Egit and the the curious case of R.java.
Problem:
You are unable to merge branches because your workspace always shows as dirty because of the generated R.java file in android project.
How to fix:
1. Disable "Build Automatically" button on your eclipse.
2. Click on project> clean option in eclipse.
3. Disable the checkbox "Build immediately" at the bottom of the clean window.
4. Restart eclipse.
5. Merge the branches with no error.
6. Resume to build automatically option, and your normal life.