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Scenario: 0. Create a project and share it using EGit; add example file eg: <pre> public class Main { /** * @param args */ public static void main(String[] args) { // TODO Auto-generated method stub } } </pre> 1. Commit changes using EGit 2. Create new branch named 'feature' and check out it 3. Checkout master branch 4. Create new branch named 'bug-fix' and check out it 5. Replace line '// TODO Auto-generated method stub' with eg. 'System.out.println("jgit merge bug");' 6. Commit changes 7. Checkout master branch and merge it with 'bug-fix' - right now everything is OK 8. Checkout 'feature' branch 9. Remove line '// TODO Auto-generated method stub' 10. Commit changes 11. Checkout master branch 12. Merge 'feature' - here we should have a conflict but instead of it line 8 (the one that had System.out in 'bug-fix' branch and was removed in 'feature' branch) was removed during merge. I test this scenario using cgit and it produce proper conflict information.
this sound like a severe bug. I'll test this now.
This was indeed a bug in the merge algorithm which was introduced during some "optimizations". It is fixed now with commit beeb1f6d08a907493b3660837fd4059322ca969a. The next nightly builds should contain this.
Thats fixed now.