thodg/libgit2

diff --git a/src/checkout.c b/src/checkout.c
index 960bc61..cfb0e72 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 04c7421..2fb1c58 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;
 
diff --git a/tests/merge/workdir/submodules.c b/tests/merge/workdir/submodules.c
new file mode 100644
index 0000000..f01faac
--- /dev/null
+++ b/tests/merge/workdir/submodules.c
@@ -0,0 +1,101 @@
+#include "clar_libgit2.h"
+#include "git2/repository.h"
+#include "git2/merge.h"
+#include "buffer.h"
+#include "merge.h"
+#include "../merge_helpers.h"
+
+static git_repository *repo;
+
+#define TEST_REPO_PATH "merge-resolve"
+
+#define SUBMODULE_MAIN_BRANCH		"submodules"
+#define SUBMODULE_OTHER_BRANCH		"submodules-branch"
+#define SUBMODULE_OTHER2_BRANCH		"submodules-branch2"
+
+#define TEST_INDEX_PATH TEST_REPO_PATH "/.git/index"
+
+// Fixture setup and teardown
+void test_merge_workdir_submodules__initialize(void)
+{
+	repo = cl_git_sandbox_init(TEST_REPO_PATH);
+}
+
+void test_merge_workdir_submodules__cleanup(void)
+{
+	cl_git_sandbox_cleanup();
+}
+
+void test_merge_workdir_submodules__automerge(void)
+{
+	git_reference *our_ref, *their_ref;
+	git_commit *our_commit;
+	git_merge_head *their_head;
+	git_merge_result *result;
+	git_merge_opts opts = GIT_MERGE_OPTS_INIT;
+	git_index *index;
+
+	struct merge_index_entry merge_index_entries[] = {
+		{ 0100644, "caff6b7d44973f53e3e0cf31d0d695188b19aec6", 0, ".gitmodules" },
+		{ 0100644, "950a663a6a7b2609eed1ed1ba9f41eb1a3192a9f", 0, "file1.txt" },
+		{ 0100644, "343e660b9cb4bee5f407c2e33fcb9df24d9407a4", 0, "file2.txt" },
+		{ 0160000, "d3d806a4bef96889117fd7ebac0e3cb5ec152932", 1, "submodule" },
+		{ 0160000, "297aa6cd028b3336c7802c7a6f49143da4e1602d", 2, "submodule" },
+		{ 0160000, "ae39c77c70cb6bad18bb471912460c4e1ba0f586", 3, "submodule" },
+	};
+
+	cl_git_pass(git_reference_lookup(&our_ref, repo, "refs/heads/" SUBMODULE_MAIN_BRANCH));
+	cl_git_pass(git_commit_lookup(&our_commit, repo, git_reference_target(our_ref)));
+	cl_git_pass(git_reset(repo, (git_object *)our_commit, GIT_RESET_HARD));
+
+	cl_git_pass(git_reference_lookup(&their_ref, repo, "refs/heads/" SUBMODULE_OTHER_BRANCH));
+	cl_git_pass(git_merge_head_from_ref(&their_head, repo, their_ref));
+
+	cl_git_pass(git_merge(&result, repo, (const git_merge_head **)&their_head, 1, &opts));
+
+	cl_git_pass(git_repository_index(&index, repo));
+	cl_assert(merge_test_index(index, merge_index_entries, 6));
+
+	git_index_free(index);
+	git_merge_result_free(result);
+	git_merge_head_free(their_head);
+	git_commit_free(our_commit);
+	git_reference_free(their_ref);
+	git_reference_free(our_ref);
+}
+
+void test_merge_workdir_submodules__take_changed(void)
+{
+	git_reference *our_ref, *their_ref;
+	git_commit *our_commit;
+	git_merge_head *their_head;
+	git_merge_result *result;
+	git_merge_opts opts = GIT_MERGE_OPTS_INIT;
+	git_index *index;
+
+	struct merge_index_entry merge_index_entries[] = {
+		{ 0100644, "caff6b7d44973f53e3e0cf31d0d695188b19aec6", 0, ".gitmodules" },
+		{ 0100644, "b438ff23300b2e0f80b84a6f30140dfa91e71423", 0, "file1.txt" },
+		{ 0100644, "f27fbafdfa6693f8f7a5128506fe3e338dbfcad2", 0, "file2.txt" },
+		{ 0160000, "297aa6cd028b3336c7802c7a6f49143da4e1602d", 0, "submodule" },
+	};
+
+	cl_git_pass(git_reference_lookup(&our_ref, repo, "refs/heads/" SUBMODULE_MAIN_BRANCH));
+	cl_git_pass(git_commit_lookup(&our_commit, repo, git_reference_target(our_ref)));
+	cl_git_pass(git_reset(repo, (git_object *)our_commit, GIT_RESET_HARD));
+
+	cl_git_pass(git_reference_lookup(&their_ref, repo, "refs/heads/" SUBMODULE_OTHER2_BRANCH));
+	cl_git_pass(git_merge_head_from_ref(&their_head, repo, their_ref));
+
+	cl_git_pass(git_merge(&result, repo, (const git_merge_head **)&their_head, 1, &opts));
+
+	cl_git_pass(git_repository_index(&index, repo));
+	cl_assert(merge_test_index(index, merge_index_entries, 4));
+
+	git_index_free(index);
+	git_merge_result_free(result);
+	git_merge_head_free(their_head);
+	git_commit_free(our_commit);
+	git_reference_free(their_ref);
+	git_reference_free(our_ref);
+}
diff --git a/tests/resources/merge-resolve/.gitted/config b/tests/resources/merge-resolve/.gitted/config
index af10792..26c4842 100644
--- a/tests/resources/merge-resolve/.gitted/config
+++ b/tests/resources/merge-resolve/.gitted/config
@@ -4,3 +4,5 @@
 	bare = false
 	logallrefupdates = true
 	ignorecase = true
+[submodule "submodule"]
+	url = ../submodule
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/HEAD b/tests/resources/merge-resolve/.gitted/modules/submodule/HEAD
new file mode 100644
index 0000000..cb089cd
--- /dev/null
+++ b/tests/resources/merge-resolve/.gitted/modules/submodule/HEAD
@@ -0,0 +1 @@
+ref: refs/heads/master
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/ORIG_HEAD b/tests/resources/merge-resolve/.gitted/modules/submodule/ORIG_HEAD
new file mode 100644
index 0000000..d1bfcf0
--- /dev/null
+++ b/tests/resources/merge-resolve/.gitted/modules/submodule/ORIG_HEAD
@@ -0,0 +1 @@
+ae39c77c70cb6bad18bb471912460c4e1ba0f586
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/config b/tests/resources/merge-resolve/.gitted/modules/submodule/config
new file mode 100644
index 0000000..575cc85
--- /dev/null
+++ b/tests/resources/merge-resolve/.gitted/modules/submodule/config
@@ -0,0 +1,15 @@
+[core]
+	repositoryformatversion = 0
+	filemode = false
+	bare = false
+	logallrefupdates = true
+	worktree = ../../../submodule
+	symlinks = false
+	ignorecase = true
+	hideDotFiles = dotGitOnly
+[remote "origin"]
+	url = c:/Temp/TestRepos/submodule
+	fetch = +refs/heads/*:refs/remotes/origin/*
+[branch "master"]
+	remote = origin
+	merge = refs/heads/master
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/index b/tests/resources/merge-resolve/.gitted/modules/submodule/index
new file mode 100644
index 0000000..e948afb
Binary files /dev/null and b/tests/resources/merge-resolve/.gitted/modules/submodule/index differ
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/info/exclude b/tests/resources/merge-resolve/.gitted/modules/submodule/info/exclude
new file mode 100644
index 0000000..a5196d1
--- /dev/null
+++ b/tests/resources/merge-resolve/.gitted/modules/submodule/info/exclude
@@ -0,0 +1,6 @@
+# git ls-files --others --exclude-from=.git/info/exclude
+# Lines that start with '#' are comments.
+# For a project mostly in C, the following would be a good set of
+# exclude patterns (uncomment them if you want to use them):
+# *.[oa]
+# *~
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/objects/18/fae1354bba0a5f1e6a531f9988369142c24a9e b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/18/fae1354bba0a5f1e6a531f9988369142c24a9e
new file mode 100644
index 0000000..fcf1c63
Binary files /dev/null and b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/18/fae1354bba0a5f1e6a531f9988369142c24a9e differ
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/objects/29/7aa6cd028b3336c7802c7a6f49143da4e1602d b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/29/7aa6cd028b3336c7802c7a6f49143da4e1602d
new file mode 100644
index 0000000..aa9fc50
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diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/objects/38/6c80dc813b89d719797668f40c1be0a6efa996 b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/38/6c80dc813b89d719797668f40c1be0a6efa996
new file mode 100644
index 0000000..bc9a32e
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diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/objects/ab/435a147bae6d5906ecfd0916a570c4ab3eeea8 b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/ab/435a147bae6d5906ecfd0916a570c4ab3eeea8
new file mode 100644
index 0000000..65a8d75
Binary files /dev/null and b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/ab/435a147bae6d5906ecfd0916a570c4ab3eeea8 differ
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/objects/ad/16e0a7684ea95bf892980a2ee412293ae979cc b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/ad/16e0a7684ea95bf892980a2ee412293ae979cc
new file mode 100644
index 0000000..49e1aaf
Binary files /dev/null and b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/ad/16e0a7684ea95bf892980a2ee412293ae979cc differ
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/objects/ae/39c77c70cb6bad18bb471912460c4e1ba0f586 b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/ae/39c77c70cb6bad18bb471912460c4e1ba0f586
new file mode 100644
index 0000000..6ceffdd
--- /dev/null
+++ b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/ae/39c77c70cb6bad18bb471912460c4e1ba0f586
@@ -0,0 +1,2 @@
+x
���
!@=S
hf�%�x��!�� ��]k���/�{k��-�a]
xW�s	=,l�P��
+��#g0K��IC�����,5��1�� �9;a�lB��=�>��|h}_{{�M�e�?�����u����6�����"���>:叄ʃ6^���Kd
\ No newline at end of file
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/objects/c2/0765f6e24e8bbb63a648d0d11d84da63170190 b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/c2/0765f6e24e8bbb63a648d0d11d84da63170190
new file mode 100644
index 0000000..1478103
Binary files /dev/null and b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/c2/0765f6e24e8bbb63a648d0d11d84da63170190 differ
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/objects/d3/d806a4bef96889117fd7ebac0e3cb5ec152932 b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/d3/d806a4bef96889117fd7ebac0e3cb5ec152932
new file mode 100644
index 0000000..8df72a4
--- /dev/null
+++ b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/d3/d806a4bef96889117fd7ebac0e3cb5ec152932
@@ -0,0 +1,3 @@
+x
��A
+�0E]�s
e�m�D�x��$�҂�@����gp����Qs^+���ZD���[�a
+,c�G�sBO#�	���v���h�G�pI�Z4��U���{^c�]�z��o@�ǎ\���M�-\��<B�t�流���A�
\ No newline at end of file
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/objects/f1/065ff5593604072837fecaad3e2e268cb0147b b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/f1/065ff5593604072837fecaad3e2e268cb0147b
new file mode 100644
index 0000000..e0d73e1
Binary files /dev/null and b/tests/resources/merge-resolve/.gitted/modules/submodule/objects/f1/065ff5593604072837fecaad3e2e268cb0147b differ
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/packed-refs b/tests/resources/merge-resolve/.gitted/modules/submodule/packed-refs
new file mode 100644
index 0000000..992c4ee
--- /dev/null
+++ b/tests/resources/merge-resolve/.gitted/modules/submodule/packed-refs
@@ -0,0 +1,3 @@
+# pack-refs with: peeled 
+297aa6cd028b3336c7802c7a6f49143da4e1602d refs/remotes/origin/master
+ae39c77c70cb6bad18bb471912460c4e1ba0f586 refs/remotes/origin/submodule-branch
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/refs/heads/master b/tests/resources/merge-resolve/.gitted/modules/submodule/refs/heads/master
new file mode 100644
index 0000000..fe28256
--- /dev/null
+++ b/tests/resources/merge-resolve/.gitted/modules/submodule/refs/heads/master
@@ -0,0 +1 @@
+297aa6cd028b3336c7802c7a6f49143da4e1602d
diff --git a/tests/resources/merge-resolve/.gitted/modules/submodule/refs/remotes/origin/HEAD b/tests/resources/merge-resolve/.gitted/modules/submodule/refs/remotes/origin/HEAD
new file mode 100644
index 0000000..6efe28f
--- /dev/null
+++ b/tests/resources/merge-resolve/.gitted/modules/submodule/refs/remotes/origin/HEAD
@@ -0,0 +1 @@
+ref: refs/remotes/origin/master
diff --git a/tests/resources/merge-resolve/.gitted/objects/0f/3fc5dddc8964b9ac1040d0e957f9eb02d9efb3 b/tests/resources/merge-resolve/.gitted/objects/0f/3fc5dddc8964b9ac1040d0e957f9eb02d9efb3
new file mode 100644
index 0000000..d0ca42d
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diff --git a/tests/resources/merge-resolve/.gitted/objects/27/4bbe983022fb4c02f8a2bf2ebe8da4fe130054 b/tests/resources/merge-resolve/.gitted/objects/27/4bbe983022fb4c02f8a2bf2ebe8da4fe130054
new file mode 100644
index 0000000..c7afad2
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diff --git a/tests/resources/merge-resolve/.gitted/objects/2b/fdd7e1b6c6ae993f23dfe8e84a8e06a772fa2a b/tests/resources/merge-resolve/.gitted/objects/2b/fdd7e1b6c6ae993f23dfe8e84a8e06a772fa2a
new file mode 100644
index 0000000..c86edfb
Binary files /dev/null and b/tests/resources/merge-resolve/.gitted/objects/2b/fdd7e1b6c6ae993f23dfe8e84a8e06a772fa2a differ
diff --git a/tests/resources/merge-resolve/.gitted/objects/42/18670ab81cc219a9f94befb5c5dad90ec52648 b/tests/resources/merge-resolve/.gitted/objects/42/18670ab81cc219a9f94befb5c5dad90ec52648
new file mode 100644
index 0000000..33ead61
Binary files /dev/null and b/tests/resources/merge-resolve/.gitted/objects/42/18670ab81cc219a9f94befb5c5dad90ec52648 differ
diff --git a/tests/resources/merge-resolve/.gitted/objects/49/fd9edac79d15c8fbfca2d481cbb900beba22a6 b/tests/resources/merge-resolve/.gitted/objects/49/fd9edac79d15c8fbfca2d481cbb900beba22a6
new file mode 100644
index 0000000..d808d9f
--- /dev/null
+++ b/tests/resources/merge-resolve/.gitted/objects/49/fd9edac79d15c8fbfca2d481cbb900beba22a6
@@ -0,0 +1,3 @@
+x
U��
+�0D=�+����
+����f�5�dI�~��Eh�e3��x������2?���ذ�$Ɂ�%+�"S�RA��WR�m K�n��\tXZ/��h�����MƱߙ��g2���j>#
\ No newline at end of file
diff --git a/tests/resources/merge-resolve/.gitted/objects/58/87a5e516c53bd58efb0f02ec6aa031b6fe9ad7 b/tests/resources/merge-resolve/.gitted/objects/58/87a5e516c53bd58efb0f02ec6aa031b6fe9ad7
new file mode 100644
index 0000000..550d288
Binary files /dev/null and b/tests/resources/merge-resolve/.gitted/objects/58/87a5e516c53bd58efb0f02ec6aa031b6fe9ad7 differ
diff --git a/tests/resources/merge-resolve/.gitted/objects/60/61fe116ecba0800c26113ea1a7dfac2e16eeaf b/tests/resources/merge-resolve/.gitted/objects/60/61fe116ecba0800c26113ea1a7dfac2e16eeaf
new file mode 100644
index 0000000..3f266f6
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diff --git a/tests/resources/merge-resolve/.gitted/objects/62/33c6a0670228627f93c01cef32485a30403670 b/tests/resources/merge-resolve/.gitted/objects/62/33c6a0670228627f93c01cef32485a30403670
new file mode 100644
index 0000000..81428dd
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diff --git a/tests/resources/merge-resolve/.gitted/objects/67/110d77886b2af6309b9212961e72b8583e5fa9 b/tests/resources/merge-resolve/.gitted/objects/67/110d77886b2af6309b9212961e72b8583e5fa9
new file mode 100644
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