Similar to commit c641ca670729 ("merge-recursive: handle addition of submodule on our side of history", 2017-11-14) a submodule can be confused for a D/F conflict for modify/delete and rename/delete conflicts. (To the code, it appears there is a directory in the way of us writing our expected path to the working tree, because our path is a submodule; i.e. the submodule is itself the directory and any directory is assumed to be a D/F conflict that is in the way.) So, when we are dealing with a submodule, avoid checking the working copy for a directory being in the way. Signed-off-by: Elijah Newren <newren@xxxxxxxxx> --- It might be better to first check that the submodule existed on the HEAD side of the merge, because there could be a directory in the way of the submodule. But that's starting to get ugly quick, and the real fix to make this cleaner is the rewrite of merge-recursive that does an index-only merge first, then updates the working copy later... merge-recursive.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/merge-recursive.c b/merge-recursive.c index 1446e92bea..4832234073 100644 --- a/merge-recursive.c +++ b/merge-recursive.c @@ -1466,7 +1466,7 @@ static int handle_change_delete(struct merge_options *o, const char *update_path = path; int ret = 0; - if (dir_in_way(path, !o->call_depth, 0) || + if (dir_in_way(path, !o->call_depth && !S_ISGITLINK(changed_mode), 0) || (!o->call_depth && would_lose_untracked(path))) { update_path = alt_path = unique_path(o, path, change_branch); } -- 2.18.0.550.g44d6daf40a.dirty