thodg/libgit2

diff --git a/include/git2/errors.h b/include/git2/errors.h
index 5ff0f35..a81aa05 100644
--- a/include/git2/errors.h
+++ b/include/git2/errors.h
@@ -47,6 +47,7 @@ typedef enum {
 	GIT_EPEEL           = -19,      /**< The requested peel operation is not possible */
 	GIT_EEOF            = -20,      /**< Unexpected EOF */
 	GIT_EINVALID        = -21,      /**< Invalid operation or input */
+	GIT_EUNCOMMITTED    = -22,	/**< Uncommitted changes in index prevented operation */
 
 	GIT_PASSTHROUGH     = -30,	/**< Internal only */
 	GIT_ITEROVER        = -31,	/**< Signals end of iteration with iterator */
diff --git a/src/iterator.c b/src/iterator.c
index d5f7eec..45eba39 100644
--- a/src/iterator.c
+++ b/src/iterator.c
@@ -1843,3 +1843,91 @@ int git_iterator_advance_over_with_status(
 	return error;
 }
 
+int git_iterator_walk(
+	git_iterator **iterators,
+	size_t cnt,
+	git_iterator_walk_cb cb,
+	void *data)
+{
+	const git_index_entry **iterator_item;	/* next in each iterator */
+	const git_index_entry **cur_items;		/* current path in each iter */
+	const git_index_entry *first_match;
+	int cur_item_modified;
+	size_t i, j;
+	int error = 0;
+
+	iterator_item = git__calloc(cnt, sizeof(git_index_entry *));
+	cur_items = git__calloc(cnt, sizeof(git_index_entry *));
+
+	GITERR_CHECK_ALLOC(iterator_item);
+	GITERR_CHECK_ALLOC(cur_items);
+
+	/* Set up the iterators */
+	for (i = 0; i < cnt; i++) {
+		error = git_iterator_current(&iterator_item[i], iterators[i]);
+
+		if (error < 0 && error != GIT_ITEROVER)
+			goto done;
+	}
+
+	while (true) {
+		for (i = 0; i < cnt; i++)
+			cur_items[i] = NULL;
+
+		first_match = NULL;
+		cur_item_modified = 0;
+
+		/* Find the next path(s) to consume from each iterator */
+		for (i = 0; i < cnt; i++) {
+			if (iterator_item[i] == NULL)
+				continue;
+
+			if (first_match == NULL) {
+				first_match = iterator_item[i];
+				cur_items[i] = iterator_item[i];
+			} else {
+				int path_diff = git_index_entry_cmp(iterator_item[i], first_match);
+
+				if (path_diff < 0) {
+					/* Found an index entry that sorts before the one we're
+					 * looking at.  Forget that we've seen the other and
+					 * look at the other iterators for this path.
+					 */
+					for (j = 0; j < i; j++)
+						cur_items[j] = NULL;
+
+					first_match = iterator_item[i];
+					cur_items[i] = iterator_item[i];
+				} else if (path_diff > 0) {
+					/* No entry for the current item, this is modified */
+					cur_item_modified = 1;
+				} else if (path_diff == 0) {
+					cur_items[i] = iterator_item[i];
+				}
+			}
+		}
+
+		if (first_match == NULL)
+			break;
+
+		if ((error = cb(cur_items, data)) != 0)
+			goto done;
+
+		/* Advance each iterator that participated */
+		for (i = 0; i < cnt; i++) {
+			if (cur_items[i] == NULL)
+				continue;
+
+			error = git_iterator_advance(&iterator_item[i], iterators[i]);
+
+			if (error < 0 && error != GIT_ITEROVER)
+				goto done;
+		}
+	}
+
+done:
+	if (error == GIT_ITEROVER)
+		error = 0;
+
+	return error;
+}
diff --git a/src/iterator.h b/src/iterator.h
index 57f8241..893e5db 100644
--- a/src/iterator.h
+++ b/src/iterator.h
@@ -294,4 +294,19 @@ extern int git_iterator_advance_over_with_status(
  */
 extern int git_iterator_index(git_index **out, git_iterator *iter);
 
+typedef int (*git_iterator_walk_cb)(
+	const git_index_entry **entries,
+	void *data);
+
+/**
+ * Walk the given iterators in lock-step.  The given callback will be
+ * called for each unique path, with the index entry in each iterator
+ * (or NULL if the given iterator does not contain that path).
+ */
+extern int git_iterator_walk(
+	git_iterator **iterators,
+	size_t cnt,
+	git_iterator_walk_cb cb,
+	void *data);
+
 #endif
diff --git a/src/merge.c b/src/merge.c
index 517d317..9d6252e 100644
--- a/src/merge.c
+++ b/src/merge.c
@@ -1449,6 +1449,34 @@ static int merge_diff_list_insert_unmodified(
 	return error;
 }
 
+struct merge_diff_find_data {
+	git_merge_diff_list *diff_list;
+	struct merge_diff_df_data df_data;
+};
+
+static int queue_difference(const git_index_entry **entries, void *data)
+{
+	struct merge_diff_find_data *find_data = data;
+	bool item_modified = false;
+	size_t i;
+
+	if (!entries[0] || !entries[1] || !entries[2]) {
+		item_modified = true;
+	} else {
+		for (i = 1; i < 3; i++) {
+			if (index_entry_cmp(entries[0], entries[i]) != 0) {
+				item_modified = true;
+				break;
+			}
+		}
+	}
+
+	return item_modified ?
+		merge_diff_list_insert_conflict(
+			find_data->diff_list, &find_data->df_data, entries) :
+		merge_diff_list_insert_unmodified(find_data->diff_list, entries);
+}
+
 int git_merge_diff_list__find_differences(
 	git_merge_diff_list *diff_list,
 	git_iterator *ancestor_iter,
@@ -1456,93 +1484,9 @@ int git_merge_diff_list__find_differences(
 	git_iterator *their_iter)
 {
 	git_iterator *iterators[3] = { ancestor_iter, our_iter, their_iter };
-	const git_index_entry *items[3] = {0}, *best_cur_item, *cur_items[3];
-	git_vector_cmp entry_compare = git_index_entry_cmp;
-	struct merge_diff_df_data df_data = {0};
-	int cur_item_modified;
-	size_t i, j;
-	int error = 0;
-
-	assert(diff_list && (our_iter || their_iter));
-
-	/* Set up the iterators */
-	for (i = 0; i < 3; i++) {
-		error = git_iterator_current(&items[i], iterators[i]);
-
-		if (error < 0 && error != GIT_ITEROVER)
-			goto done;
-	}
-
-	while (true) {
-		for (i = 0; i < 3; i++)
-			cur_items[i] = NULL;
-
-		best_cur_item = NULL;
-		cur_item_modified = 0;
-
-		/* Find the next path(s) to consume from each iterator */
-		for (i = 0; i < 3; i++) {
-			if (items[i] == NULL) {
-				cur_item_modified = 1;
-				continue;
-			}
-
-			if (best_cur_item == NULL) {
-				best_cur_item = items[i];
-				cur_items[i] = items[i];
-			} else {
-				int path_diff = entry_compare(items[i], best_cur_item);
-
-				if (path_diff < 0) {
-					/*
-					 * Found an item that sorts before our current item, make
-					 * our current item this one.
-					 */
-					for (j = 0; j < i; j++)
-						cur_items[j] = NULL;
-
-					cur_item_modified = 1;
-					best_cur_item = items[i];
-					cur_items[i] = items[i];
-				} else if (path_diff > 0) {
-					/* No entry for the current item, this is modified */
-					cur_item_modified = 1;
-				} else if (path_diff == 0) {
-					cur_items[i] = items[i];
-
-					if (!cur_item_modified)
-						cur_item_modified = index_entry_cmp(best_cur_item, items[i]);
-				}
-			}
-		}
-
-		if (best_cur_item == NULL)
-			break;
-
-		if (cur_item_modified)
-			error = merge_diff_list_insert_conflict(diff_list, &df_data, cur_items);
-		else
-			error = merge_diff_list_insert_unmodified(diff_list, cur_items);
-		if (error < 0)
-			goto done;
+	struct merge_diff_find_data find_data = { diff_list };
 
-		/* Advance each iterator that participated */
-		for (i = 0; i < 3; i++) {
-			if (cur_items[i] == NULL)
-				continue;
-
-			error = git_iterator_advance(&items[i], iterators[i]);
-
-			if (error < 0 && error != GIT_ITEROVER)
-				goto done;
-		}
-	}
-
-done:
-	if (error == GIT_ITEROVER)
-		error = 0;
-
-	return error;
+	return git_iterator_walk(iterators, 3, queue_difference, &find_data);
 }
 
 git_merge_diff_list *git_merge_diff_list__alloc(git_repository *repo)
diff --git a/src/stash.c b/src/stash.c
index 9010c47..59ecd3b 100644
--- a/src/stash.c
+++ b/src/stash.c
@@ -671,6 +671,31 @@ cleanup:
 	return error;
 }
 
+static int merge_indexes(
+	git_index **out,
+	git_repository *repo,
+	git_tree *ancestor_tree,
+	git_index *ours_index,
+	git_index *theirs_index)
+{
+	git_iterator *ancestor = NULL, *ours = NULL, *theirs = NULL;
+	const git_iterator_flag_t flags = GIT_ITERATOR_DONT_IGNORE_CASE;
+	int error;
+
+	if ((error = git_iterator_for_tree(&ancestor, ancestor_tree, flags, NULL, NULL)) < 0 ||
+		(error = git_iterator_for_index(&ours, ours_index, flags, NULL, NULL)) < 0 ||
+		(error = git_iterator_for_index(&theirs, theirs_index, flags, NULL, NULL)) < 0)
+		goto done;
+
+	error = git_merge__iterators(out, repo, ancestor, ours, theirs, NULL);
+
+done:
+	git_iterator_free(ancestor);
+	git_iterator_free(ours);
+	git_iterator_free(theirs);
+	return error;
+}
+
 static int merge_index_and_tree(
 	git_index **out,
 	git_repository *repo,
@@ -733,6 +758,70 @@ int git_stash_apply_init_options(git_stash_apply_options *opts, unsigned int ver
 		}							\
 	} while(false);
 
+static int ensure_clean_index(git_repository *repo, git_index *index)
+{
+	git_tree *head_tree = NULL;
+	git_diff *index_diff = NULL;
+	int error = 0;
+
+	if ((error = git_repository_head_tree(&head_tree, repo)) < 0 ||
+		(error = git_diff_tree_to_index(
+			&index_diff, repo, head_tree, index, NULL)) < 0)
+		goto done;
+
+	if (git_diff_num_deltas(index_diff) > 0) {
+		giterr_set(GITERR_STASH, "%d uncommitted changes exist in the index",
+			git_diff_num_deltas(index_diff));
+		error = GIT_EUNCOMMITTED;
+	}
+
+done:
+	git_diff_free(index_diff);
+	git_tree_free(head_tree);
+	return error;
+}
+
+static int stage_new_file(const git_index_entry **entries, void *data)
+{
+	git_index *index = data;
+
+	if(entries[0] == NULL)
+		return git_index_add(index, entries[1]);
+	else
+		return git_index_add(index, entries[0]);
+}
+
+static int stage_new_files(
+	git_index **out,
+	git_repository *repo,
+	git_tree *parent_tree,
+	git_tree *tree)
+{
+	git_iterator *iterators[2] = { NULL, NULL };
+	git_index *index = NULL;
+	int error;
+
+	if ((error = git_index_new(&index)) < 0 ||
+		(error = git_iterator_for_tree(&iterators[0], parent_tree,
+			GIT_ITERATOR_DONT_IGNORE_CASE, NULL, NULL)) < 0 ||
+		(error = git_iterator_for_tree(&iterators[1], tree,
+			GIT_ITERATOR_DONT_IGNORE_CASE, NULL, NULL)) < 0)
+		goto done;
+
+	error = git_iterator_walk(iterators, 2, stage_new_file, index);
+
+done:
+	if (error < 0)
+		git_index_free(index);
+	else
+		*out = index;
+
+	git_iterator_free(iterators[0]);
+	git_iterator_free(iterators[1]);
+
+	return error;
+}
+
 int git_stash_apply(
 	git_repository *repo,
 	size_t index,
@@ -746,6 +835,7 @@ int git_stash_apply(
 	git_tree *index_tree = NULL;
 	git_tree *index_parent_tree = NULL;
 	git_tree *untracked_tree = NULL;
+	git_index *stash_adds = NULL;
 	git_index *repo_index = NULL;
 	git_index *unstashed_index = NULL;
 	git_index *modified_index = NULL;
@@ -775,6 +865,9 @@ int git_stash_apply(
 
 	NOTIFY_PROGRESS(opts, GIT_STASH_APPLY_PROGRESS_ANALYZE_INDEX);
 
+	if ((error = ensure_clean_index(repo, repo_index)) < 0)
+		goto cleanup;
+
 	/* Restore index if required */
 	if ((opts.flags & GIT_STASH_APPLY_REINSTATE_INDEX) &&
 		git_oid_cmp(git_tree_id(stash_parent_tree), git_tree_id(index_tree))) {
@@ -787,6 +880,16 @@ int git_stash_apply(
 			error = GIT_ECONFLICT;
 			goto cleanup;
 		}
+
+	/* Otherwise, stage any new files in the stash tree.  (Note: their
+	 * previously unstaged contents are staged, not the previously staged.)
+	 */
+	} else if ((opts.flags & GIT_STASH_APPLY_REINSTATE_INDEX) == 0) {
+		if ((error = stage_new_files(
+				&stash_adds, repo, stash_parent_tree, stash_tree)) < 0 ||
+			(error = merge_indexes(
+				&unstashed_index, repo, stash_parent_tree, repo_index, stash_adds)) < 0)
+			goto cleanup;
 	}
 
 	NOTIFY_PROGRESS(opts, GIT_STASH_APPLY_PROGRESS_ANALYZE_MODIFIED);
@@ -848,6 +951,7 @@ cleanup:
 	git_index_free(untracked_index);
 	git_index_free(modified_index);
 	git_index_free(unstashed_index);
+	git_index_free(stash_adds);
 	git_index_free(repo_index);
 	git_tree_free(untracked_tree);
 	git_tree_free(index_parent_tree);
diff --git a/tests/stash/apply.c b/tests/stash/apply.c
index c22a31b..901667d 100644
--- a/tests/stash/apply.c
+++ b/tests/stash/apply.c
@@ -10,14 +10,14 @@ void test_stash_apply__initialize(void)
 {
 	git_oid oid;
 
-	cl_git_pass(git_signature_new(&signature, "nulltoken", "emeric.fermas@gmail.com", 1323847743, 60)); /* Wed Dec 14 08:29:03 2011 +0100 */
-
-	cl_git_pass(git_repository_init(&repo, "stash", 0));
+	repo = cl_git_sandbox_init_new("stash");
 	cl_git_pass(git_repository_index(&repo_index, repo));
+	cl_git_pass(git_signature_new(&signature, "nulltoken", "emeric.fermas@gmail.com", 1323847743, 60)); /* Wed Dec 14 08:29:03 2011 +0100 */
 
 	cl_git_mkfile("stash/what", "hello\n");
 	cl_git_mkfile("stash/how", "small\n");
 	cl_git_mkfile("stash/who", "world\n");
+	cl_git_mkfile("stash/where", "meh\n");
 
 	cl_git_pass(git_index_add_bypath(repo_index, "what"));
 	cl_git_pass(git_index_add_bypath(repo_index, "how"));
@@ -28,14 +28,23 @@ void test_stash_apply__initialize(void)
 	cl_git_rewritefile("stash/what", "goodbye\n");
 	cl_git_rewritefile("stash/who", "funky world\n");
 	cl_git_mkfile("stash/when", "tomorrow\n");
+	cl_git_mkfile("stash/why", "would anybody use stash?\n");
+	cl_git_mkfile("stash/where", "????\n");
 
 	cl_git_pass(git_index_add_bypath(repo_index, "who"));
+	cl_git_pass(git_index_add_bypath(repo_index, "why"));
+	cl_git_pass(git_index_add_bypath(repo_index, "where"));
+	git_index_write(repo_index);
+
+	cl_git_rewritefile("stash/where", "....\n");
 
 	/* Pre-stash state */
 	assert_status(repo, "what", GIT_STATUS_WT_MODIFIED);
 	assert_status(repo, "how", GIT_STATUS_CURRENT);
 	assert_status(repo, "who", GIT_STATUS_INDEX_MODIFIED);
 	assert_status(repo, "when", GIT_STATUS_WT_NEW);
+	assert_status(repo, "why", GIT_STATUS_INDEX_NEW);
+	assert_status(repo, "where", GIT_STATUS_INDEX_NEW|GIT_STATUS_WT_MODIFIED);
 
 	cl_git_pass(git_stash_save(&oid, repo, signature, NULL, GIT_STASH_INCLUDE_UNTRACKED));
 
@@ -44,6 +53,8 @@ void test_stash_apply__initialize(void)
 	assert_status(repo, "how", GIT_STATUS_CURRENT);
 	assert_status(repo, "who", GIT_STATUS_CURRENT);
 	assert_status(repo, "when", GIT_ENOTFOUND);
+	assert_status(repo, "why", GIT_ENOTFOUND);
+	assert_status(repo, "where", GIT_ENOTFOUND);
 }
 
 void test_stash_apply__cleanup(void)
@@ -54,15 +65,13 @@ void test_stash_apply__cleanup(void)
 	git_index_free(repo_index);
 	repo_index = NULL;
 
-	git_repository_free(repo);
-	repo = NULL;
-
-	cl_git_pass(git_futils_rmdir_r("stash", NULL, GIT_RMDIR_REMOVE_FILES));
-	cl_fixture_cleanup("sorry-it-is-a-non-bare-only-party");
+	cl_git_sandbox_cleanup();
 }
 
 void test_stash_apply__with_default(void)
 {
+	git_buf where = GIT_BUF_INIT;
+
 	cl_git_pass(git_stash_apply(repo, 0, NULL));
 
 	cl_assert_equal_i(git_index_has_conflicts(repo_index), 0);
@@ -70,10 +79,42 @@ void test_stash_apply__with_default(void)
 	assert_status(repo, "how", GIT_STATUS_CURRENT);
 	assert_status(repo, "who", GIT_STATUS_WT_MODIFIED);
 	assert_status(repo, "when", GIT_STATUS_WT_NEW);
+	assert_status(repo, "why", GIT_STATUS_INDEX_NEW);
+	assert_status(repo, "where", GIT_STATUS_INDEX_NEW);
+
+	cl_git_pass(git_futils_readbuffer(&where, "stash/where"));
+	cl_assert_equal_s("....\n", where.ptr);
+
+	git_buf_free(&where);
+}
+
+void test_stash_apply__with_existing_file(void)
+{
+	cl_git_mkfile("stash/where", "oops!\n");
+	cl_git_fail(git_stash_apply(repo, 0, NULL));
+}
+
+void test_stash_apply__merges_new_file(void)
+{
+	git_index_entry *ancestor, *our, *their;
+
+	cl_git_mkfile("stash/where", "committed before stash\n");
+	cl_git_pass(git_index_add_bypath(repo_index, "where"));
+	cl_repo_commit_from_index(NULL, repo, signature, 0, "Other commit");
+
+	cl_git_pass(git_stash_apply(repo, 0, NULL));
+
+	cl_assert_equal_i(1, git_index_has_conflicts(repo_index));
+	assert_status(repo, "what", GIT_STATUS_INDEX_MODIFIED);
+	cl_git_pass(git_index_conflict_get(&ancestor, &our, &their, repo_index, "where")); /* unmerged */
+	assert_status(repo, "who", GIT_STATUS_INDEX_MODIFIED);
+	assert_status(repo, "when", GIT_STATUS_WT_NEW);
+	assert_status(repo, "why", GIT_STATUS_INDEX_NEW);
 }
 
 void test_stash_apply__with_reinstate_index(void)
 {
+	git_buf where = GIT_BUF_INIT;
 	git_stash_apply_options opts = GIT_STASH_APPLY_OPTIONS_INIT;
 
 	opts.flags = GIT_STASH_APPLY_REINSTATE_INDEX;
@@ -85,6 +126,13 @@ void test_stash_apply__with_reinstate_index(void)
 	assert_status(repo, "how", GIT_STATUS_CURRENT);
 	assert_status(repo, "who", GIT_STATUS_INDEX_MODIFIED);
 	assert_status(repo, "when", GIT_STATUS_WT_NEW);
+	assert_status(repo, "why", GIT_STATUS_INDEX_NEW);
+	assert_status(repo, "where", GIT_STATUS_INDEX_NEW | GIT_STATUS_WT_MODIFIED);
+
+	cl_git_pass(git_futils_readbuffer(&where, "stash/where"));
+	cl_assert_equal_s("....\n", where.ptr);
+
+	git_buf_free(&where);
 }
 
 void test_stash_apply__conflict_index_with_default(void)
@@ -96,6 +144,7 @@ void test_stash_apply__conflict_index_with_default(void)
 	cl_git_rewritefile("stash/who", "nothing\n");
 	cl_git_pass(git_index_add_bypath(repo_index, "who"));
 	cl_git_pass(git_index_write(repo_index));
+	cl_repo_commit_from_index(NULL, repo, signature, 0, "Other commit");
 
 	cl_git_pass(git_stash_apply(repo, 0, NULL));
 
@@ -104,6 +153,7 @@ void test_stash_apply__conflict_index_with_default(void)
 	assert_status(repo, "how", GIT_STATUS_CURRENT);
 	cl_git_pass(git_index_conflict_get(&ancestor, &our, &their, repo_index, "who")); /* unmerged */
 	assert_status(repo, "when", GIT_STATUS_WT_NEW);
+	assert_status(repo, "why", GIT_STATUS_INDEX_NEW);
 }
 
 void test_stash_apply__conflict_index_with_reinstate_index(void)
@@ -115,14 +165,16 @@ void test_stash_apply__conflict_index_with_reinstate_index(void)
 	cl_git_rewritefile("stash/who", "nothing\n");
 	cl_git_pass(git_index_add_bypath(repo_index, "who"));
 	cl_git_pass(git_index_write(repo_index));
+	cl_repo_commit_from_index(NULL, repo, signature, 0, "Other commit");
 
 	cl_git_fail_with(git_stash_apply(repo, 0, &opts), GIT_ECONFLICT);
 
 	cl_assert_equal_i(git_index_has_conflicts(repo_index), 0);
 	assert_status(repo, "what", GIT_STATUS_CURRENT);
 	assert_status(repo, "how", GIT_STATUS_CURRENT);
-	assert_status(repo, "who", GIT_STATUS_INDEX_MODIFIED);
+	assert_status(repo, "who", GIT_STATUS_CURRENT);
 	assert_status(repo, "when", GIT_ENOTFOUND);
+	assert_status(repo, "why", GIT_ENOTFOUND);
 }
 
 void test_stash_apply__conflict_untracked_with_default(void)
@@ -138,6 +190,7 @@ void test_stash_apply__conflict_untracked_with_default(void)
 	assert_status(repo, "how", GIT_STATUS_CURRENT);
 	assert_status(repo, "who", GIT_STATUS_CURRENT);
 	assert_status(repo, "when", GIT_STATUS_WT_NEW);
+	assert_status(repo, "why", GIT_ENOTFOUND);
 }
 
 void test_stash_apply__conflict_untracked_with_reinstate_index(void)
@@ -155,6 +208,7 @@ void test_stash_apply__conflict_untracked_with_reinstate_index(void)
 	assert_status(repo, "how", GIT_STATUS_CURRENT);
 	assert_status(repo, "who", GIT_STATUS_CURRENT);
 	assert_status(repo, "when", GIT_STATUS_WT_NEW);
+	assert_status(repo, "why", GIT_ENOTFOUND);
 }
 
 void test_stash_apply__conflict_workdir_with_default(void)
@@ -168,6 +222,7 @@ void test_stash_apply__conflict_workdir_with_default(void)
 	assert_status(repo, "how", GIT_STATUS_CURRENT);
 	assert_status(repo, "who", GIT_STATUS_CURRENT);
 	assert_status(repo, "when", GIT_STATUS_WT_NEW);
+	assert_status(repo, "why", GIT_ENOTFOUND);
 }
 
 void test_stash_apply__conflict_workdir_with_reinstate_index(void)
@@ -185,6 +240,7 @@ void test_stash_apply__conflict_workdir_with_reinstate_index(void)
 	assert_status(repo, "how", GIT_STATUS_CURRENT);
 	assert_status(repo, "who", GIT_STATUS_CURRENT);
 	assert_status(repo, "when", GIT_STATUS_WT_NEW);
+	assert_status(repo, "why", GIT_ENOTFOUND);
 }
 
 void test_stash_apply__conflict_commit_with_default(void)
@@ -204,6 +260,7 @@ void test_stash_apply__conflict_commit_with_default(void)
 	assert_status(repo, "how", GIT_STATUS_CURRENT);
 	assert_status(repo, "who", GIT_STATUS_INDEX_MODIFIED);
 	assert_status(repo, "when", GIT_STATUS_WT_NEW);
+	assert_status(repo, "why", GIT_STATUS_INDEX_NEW);
 }
 
 void test_stash_apply__conflict_commit_with_reinstate_index(void)
@@ -226,6 +283,23 @@ void test_stash_apply__conflict_commit_with_reinstate_index(void)
 	assert_status(repo, "how", GIT_STATUS_CURRENT);
 	assert_status(repo, "who", GIT_STATUS_INDEX_MODIFIED);
 	assert_status(repo, "when", GIT_STATUS_WT_NEW);
+	assert_status(repo, "why", GIT_STATUS_INDEX_NEW);
+}
+
+void test_stash_apply__fails_with_uncommitted_changes_in_index(void)
+{
+	cl_git_rewritefile("stash/who", "nothing\n");
+	cl_git_pass(git_index_add_bypath(repo_index, "who"));
+	cl_git_pass(git_index_write(repo_index));
+
+	cl_git_fail_with(git_stash_apply(repo, 0, NULL), GIT_EUNCOMMITTED);
+
+	cl_assert_equal_i(git_index_has_conflicts(repo_index), 0);
+	assert_status(repo, "what", GIT_STATUS_CURRENT);
+	assert_status(repo, "how", GIT_STATUS_CURRENT);
+	assert_status(repo, "who", GIT_STATUS_INDEX_MODIFIED);
+	assert_status(repo, "when", GIT_ENOTFOUND);
+	assert_status(repo, "why", GIT_ENOTFOUND);
 }
 
 void test_stash_apply__pop(void)
@@ -285,6 +359,8 @@ void test_stash_apply__executes_notify_cb(void)
 	assert_status(repo, "how", GIT_STATUS_CURRENT);
 	assert_status(repo, "who", GIT_STATUS_WT_MODIFIED);
 	assert_status(repo, "when", GIT_STATUS_WT_NEW);
+	assert_status(repo, "why", GIT_STATUS_INDEX_NEW);
+	assert_status(repo, "where", GIT_STATUS_INDEX_NEW);
 
 	cl_assert_equal_b(true, seen_paths.what);
 	cl_assert_equal_b(false, seen_paths.how);