thodg/libgit2

diff --git a/src/index.c b/src/index.c
index 32f585f..6546ea1 100644
--- a/src/index.c
+++ b/src/index.c
@@ -2925,38 +2925,39 @@ cleanup:
 	return error;
 }
 
-int git_index_read_index(
+static int git_index_read_iterator(
 	git_index *index,
-	const git_index *new_index)
+	git_iterator *new_iterator,
+	size_t new_length_hint)
 {
 	git_vector new_entries = GIT_VECTOR_INIT,
 		remove_entries = GIT_VECTOR_INIT;
 	git_idxmap *new_entries_map = NULL;
 	git_iterator *index_iterator = NULL;
-	git_iterator *new_iterator = NULL;
 	git_iterator_options opts = GIT_ITERATOR_OPTIONS_INIT;
 	const git_index_entry *old_entry, *new_entry;
 	git_index_entry *entry;
 	size_t i;
 	int error;
 
-	if ((error = git_vector_init(&new_entries, new_index->entries.length, index->entries._cmp)) < 0 ||
+	assert((new_iterator->flags & GIT_ITERATOR_DONT_IGNORE_CASE));
+
+	if ((error = git_vector_init(&new_entries, new_length_hint, index->entries._cmp)) < 0 ||
 		(error = git_vector_init(&remove_entries, index->entries.length, NULL)) < 0 ||
 		(error = git_idxmap_alloc(&new_entries_map)) < 0)
 		goto done;
 
-	if (index->ignore_case)
-		kh_resize(idxicase, (khash_t(idxicase) *) new_entries_map, new_index->entries.length);
-	else
-		kh_resize(idx, new_entries_map, new_index->entries.length);
+	if (index->ignore_case && new_length_hint)
+		kh_resize(idxicase, (khash_t(idxicase) *) new_entries_map, new_length_hint);
+	else if (new_length_hint)
+		kh_resize(idx, new_entries_map, new_length_hint);
 
-	opts.flags = GIT_ITERATOR_DONT_IGNORE_CASE;
+	opts.flags = GIT_ITERATOR_DONT_IGNORE_CASE |
+		GIT_ITERATOR_INCLUDE_CONFLICTS;
 
-	if ((error = git_iterator_for_index(&index_iterator, git_index_owner(index), index, &opts)) < 0 ||
-		(error = git_iterator_for_index(&new_iterator, git_index_owner(new_index), (git_index *)new_index, &opts)) < 0)
-		goto done;
-
-	if (((error = git_iterator_current(&old_entry, index_iterator)) < 0 &&
+	if ((error = git_iterator_for_index(&index_iterator,
+			git_index_owner(index), index, &opts)) < 0 ||
+		((error = git_iterator_current(&old_entry, index_iterator)) < 0 &&
 			error != GIT_ITEROVER) ||
 		((error = git_iterator_current(&new_entry, new_iterator)) < 0 &&
 			error != GIT_ITEROVER))
@@ -3050,6 +3051,8 @@ int git_index_read_index(
 		index_entry_free(entry);
 	}
 
+	clear_uptodate(index);
+
 	error = 0;
 
 done:
@@ -3057,6 +3060,27 @@ done:
 	git_vector_free(&new_entries);
 	git_vector_free(&remove_entries);
 	git_iterator_free(index_iterator);
+	return error;
+}
+
+int git_index_read_index(
+	git_index *index,
+	const git_index *new_index)
+{
+	git_iterator *new_iterator = NULL;
+	git_iterator_options opts = GIT_ITERATOR_OPTIONS_INIT;
+	int error;
+
+	opts.flags = GIT_ITERATOR_DONT_IGNORE_CASE |
+		GIT_ITERATOR_INCLUDE_CONFLICTS;
+
+	if ((error = git_iterator_for_index(&new_iterator,
+		git_index_owner(new_index), (git_index *)new_index, &opts)) < 0 ||
+		(error = git_index_read_iterator(index, new_iterator,
+		new_index->entries.length)) < 0)
+		goto done;
+
+done:
 	git_iterator_free(new_iterator);
 	return error;
 }
diff --git a/tests/index/conflicts.c b/tests/index/conflicts.c
index d400468..cabef88 100644
--- a/tests/index/conflicts.c
+++ b/tests/index/conflicts.c
@@ -1,6 +1,7 @@
 #include "clar_libgit2.h"
 #include "index.h"
 #include "git2/repository.h"
+#include "conflicts.h"
 
 static git_repository *repo;
 static git_index *repo_index;
@@ -8,14 +9,6 @@ static git_index *repo_index;
 #define TEST_REPO_PATH "mergedrepo"
 #define TEST_INDEX_PATH TEST_REPO_PATH "/.git/index"
 
-#define CONFLICTS_ONE_ANCESTOR_OID "1f85ca51b8e0aac893a621b61a9c2661d6aa6d81"
-#define CONFLICTS_ONE_OUR_OID "6aea5f295304c36144ad6e9247a291b7f8112399"
-#define CONFLICTS_ONE_THEIR_OID "516bd85f78061e09ccc714561d7b504672cb52da"
-
-#define CONFLICTS_TWO_ANCESTOR_OID "84af62840be1b1c47b778a8a249f3ff45155038c"
-#define CONFLICTS_TWO_OUR_OID "8b3f43d2402825c200f835ca1762413e386fd0b2"
-#define CONFLICTS_TWO_THEIR_OID "220bd62631c8cf7a83ef39c6b94595f00517211e"
-
 // Fixture setup and teardown
 void test_index_conflicts__initialize(void)
 {
diff --git a/tests/index/conflicts.h b/tests/index/conflicts.h
new file mode 100644
index 0000000..3e26e6d
--- /dev/null
+++ b/tests/index/conflicts.h
@@ -0,0 +1,7 @@
+#define CONFLICTS_ONE_ANCESTOR_OID "1f85ca51b8e0aac893a621b61a9c2661d6aa6d81"
+#define CONFLICTS_ONE_OUR_OID "6aea5f295304c36144ad6e9247a291b7f8112399"
+#define CONFLICTS_ONE_THEIR_OID "516bd85f78061e09ccc714561d7b504672cb52da"
+
+#define CONFLICTS_TWO_ANCESTOR_OID "84af62840be1b1c47b778a8a249f3ff45155038c"
+#define CONFLICTS_TWO_OUR_OID "8b3f43d2402825c200f835ca1762413e386fd0b2"
+#define CONFLICTS_TWO_THEIR_OID "220bd62631c8cf7a83ef39c6b94595f00517211e"
diff --git a/tests/index/read_index.c b/tests/index/read_index.c
index 6d14bc9..2df7cc8 100644
--- a/tests/index/read_index.c
+++ b/tests/index/read_index.c
@@ -1,6 +1,7 @@
 #include "clar_libgit2.h"
 #include "posix.h"
 #include "index.h"
+#include "conflicts.h"
 
 static git_repository *_repo;
 static git_index *_index;
@@ -126,3 +127,106 @@ void test_index_read_index__read_and_writes(void)
 	git_index_free(tree_index);
 	git_index_free(new_index);
 }
+
+static void add_conflicts(git_index *index, const char *filename)
+{
+	git_index_entry ancestor_entry, our_entry, their_entry;
+	static int conflict_idx = 0;
+	char *ancestor_ids[] =
+		{ CONFLICTS_ONE_ANCESTOR_OID, CONFLICTS_TWO_ANCESTOR_OID };
+	char *our_ids[] =
+		{ CONFLICTS_ONE_OUR_OID, CONFLICTS_TWO_OUR_OID };
+	char *their_ids[] =
+		{ CONFLICTS_ONE_THEIR_OID, CONFLICTS_TWO_THEIR_OID };
+
+	conflict_idx = (conflict_idx + 1) % 2;
+
+	memset(&ancestor_entry, 0x0, sizeof(git_index_entry));
+	memset(&our_entry, 0x0, sizeof(git_index_entry));
+	memset(&their_entry, 0x0, sizeof(git_index_entry));
+
+	ancestor_entry.path = filename;
+	ancestor_entry.mode = 0100644;
+	GIT_IDXENTRY_STAGE_SET(&ancestor_entry, 1);
+	git_oid_fromstr(&ancestor_entry.id, ancestor_ids[conflict_idx]);
+
+	our_entry.path = filename;
+	our_entry.mode = 0100644;
+	GIT_IDXENTRY_STAGE_SET(&our_entry, 2);
+	git_oid_fromstr(&our_entry.id, our_ids[conflict_idx]);
+
+	their_entry.path = filename;
+	their_entry.mode = 0100644;
+	GIT_IDXENTRY_STAGE_SET(&ancestor_entry, 2);
+	git_oid_fromstr(&their_entry.id, their_ids[conflict_idx]);
+
+	cl_git_pass(git_index_conflict_add(index, &ancestor_entry,
+		&our_entry, &their_entry));
+}
+
+void test_index_read_index__handles_conflicts(void)
+{
+	git_oid tree_id;
+	git_tree *tree;
+	git_index *index, *new_index;
+	git_index_conflict_iterator *conflict_iterator;
+	const git_index_entry *ancestor, *ours, *theirs;
+
+	cl_git_pass(git_oid_fromstr(&tree_id, "ae90f12eea699729ed24555e40b9fd669da12a12"));
+	cl_git_pass(git_tree_lookup(&tree, _repo, &tree_id));
+	cl_git_pass(git_index_new(&index));
+	cl_git_pass(git_index_new(&new_index));
+	cl_git_pass(git_index_read_tree(index, tree));
+	cl_git_pass(git_index_read_tree(new_index, tree));
+
+	/* put some conflicts in only the old side, these should be removed */
+	add_conflicts(index, "orig_side-1.txt");
+	add_conflicts(index, "orig_side-2.txt");
+
+	/* put some conflicts in both indexes, these should be unchanged */
+	add_conflicts(index, "both_sides-1.txt");
+	add_conflicts(new_index,  "both_sides-1.txt");
+	add_conflicts(index, "both_sides-2.txt");
+	add_conflicts(new_index,  "both_sides-2.txt");
+
+	/* put some conflicts in the new index, these should be added */
+	add_conflicts(new_index, "new_side-1.txt");
+	add_conflicts(new_index, "new_side-2.txt");
+
+	cl_git_pass(git_index_read_index(index, new_index));
+	cl_git_pass(git_index_conflict_iterator_new(&conflict_iterator, index));
+
+	cl_git_pass(git_index_conflict_next(
+		&ancestor, &ours, &theirs, conflict_iterator));
+	cl_assert_equal_s("both_sides-1.txt", ancestor->path);
+	cl_assert_equal_s("both_sides-1.txt", ours->path);
+	cl_assert_equal_s("both_sides-1.txt", theirs->path);
+
+	cl_git_pass(git_index_conflict_next(
+		&ancestor, &ours, &theirs, conflict_iterator));
+	cl_assert_equal_s("both_sides-2.txt", ancestor->path);
+	cl_assert_equal_s("both_sides-2.txt", ours->path);
+	cl_assert_equal_s("both_sides-2.txt", theirs->path);
+
+	cl_git_pass(git_index_conflict_next(
+		&ancestor, &ours, &theirs, conflict_iterator));
+	cl_assert_equal_s("new_side-1.txt", ancestor->path);
+	cl_assert_equal_s("new_side-1.txt", ours->path);
+	cl_assert_equal_s("new_side-1.txt", theirs->path);
+
+	cl_git_pass(git_index_conflict_next(
+		&ancestor, &ours, &theirs, conflict_iterator));
+	cl_assert_equal_s("new_side-2.txt", ancestor->path);
+	cl_assert_equal_s("new_side-2.txt", ours->path);
+	cl_assert_equal_s("new_side-2.txt", theirs->path);
+
+
+	cl_git_fail_with(GIT_ITEROVER, git_index_conflict_next(
+		&ancestor, &ours, &theirs, conflict_iterator));
+
+	git_index_conflict_iterator_free(conflict_iterator);
+
+	git_tree_free(tree);
+	git_index_free(new_index);
+	git_index_free(index);
+}