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

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.

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