I have two branches, A and B, both of which have a file X. These branches started from one code base but have since then interweaved merges into each other because they're branched for different implementations of the project. X has been updated in A, and also in B. When I do git merge (using the default recursive strategy) I get a merge conflict (regardless of whether I merge B into A or A into B) that A's version of the file has been added, and B's version of the file has been deleted.
I have tested this with the shell (Mac) Using git version 1.8.2.