase on a branch you have pushed to a shared repository will cause grief for everyone who is pulling from that repository.

I prefer to use git stash in these cases, but I only use it if the merge changes files that I have edited and not committed.