Git merge error "commit is not possible because you have unmerged files"

You can use git stash to save the current repository before doing the commit you want to make (after merging the changes from the upstream repo with git stash pop). I had to do this yesterday when I had the same problem.

If you have fixed the conflicts you need to add the files to the stage with git add [filename], then commit as normal.

You need to do two things. First add the changes with

git add .
git stash  

git checkout <some branch>

It should solve your issue as it solved to me.