Here's an example.
$ git pull First, rewinding head to replay your work on top of it... Applying: Some commit message Using index info to reconstruct a base tree... M some-service/pom.xml Falling back to patching base and 3-way merge... Auto-merging some-service/pom.xml CONFLICT (content): Merge conflict in some-service/pom.xml Patch failed at 0001 some commit message The copy of the patch that failed is found in: /home/rroller/workspaces/some-service/.git/rebase-apply/patch When you have resolved this problem, run "git rebase --continue". If you prefer to skip this patch, run "git rebase --skip" instead. To check out the original branch and stop rebasing, run "git rebase --abort".
Edit each of the files that failed to merge and save them.
Now, for each fixed file, git add it.
git add some-service/pom.xml
Now just continue the rebase and you are back to normal.
git rebase --continue
Relax, you didn't lose your work.