thodg/libgit2

diff --git a/include/git2/stash.h b/include/git2/stash.h
index f69ba30..428d9f2 100644
--- a/include/git2/stash.h
+++ b/include/git2/stash.h
@@ -97,10 +97,9 @@ typedef enum {
  * the workdir and index will be left untouched.
  *
  * @param repo The owning repository.
- *
  * @param index The position within the stash list. 0 points to the
- * most recent stashed state.
- *
+ *              most recent stashed state.
+ * @param checkout_options Options to control how files are checked out
  * @param flags Flags to control the applying process. (see GIT_APPLY_* above)
  *
  * @return 0 on success, GIT_ENOTFOUND if there's no stashed state for the given
@@ -109,6 +108,7 @@ typedef enum {
 GIT_EXTERN(int) git_stash_apply(
 	git_repository *repo,
 	size_t index,
+	const git_checkout_options *checkout_options,
 	unsigned int flags);
 
 /**
@@ -167,10 +167,9 @@ GIT_EXTERN(int) git_stash_drop(
  * if successful.
  *
  * @param repo The owning repository.
- *
  * @param index The position within the stash list. 0 points to the
- * most recent stashed state.
- *
+ *              most recent stashed state.
+ * @param checkout_options Options to control how files are checked out
  * @param flags Flags to control the applying process. (see GIT_APPLY_* above)
  *
  * @return 0 on success, GIT_ENOTFOUND if there's no stashed state for the given
@@ -179,6 +178,7 @@ GIT_EXTERN(int) git_stash_drop(
 GIT_EXTERN(int) git_stash_pop(
 	git_repository *repo,
 	size_t index,
+	const git_checkout_options *checkout_options,
 	unsigned int flags);
 
 /** @} */
diff --git a/src/stash.c b/src/stash.c
index 899156d..d53c22c 100644
--- a/src/stash.c
+++ b/src/stash.c
@@ -18,7 +18,10 @@
 #include "git2/index.h"
 #include "git2/transaction.h"
 #include "git2/merge.h"
+#include "index.h"
 #include "signature.h"
+#include "iterator.h"
+#include "merge.h"
 
 static int create_error(int error, const char *msg)
 {
@@ -645,187 +648,81 @@ cleanup:
 	return error;
 }
 
-static int apply_index(
-	git_tree **unstashed_tree,
+static int merge_index_and_tree(
+	git_index **out,
 	git_repository *repo,
-	git_tree *start_index_tree,
-	git_tree *index_parent_tree,
-	git_tree *index_tree)
+	git_tree *ancestor_tree,
+	git_index *ours_index,
+	git_tree *theirs_tree)
 {
-	git_index *unstashed_index = NULL;
-	git_merge_options options = GIT_MERGE_OPTIONS_INIT;
+	git_iterator *ancestor = NULL, *ours = NULL, *theirs = NULL;
+	const git_iterator_flag_t flags = GIT_ITERATOR_DONT_IGNORE_CASE;
 	int error;
-	git_oid oid;
-
-	if ((error = git_merge_trees(
-			&unstashed_index, repo, index_parent_tree,
-			start_index_tree, index_tree, &options)) < 0)
-		goto cleanup;
-
-	if ((error = git_index_write_tree_to(&oid, unstashed_index, repo)) < 0)
-		goto cleanup;
-
-	if ((error = git_tree_lookup(unstashed_tree, repo, &oid)) < 0)
-		goto cleanup;
-
-cleanup:
-	git_index_free(unstashed_index);
-	return error;
-}
-
-static int apply_untracked(
-	git_repository *repo,
-	git_tree *start_index_tree,
-	git_tree *untracked_tree)
-{
-	git_checkout_options options = GIT_CHECKOUT_OPTIONS_INIT;
-	git_index *merged_index = NULL;
-	int error;
-
-	options.checkout_strategy =
-		GIT_CHECKOUT_SAFE | GIT_CHECKOUT_DONT_UPDATE_INDEX;
-
-	if ((error = git_merge_trees(&merged_index,
-			repo, NULL, start_index_tree, untracked_tree, NULL)) == 0)
-		error = git_checkout_index(repo, merged_index, &options);
-
-	git_index_free(merged_index);
-	return error;
-}
 
-static int checkout_modified_notify_callback(
-	git_checkout_notify_t why,
-	const char *path,
-	const git_diff_file *baseline,
-	const git_diff_file *target,
-	const git_diff_file *workdir,
-	void *payload)
-{
-	unsigned int status;
-	int error;
-
-	GIT_UNUSED(why);
-	GIT_UNUSED(baseline);
-	GIT_UNUSED(target);
-	GIT_UNUSED(workdir);
-
-	if ((error = git_status_file(&status, payload, path)) < 0)
-		return error;
-
-	if (status & GIT_STATUS_WT_MODIFIED) {
-		giterr_set(GITERR_STASH, "Local changes to '%s' would be overwritten", path);
-		return GIT_EMERGECONFLICT;
-	}
-
-	return 0;
-}
-
-static int apply_modified(
-	int *has_conflicts,
-	git_repository *repo,
-	git_tree *base_tree,
-	git_tree *start_index_tree,
-	git_tree *stash_tree,
-	unsigned int flags)
-{
-	git_index *index = NULL;
-	git_merge_options merge_options = GIT_MERGE_OPTIONS_INIT;
-	git_checkout_options checkout_options = GIT_CHECKOUT_OPTIONS_INIT;
-	int error;
-
-	if ((error = git_merge_trees(
-			&index, repo, base_tree,
-			start_index_tree, stash_tree, &merge_options)) < 0)
-		goto cleanup;
-
-	checkout_options.checkout_strategy = GIT_CHECKOUT_SAFE | GIT_CHECKOUT_ALLOW_CONFLICTS;
-	if ((flags & GIT_APPLY_REINSTATE_INDEX) && !git_index_has_conflicts(index)) {
-		/* No need to update the index if it will be overridden later on */
-		checkout_options.checkout_strategy |= GIT_CHECKOUT_DONT_UPDATE_INDEX;
-	}
-	checkout_options.notify_flags = GIT_CHECKOUT_NOTIFY_CONFLICT;
-	checkout_options.notify_cb = checkout_modified_notify_callback;
-	checkout_options.notify_payload = repo;
-	checkout_options.our_label = "Updated upstream";
-	checkout_options.their_label = "Stashed changes";
-	if ((error = git_checkout_index(repo, index, &checkout_options)) < 0)
-		goto cleanup;
+	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_tree(&theirs, theirs_tree, flags, NULL, NULL)) < 0)
+		goto done;
 
-	*has_conflicts = git_index_has_conflicts(index);
+	error = git_merge__iterators(out, repo, ancestor, ours, theirs, NULL);
 
-cleanup:
-	git_index_free(index);
+done:
+	git_iterator_free(ancestor);
+	git_iterator_free(ours);
+	git_iterator_free(theirs);
 	return error;
 }
 
-static int unstage_modified_files(
-	git_repository *repo,
-	git_index *repo_index,
-	git_tree *unstashed_tree,
-	git_tree *start_index_tree)
-{
-	git_diff *diff = NULL;
-	git_diff_options options = GIT_DIFF_OPTIONS_INIT;
-	size_t i, count;
-	int error;
-
-	if (unstashed_tree) {
-		if ((error = git_index_read_tree(repo_index, unstashed_tree)) < 0)
-			goto cleanup;
+static void normalize_checkout_options(
+	git_checkout_options *checkout_opts,
+	const git_checkout_options *given_checkout_opts)
+{	
+	if (given_checkout_opts != NULL) {
+		memcpy(checkout_opts, given_checkout_opts, sizeof(git_checkout_options));
 	} else {
-		options.flags = GIT_DIFF_FORCE_BINARY;
-		if ((error = git_diff_tree_to_index(&diff, repo, start_index_tree,
-				repo_index, &options)) < 0)
-			goto cleanup;
-
-		/*
-		 This behavior is not 100% similar to "git stash apply" as the latter uses
-		 "git-read-tree --reset {treeish}" which preserves the stat()s from the
-		 index instead of replacing them with the tree ones for identical files.
-		 */
+		git_checkout_options default_checkout_opts = GIT_CHECKOUT_OPTIONS_INIT;
+		default_checkout_opts.checkout_strategy =  GIT_CHECKOUT_SAFE;
 
-		if ((error = git_index_read_tree(repo_index, start_index_tree)) < 0)
-			goto cleanup;
-
-		for (i = 0, count = git_diff_num_deltas(diff); i < count; ++i) {
-			const git_diff_delta* delta = git_diff_get_delta(diff, i);
-			if (delta->status == GIT_DELTA_ADDED) {
-				if ((error = git_index_add_bypath(
-						repo_index, delta->new_file.path)) < 0)
-					goto cleanup;
-			}
-		}
+		memcpy(checkout_opts, &default_checkout_opts, sizeof(git_checkout_options));
 	}
 
-cleanup:
-	git_diff_free(diff);
-	return error;
+	if (!checkout_opts->our_label)
+		checkout_opts->our_label = "Updated upstream";
+
+	if (!checkout_opts->their_label)
+		checkout_opts->their_label = "Stashed changes";
 }
 
 int git_stash_apply(
 	git_repository *repo,
 	size_t index,
+	const git_checkout_options *given_checkout_opts,
 	unsigned int flags)
 {
+	git_checkout_options checkout_opts;
+	unsigned int checkout_strategy;
 	git_commit *stash_commit = NULL;
 	git_tree *stash_tree = NULL;
-	git_tree *base_tree = NULL;
+	git_tree *stash_parent_tree = NULL;
 	git_tree *index_tree = NULL;
 	git_tree *index_parent_tree = NULL;
 	git_tree *untracked_tree = NULL;
 	git_index *repo_index = NULL;
-	git_tree *start_index_tree = NULL;
-	git_tree *unstashed_tree = NULL;
-	int has_conflicts;
+	git_index *unstashed_index = NULL;
+	git_index *modified_index = NULL;
+	git_index *untracked_index = NULL;
 	int error;
 
+	normalize_checkout_options(&checkout_opts, given_checkout_opts);
+	checkout_strategy = checkout_opts.checkout_strategy;
+
 	/* Retrieve commit corresponding to the given stash */
 	if ((error = retrieve_stash_commit(&stash_commit, repo, index)) < 0)
 		goto cleanup;
 
 	/* Retrieve all trees in the stash */
 	if ((error = retrieve_stash_trees(
-			&stash_tree, &base_tree, &index_tree,
+			&stash_tree, &stash_parent_tree, &index_tree,
 			&index_parent_tree, &untracked_tree, stash_commit)) < 0)
 		goto cleanup;
 
@@ -833,50 +730,73 @@ int git_stash_apply(
 	if ((error = git_repository_index(&repo_index, repo)) < 0)
 		goto cleanup;
 
-	/* Create tree from index */
-	if ((error = build_tree_from_index(&start_index_tree, repo_index)) < 0)
-		goto cleanup;
-
 	/* Restore index if required */
 	if ((flags & GIT_APPLY_REINSTATE_INDEX) &&
-		git_oid_cmp(git_tree_id(base_tree), git_tree_id(index_tree)) &&
-		git_oid_cmp(git_tree_id(start_index_tree), git_tree_id(index_tree))) {
+		git_oid_cmp(git_tree_id(stash_parent_tree), git_tree_id(index_tree))) {
 
-		if ((error = apply_index(
-				&unstashed_tree, repo, start_index_tree,
-				index_parent_tree, index_tree)) < 0)
+		if ((error = merge_index_and_tree(
+				&unstashed_index, repo, index_parent_tree, repo_index, index_tree)) < 0)
 			goto cleanup;
-	}
 
-	/* If applicable, restore untracked / ignored files in workdir */
-	if (untracked_tree) {
-		if ((error = apply_untracked(repo, start_index_tree, untracked_tree)) < 0)
+
+		/* TODO: GIT_EMERGECONFLICT  */
+		if (git_index_has_conflicts(unstashed_index)) {
+			error = GIT_EUNMERGED;
 			goto cleanup;
+		}
 	}
 
 	/* Restore modified files in workdir */
-	if ((error = apply_modified(
-			&has_conflicts, repo, base_tree, start_index_tree,
-			stash_tree, flags)) < 0)
+	if ((error = merge_index_and_tree(
+			&modified_index, repo, stash_parent_tree, repo_index, stash_tree)) < 0)
 		goto cleanup;
 
-	/* Unstage modified files from index unless there were merge conflicts */
-	if (!has_conflicts && (error = unstage_modified_files(
-			repo, repo_index, unstashed_tree, start_index_tree)) < 0)
+	/* If applicable, restore untracked / ignored files in workdir */
+	if (untracked_tree &&
+		(error = merge_index_and_tree(&untracked_index, repo, NULL, repo_index, untracked_tree)) < 0)
 		goto cleanup;
 
-	/* Write updated index */
-	if ((error = git_index_write(repo_index)) < 0)
+	if (untracked_index) {
+		checkout_opts.checkout_strategy |= GIT_CHECKOUT_DONT_UPDATE_INDEX;
+
+		if ((error = git_checkout_index(repo, untracked_index, &checkout_opts)) < 0)
+			goto cleanup;
+
+		checkout_opts.checkout_strategy = checkout_strategy;
+	}
+
+
+	/* If there are conflicts in the modified index, then we need to actually
+	 * check that out as the repo's index.  Otherwise, we don't update the
+	 * index.
+	 */
+
+	if (!git_index_has_conflicts(modified_index))
+		checkout_opts.checkout_strategy |= GIT_CHECKOUT_DONT_UPDATE_INDEX;
+
+	/* Check out the modified index using the existing repo index as baseline,
+	 * so that existing modifications in the index can be rewritten even when
+	 * checking out safely.
+	 */
+	checkout_opts.baseline_index = repo_index;
+
+	if ((error = git_checkout_index(repo, modified_index, &checkout_opts)) < 0)
 		goto cleanup;
 
+	if (unstashed_index && !git_index_has_conflicts(modified_index)) {
+		if ((error = git_index_read_index(repo_index, unstashed_index)) < 0)
+			goto cleanup;
+	}
+
 cleanup:
-	git_tree_free(unstashed_tree);
-	git_tree_free(start_index_tree);
+	git_index_free(untracked_index);
+	git_index_free(modified_index);
+	git_index_free(unstashed_index);
 	git_index_free(repo_index);
 	git_tree_free(untracked_tree);
 	git_tree_free(index_parent_tree);
 	git_tree_free(index_tree);
-	git_tree_free(base_tree);
+	git_tree_free(stash_parent_tree);
 	git_tree_free(stash_tree);
 	git_commit_free(stash_commit);
 	return error;
@@ -984,11 +904,12 @@ cleanup:
 int git_stash_pop(
 	git_repository *repo,
 	size_t index,
+	const git_checkout_options *checkout_options,
 	unsigned int flags)
 {
 	int error;
 
-	if ((error = git_stash_apply(repo, index, flags)) < 0)
+	if ((error = git_stash_apply(repo, index, checkout_options, flags)) < 0)
 		return error;
 
 	return git_stash_drop(repo, index);
diff --git a/tests/stash/apply.c b/tests/stash/apply.c
index c0cdcab..efe7852 100644
--- a/tests/stash/apply.c
+++ b/tests/stash/apply.c
@@ -63,7 +63,7 @@ void test_stash_apply__cleanup(void)
 
 void test_stash_apply__with_default(void)
 {
-	cl_git_pass(git_stash_apply(repo, 0, GIT_APPLY_DEFAULT));
+	cl_git_pass(git_stash_apply(repo, 0, NULL, GIT_APPLY_DEFAULT));
 
 	cl_assert_equal_i(git_index_has_conflicts(repo_index), 0);
 	assert_status(repo, "what", GIT_STATUS_WT_MODIFIED);
@@ -74,7 +74,7 @@ void test_stash_apply__with_default(void)
 
 void test_stash_apply__with_reinstate_index(void)
 {
-	cl_git_pass(git_stash_apply(repo, 0, GIT_APPLY_REINSTATE_INDEX));
+	cl_git_pass(git_stash_apply(repo, 0, NULL, GIT_APPLY_REINSTATE_INDEX));
 
 	cl_assert_equal_i(git_index_has_conflicts(repo_index), 0);
 	assert_status(repo, "what", GIT_STATUS_WT_MODIFIED);
@@ -93,7 +93,7 @@ void test_stash_apply__conflict_index_with_default(void)
 	cl_git_pass(git_index_add_bypath(repo_index, "who"));
 	cl_git_pass(git_index_write(repo_index));
 
-	cl_git_pass(git_stash_apply(repo, 0, GIT_APPLY_DEFAULT));
+	cl_git_pass(git_stash_apply(repo, 0, NULL, GIT_APPLY_DEFAULT));
 
 	cl_assert_equal_i(git_index_has_conflicts(repo_index), 1);
 	assert_status(repo, "what", GIT_STATUS_INDEX_MODIFIED);
@@ -108,7 +108,7 @@ void test_stash_apply__conflict_index_with_reinstate_index(void)
 	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, GIT_APPLY_REINSTATE_INDEX), GIT_EUNMERGED);
+	cl_git_fail_with(git_stash_apply(repo, 0, NULL, GIT_APPLY_REINSTATE_INDEX), GIT_EUNMERGED);
 
 	cl_assert_equal_i(git_index_has_conflicts(repo_index), 0);
 	assert_status(repo, "what", GIT_STATUS_CURRENT);
@@ -121,7 +121,7 @@ void test_stash_apply__conflict_untracked_with_default(void)
 {
 	cl_git_mkfile("stash/when", "nothing\n");
 
-	cl_git_fail_with(git_stash_apply(repo, 0, GIT_APPLY_DEFAULT), GIT_EMERGECONFLICT);
+	cl_git_fail_with(git_stash_apply(repo, 0, NULL, GIT_APPLY_DEFAULT), GIT_EMERGECONFLICT);
 
 	cl_assert_equal_i(git_index_has_conflicts(repo_index), 0);
 	assert_status(repo, "what", GIT_STATUS_CURRENT);
@@ -134,7 +134,7 @@ void test_stash_apply__conflict_untracked_with_reinstate_index(void)
 {
 	cl_git_mkfile("stash/when", "nothing\n");
 
-	cl_git_fail_with(git_stash_apply(repo, 0, GIT_APPLY_REINSTATE_INDEX), GIT_EMERGECONFLICT);
+	cl_git_fail_with(git_stash_apply(repo, 0, NULL, GIT_APPLY_REINSTATE_INDEX), GIT_EMERGECONFLICT);
 
 	cl_assert_equal_i(git_index_has_conflicts(repo_index), 0);
 	assert_status(repo, "what", GIT_STATUS_CURRENT);
@@ -147,7 +147,7 @@ void test_stash_apply__conflict_workdir_with_default(void)
 {
 	cl_git_rewritefile("stash/what", "ciao\n");
 
-	cl_git_fail_with(git_stash_apply(repo, 0, GIT_APPLY_DEFAULT), GIT_EMERGECONFLICT);
+	cl_git_fail_with(git_stash_apply(repo, 0, NULL, GIT_APPLY_DEFAULT), GIT_EMERGECONFLICT);
 
 	cl_assert_equal_i(git_index_has_conflicts(repo_index), 0);
 	assert_status(repo, "what", GIT_STATUS_WT_MODIFIED);
@@ -160,7 +160,7 @@ void test_stash_apply__conflict_workdir_with_reinstate_index(void)
 {
 	cl_git_rewritefile("stash/what", "ciao\n");
 
-	cl_git_fail_with(git_stash_apply(repo, 0, GIT_APPLY_REINSTATE_INDEX), GIT_EMERGECONFLICT);
+	cl_git_fail_with(git_stash_apply(repo, 0, NULL, GIT_APPLY_REINSTATE_INDEX), GIT_EMERGECONFLICT);
 
 	cl_assert_equal_i(git_index_has_conflicts(repo_index), 0);
 	assert_status(repo, "what", GIT_STATUS_WT_MODIFIED);
@@ -179,7 +179,7 @@ void test_stash_apply__conflict_commit_with_default(void)
 	cl_git_pass(git_index_add_bypath(repo_index, "what"));
 	cl_repo_commit_from_index(NULL, repo, signature, 0, "Other commit");
 
-	cl_git_pass(git_stash_apply(repo, 0, GIT_APPLY_DEFAULT));
+	cl_git_pass(git_stash_apply(repo, 0, NULL, GIT_APPLY_DEFAULT));
 
 	cl_assert_equal_i(git_index_has_conflicts(repo_index), 1);
 	cl_git_pass(git_index_conflict_get(&ancestor, &our, &their, repo_index, "what")); /* unmerged */
@@ -198,7 +198,7 @@ void test_stash_apply__conflict_commit_with_reinstate_index(void)
 	cl_git_pass(git_index_add_bypath(repo_index, "what"));
 	cl_repo_commit_from_index(NULL, repo, signature, 0, "Other commit");
 
-	cl_git_pass(git_stash_apply(repo, 0, GIT_APPLY_REINSTATE_INDEX));
+	cl_git_pass(git_stash_apply(repo, 0, NULL, GIT_APPLY_REINSTATE_INDEX));
 
 	cl_assert_equal_i(git_index_has_conflicts(repo_index), 1);
 	cl_git_pass(git_index_conflict_get(&ancestor, &our, &their, repo_index, "what")); /* unmerged */
@@ -209,7 +209,7 @@ void test_stash_apply__conflict_commit_with_reinstate_index(void)
 
 void test_stash_apply__pop(void)
 {
-	cl_git_pass(git_stash_pop(repo, 0, GIT_APPLY_DEFAULT));
+	cl_git_pass(git_stash_pop(repo, 0, NULL, GIT_APPLY_DEFAULT));
 
-	cl_git_fail_with(git_stash_pop(repo, 0, GIT_APPLY_DEFAULT), GIT_ENOTFOUND);
+	cl_git_fail_with(git_stash_pop(repo, 0, NULL, GIT_APPLY_DEFAULT), GIT_ENOTFOUND);
 }