2 files changed, 29 insertions, 6 deletions

diff --git a/src/checkout.c b/src/checkout.c
index 960bc6140..cfb0e72ab 100644
--- a/src/checkout.c
+++ b/src/checkout.c
@@ -71,7 +71,8 @@ typedef struct {
 	int name_collision:1,
 		directoryfile:1,
 		one_to_two:1,
-		binary:1;
+		binary:1,
+		submodule:1;
 } checkout_conflictdata;
 
 static int checkout_notify(
@@ -682,11 +683,22 @@ GIT_INLINE(bool) conflict_pathspec_match(
 	return false;
 }
 
+GIT_INLINE(int) checkout_conflict_detect_submodule(checkout_conflictdata *conflict)
+{
+	conflict->submodule = ((conflict->ancestor && S_ISGITLINK(conflict->ancestor->mode)) ||
+		(conflict->ours && S_ISGITLINK(conflict->ours->mode)) ||
+		(conflict->theirs && S_ISGITLINK(conflict->theirs->mode)));
+	return 0;
+}
+
 GIT_INLINE(int) checkout_conflict_detect_binary(git_repository *repo, checkout_conflictdata *conflict)
 {
 	git_blob *ancestor_blob = NULL, *our_blob = NULL, *their_blob = NULL;
 	int error = 0;
 
+	if (conflict->submodule)
+		return 0;
+
 	if (conflict->ancestor) {
 		if ((error = git_blob_lookup(&ancestor_blob, repo, &conflict->ancestor->oid)) < 0)
 			goto done;
@@ -740,7 +752,8 @@ static int checkout_conflicts_load(checkout_data *data, git_iterator *workdir, g
 		conflict->ours = ours;
 		conflict->theirs = theirs;
 
-		if ((error = checkout_conflict_detect_binary(data->repo, conflict)) < 0)
+		if ((error = checkout_conflict_detect_submodule(conflict)) < 0 ||
+			(error = checkout_conflict_detect_binary(data->repo, conflict)) < 0)
 			goto done;
 
 		git_vector_insert(&data->conflicts, conflict);
@@ -1791,6 +1804,10 @@ static int checkout_create_conflicts(checkout_data *data)
 		else if (S_ISLNK(conflict->theirs->mode))
 			error = checkout_write_entry(data, conflict, conflict->ours);
 
+		/* If any side is a gitlink, do nothing. */
+		else if (conflict->submodule)
+			error = 0;
+
 		/* If any side is binary, write the ours side */
 		else if (conflict->binary)
 			error = checkout_write_entry(data, conflict, conflict->ours);
diff --git a/src/merge.c b/src/merge.c
index 04c74212a..2fb1c5898 100644
--- a/src/merge.c
+++ b/src/merge.c
@@ -42,6 +42,7 @@
 #include "git2/sys/index.h"
 
 #define GIT_MERGE_INDEX_ENTRY_EXISTS(X)	((X).mode != 0)
+#define GIT_MERGE_INDEX_ENTRY_ISFILE(X) S_ISREG((X).mode)
 
 typedef enum {
 	TREE_IDX_ANCESTOR = 0,
@@ -447,7 +448,6 @@ static int merge_conflict_resolve_one_removed(
 	return error;
 }
 
-
 static int merge_conflict_resolve_one_renamed(
 	int *resolved,
 	git_merge_diff_list *diff_list,
@@ -533,6 +533,12 @@ static int merge_conflict_resolve_automerge(
 	if (conflict->type == GIT_MERGE_DIFF_DIRECTORY_FILE)
 		return 0;
 
+	/* Reject submodules. */
+	if (S_ISGITLINK(conflict->ancestor_entry.mode) ||
+		S_ISGITLINK(conflict->our_entry.mode) ||
+		S_ISGITLINK(conflict->their_entry.mode))
+		return 0;
+
 	/* Reject link/file conflicts. */
 	if ((S_ISLNK(conflict->ancestor_entry.mode) ^ S_ISLNK(conflict->our_entry.mode)) ||
 		(S_ISLNK(conflict->ancestor_entry.mode) ^ S_ISLNK(conflict->their_entry.mode)))
@@ -1156,7 +1162,7 @@ GIT_INLINE(int) merge_diff_detect_binary(
 	git_blob *ancestor_blob = NULL, *our_blob = NULL, *their_blob = NULL;
 	int error = 0;
 
-	if (GIT_MERGE_INDEX_ENTRY_EXISTS(conflict->ancestor_entry)) {
+	if (GIT_MERGE_INDEX_ENTRY_ISFILE(conflict->ancestor_entry)) {
 		if ((error = git_blob_lookup(&ancestor_blob, repo, &conflict->ancestor_entry.oid)) < 0)
 			goto done;
 
@@ -1164,7 +1170,7 @@ GIT_INLINE(int) merge_diff_detect_binary(
 	}
 
 	if (!conflict->binary &&
-		GIT_MERGE_INDEX_ENTRY_EXISTS(conflict->our_entry)) {
+		GIT_MERGE_INDEX_ENTRY_ISFILE(conflict->our_entry)) {
 		if ((error = git_blob_lookup(&our_blob, repo, &conflict->our_entry.oid)) < 0)
 			goto done;
 
@@ -1172,7 +1178,7 @@ GIT_INLINE(int) merge_diff_detect_binary(
 	}
 
 	if (!conflict->binary &&
-		GIT_MERGE_INDEX_ENTRY_EXISTS(conflict->their_entry)) {
+		GIT_MERGE_INDEX_ENTRY_ISFILE(conflict->their_entry)) {
 		if ((error = git_blob_lookup(&their_blob, repo, &conflict->their_entry.oid)) < 0)
 			goto done;