When you start a 3\-way merge with an index file that is already populated, it is assumed that it represents the state of the files in your work tree, and you can even have files with changes unrecorded in the index file\&. It is further assumed that this state is "derived" from the stage 2 tree\&. The 3\-way merge refuses to run if it finds an entry in the original index file that does not match stage 2\&.
When you start a 3\-way merge with an index file that is already populated, it is assumed that it represents the state of the files in your work tree, and you can even have files with changes unrecorded in the index file\&. It is further assumed that this state is "derived" from the stage 2 tree\&. The 3\-way merge refuses to run if it finds an entry in the original index file that does not match stage 2\&.