diff --git a/src/index.c b/src/index.c
@@ -2968,6 +2968,8 @@ int git_index_read_index(
 			*remove_entry = NULL;
 		int diff;
 
+		error = 0;
+
 		if (old_entry && new_entry)
 			diff = git_index_entry_cmp(old_entry, new_entry);
 		else if (!old_entry && new_entry)
@@ -2985,7 +2987,8 @@ int git_index_read_index(
 			/* Path and stage are equal, if the OID is equal, keep it to
 			 * keep the stat cache data.
 			 */
-			if (git_oid_equal(&old_entry->id, &new_entry->id)) {
+			if (git_oid_equal(&old_entry->id, &new_entry->id) &&
+				old_entry->mode == new_entry->mode) {
 				add_entry = (git_index_entry *)old_entry;
 			} else {
 				dup_entry = (git_index_entry *)new_entry;
@@ -2996,8 +2999,17 @@ int git_index_read_index(
 		if (dup_entry) {
 			if ((error = index_entry_dup_nocache(&add_entry, index, dup_entry)) < 0)
 				goto done;
+
+			index_entry_adjust_namemask(add_entry,
+				((struct entry_internal *)add_entry)->pathlen);
 		}
 
+		/* invalidate this path in the tree cache if this is new (to
+		 * invalidate the parent trees)
+		 */
+		if (dup_entry && !remove_entry && index->tree)
+			git_tree_cache_invalidate_path(index->tree, dup_entry->path);
+
 		if (add_entry) {
 			if ((error = git_vector_insert(&new_entries, add_entry)) == 0)
 				INSERT_IN_MAP_EX(index, new_entries_map, add_entry, error);

diff --git a/tests/index/read_index.c b/tests/index/read_index.c
@@ -71,3 +71,58 @@ void test_index_read_index__maintains_stat_cache(void)
 		}
 	}
 }
+
+static bool roundtrip_with_read_index(const char *tree_idstr)
+{
+	git_oid tree_id, new_tree_id;
+	git_tree *tree;
+	git_index *tree_index;
+
+	cl_git_pass(git_oid_fromstr(&tree_id, tree_idstr));
+	cl_git_pass(git_tree_lookup(&tree, _repo, &tree_id));
+	cl_git_pass(git_index_new(&tree_index));
+	cl_git_pass(git_index_read_tree(tree_index, tree));
+	cl_git_pass(git_index_read_index(_index, tree_index));
+	cl_git_pass(git_index_write_tree(&new_tree_id, _index));
+
+	git_tree_free(tree);
+	git_index_free(tree_index);
+
+	return git_oid_equal(&tree_id, &new_tree_id);
+}
+
+void test_index_read_index__produces_treesame_indexes(void)
+{
+	roundtrip_with_read_index("53fc32d17276939fc79ed05badaef2db09990016");
+	roundtrip_with_read_index("944c0f6e4dfa41595e6eb3ceecdb14f50fe18162");
+	roundtrip_with_read_index("1810dff58d8a660512d4832e740f692884338ccd");
+	roundtrip_with_read_index("d52a8fe84ceedf260afe4f0287bbfca04a117e83");
+	roundtrip_with_read_index("c36d8ea75da8cb510fcb0c408c1d7e53f9a99dbe");
+	roundtrip_with_read_index("7b2417a23b63e1fdde88c80e14b33247c6e5785a");
+	roundtrip_with_read_index("f82a8eb4cb20e88d1030fd10d89286215a715396");
+	roundtrip_with_read_index("fd093bff70906175335656e6ce6ae05783708765");
+	roundtrip_with_read_index("ae90f12eea699729ed24555e40b9fd669da12a12");
+}
+
+void test_index_read_index__read_and_writes(void)
+{
+	git_oid tree_id, new_tree_id;
+	git_tree *tree;
+	git_index *tree_index, *new_index;
+
+	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(&tree_index));
+	cl_git_pass(git_index_read_tree(tree_index, tree));
+	cl_git_pass(git_index_read_index(_index, tree_index));
+	cl_git_pass(git_index_write(_index));
+
+	cl_git_pass(git_index_open(&new_index, git_index_path(_index)));
+	cl_git_pass(git_index_write_tree_to(&new_tree_id, new_index, _repo));
+
+	cl_assert_equal_oid(&tree_id, &new_tree_id);
+
+	git_tree_free(tree);
+	git_index_free(tree_index);
+	git_index_free(new_index);
+}
diff --git a/tests/rebase/inmemory.c b/tests/rebase/inmemory.c
@@ -165,3 +165,46 @@ void test_rebase_inmemory__no_common_ancestor(void)
 	git_reference_free(upstream_ref);
 	git_rebase_free(rebase);
 }
+
+void test_rebase_inmemory__with_directories(void)
+{
+	git_rebase *rebase;
+	git_reference *branch_ref, *upstream_ref;
+	git_annotated_commit *branch_head, *upstream_head;
+	git_rebase_operation *rebase_operation;
+	git_oid commit_id, tree_id;
+	git_commit *commit;
+	git_rebase_options opts = GIT_REBASE_OPTIONS_INIT;
+
+	opts.inmemory = true;
+
+	git_oid_fromstr(&tree_id, "a4d6d9c3d57308fd8e320cf2525bae8f1adafa57");
+
+	cl_git_pass(git_reference_lookup(&branch_ref, repo, "refs/heads/deep_gravy"));
+	cl_git_pass(git_reference_lookup(&upstream_ref, repo, "refs/heads/veal"));
+
+	cl_git_pass(git_annotated_commit_from_ref(&branch_head, repo, branch_ref));
+	cl_git_pass(git_annotated_commit_from_ref(&upstream_head, repo, upstream_ref));
+
+	cl_git_pass(git_rebase_init(&rebase, repo, branch_head, upstream_head, NULL, &opts));
+
+	cl_git_pass(git_rebase_next(&rebase_operation, rebase));
+	cl_git_pass(git_rebase_commit(&commit_id, rebase, NULL, signature,
+		NULL, NULL));
+
+	cl_git_pass(git_rebase_next(&rebase_operation, rebase));
+	cl_git_pass(git_rebase_commit(&commit_id, rebase, NULL, signature,
+		NULL, NULL));
+
+	cl_git_fail_with(GIT_ITEROVER, git_rebase_next(&rebase_operation, rebase));
+
+	cl_git_pass(git_commit_lookup(&commit, repo, &commit_id));
+	cl_assert_equal_oid(&tree_id, git_commit_tree_id(commit));
+
+	git_commit_free(commit);
+	git_annotated_commit_free(branch_head);
+	git_annotated_commit_free(upstream_head);
+	git_reference_free(branch_ref);
+	git_reference_free(upstream_ref);
+	git_rebase_free(rebase);
+}
diff --git a/tests/rebase/merge.c b/tests/rebase/merge.c
@@ -750,3 +750,42 @@ void test_rebase_merge__custom_merge_options(void)
 	git_rebase_free(rebase);
 }
 
+void test_rebase_merge__with_directories(void)
+{
+	git_rebase *rebase;
+	git_reference *branch_ref, *upstream_ref;
+	git_annotated_commit *branch_head, *upstream_head;
+	git_rebase_operation *rebase_operation;
+	git_oid commit_id, tree_id;
+	git_commit *commit;
+
+	git_oid_fromstr(&tree_id, "a4d6d9c3d57308fd8e320cf2525bae8f1adafa57");
+
+	cl_git_pass(git_reference_lookup(&branch_ref, repo, "refs/heads/deep_gravy"));
+	cl_git_pass(git_reference_lookup(&upstream_ref, repo, "refs/heads/veal"));
+
+	cl_git_pass(git_annotated_commit_from_ref(&branch_head, repo, branch_ref));
+	cl_git_pass(git_annotated_commit_from_ref(&upstream_head, repo, upstream_ref));
+
+	cl_git_pass(git_rebase_init(&rebase, repo, branch_head, upstream_head, NULL, NULL));
+
+	cl_git_pass(git_rebase_next(&rebase_operation, rebase));
+	cl_git_pass(git_rebase_commit(&commit_id, rebase, NULL, signature,
+		NULL, NULL));
+
+	cl_git_pass(git_rebase_next(&rebase_operation, rebase));
+	cl_git_pass(git_rebase_commit(&commit_id, rebase, NULL, signature,
+		NULL, NULL));
+
+	cl_git_fail_with(GIT_ITEROVER, git_rebase_next(&rebase_operation, rebase));
+
+	cl_git_pass(git_commit_lookup(&commit, repo, &commit_id));
+	cl_assert_equal_oid(&tree_id, git_commit_tree_id(commit));
+
+	git_commit_free(commit);
+	git_annotated_commit_free(branch_head);
+	git_annotated_commit_free(upstream_head);
+	git_reference_free(branch_ref);
+	git_reference_free(upstream_ref);
+	git_rebase_free(rebase);
+}
diff --git a/tests/resources/rebase/.gitted/objects/1d/83f106355e4309a293e42ad2a2c4b8bdbe77ae b/tests/resources/rebase/.gitted/objects/1d/83f106355e4309a293e42ad2a2c4b8bdbe77ae
diff --git a/tests/resources/rebase/.gitted/objects/5a/72bf3bf964fdb176ffa4587312e69e2039695a b/tests/resources/rebase/.gitted/objects/5a/72bf3bf964fdb176ffa4587312e69e2039695a
diff --git a/tests/resources/rebase/.gitted/objects/77/0f14546ee2563a26c52afa5cc4139a96e5d360 b/tests/resources/rebase/.gitted/objects/77/0f14546ee2563a26c52afa5cc4139a96e5d360
diff --git a/tests/resources/rebase/.gitted/objects/91/4f3c604d1098847b7fe275f659ee329878153f b/tests/resources/rebase/.gitted/objects/91/4f3c604d1098847b7fe275f659ee329878153f
diff --git a/tests/resources/rebase/.gitted/objects/d9/c5185186d95d233dc007c1927cb3bdd6cde35b b/tests/resources/rebase/.gitted/objects/d9/c5185186d95d233dc007c1927cb3bdd6cde35b
diff --git a/tests/resources/rebase/.gitted/refs/heads/deep_gravy b/tests/resources/rebase/.gitted/refs/heads/deep_gravy
@@ -0,0 +1 @@
+d9c5185186d95d233dc007c1927cb3bdd6cde35b