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

I've started Eclipse EGit. In some scenarios it is really not comprehensive.

I have local file e.g. pom.xml changed. On git server this file was changed. I do pull, EGIt says:

Checkout conflict with files:

i.e. pulling stops (fetch is done, but not merge), that is OK. However the next is bad experience.

I synchronize workspace, put my changes aside and make it the same as FETCH_HEAD. But EGit doesn't want to continue. I replace the file with HEAD revision. But EGit still doesn't want to continue.

What standard expected user operation should be with EGit after conflict resolution?

UPDATE:

I added to index, then marked as Merged -> pull still can't pass.
When I select Merge I get the dialog

I can't commit the file as it is not in list of changed files.

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:

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.