Eclipse EGit Checkout conflict with files: - EGit doesn't want to continue

Situation:

• You have local uncommitted changes
• You pull from the master repo
• You get the error "Checkout conflict with files: xy"

Solution:

• Stage and commit (at least) the files xy
• Pull again
• If automerge is possible, everything is ok.
• If not, the pull merges the files and inserts the merge-conflict markers (<<<<<<, >>>>)
  • Manually edit the conflicting files
• Commit and push

This is the way I solved my problem:

1. Right click the folder that has uncommitted changes on your local
2. Click Team > Advanced > Assume Unchanged
3. Pull from master.

UPDATE:

As Hugo Zuleta rightly pointed out, you should be careful while applying this. He says that it might end up saying the branch is up to date, but the changes aren't shown, resulting in desync from the branch.

1. After closing the Conflict Error Dialog; from the Project Explorer, right click on the head of the project -> Team -> Stashes -> Stash Changes
2. Enter a name for your stash. E.G. "Conflict"
3. Try Pulling again. Hopefully there are no errors this time.
4. From the Git Repository view, expand your repository -> Stashed Commits
5. Right Click on the stash you created in step 2 -> Apply Stashed Changes
6. This brings up the merge tool if it can't automatically merge it.
7. Manually resolve the merge conflicts in the file/s.
8. Right Click on the file editor -> Team -> Add To Index
9. If you are not ready to commit the file or just don't want it in the Index, right click on the file editor -> Team -> Remove from Index.
10. Cleanup: From the Git Repository view, right Click on the stash you created in step 2 -> Delete Stashed Commit

Your local working directory file should be be merged