thodg/libgit2

diff --git a/src/merge.c b/src/merge.c
index 20cfc0e..ac973ef 100644
--- a/src/merge.c
+++ b/src/merge.c
@@ -2330,7 +2330,7 @@ done:
 
 static int merge_check_workdir(size_t *conflicts, git_repository *repo, git_index *index_new, git_vector *merged_paths)
 {
-	git_tree *head_tree = NULL;
+	git_index *index_repo = NULL;
 	git_diff *wd_diff_list = NULL;
 	git_diff_options opts = GIT_DIFF_OPTIONS_INIT;
 	int error = 0;
@@ -2341,9 +2341,6 @@ static int merge_check_workdir(size_t *conflicts, git_repository *repo, git_inde
 
 	opts.flags |= GIT_DIFF_INCLUDE_UNTRACKED;
 
-	if ((error = git_repository_head_tree(&head_tree, repo)) < 0)
-		goto done;
-
 	/* Workdir changes may exist iff they do not conflict with changes that
 	 * will be applied by the merge (including conflicts).  Ensure that there
 	 * are no changes in the workdir to these paths.
@@ -2351,13 +2348,13 @@ static int merge_check_workdir(size_t *conflicts, git_repository *repo, git_inde
 	opts.pathspec.count = merged_paths->length;
 	opts.pathspec.strings = (char **)merged_paths->contents;
 
-	if ((error = git_diff_tree_to_workdir(&wd_diff_list, repo, head_tree, &opts)) < 0)
+	if ((error = git_diff_index_to_workdir(&wd_diff_list, repo, index_repo, &opts)) < 0)
 		goto done;
 
 	*conflicts = wd_diff_list->deltas.length;
 
 done:
-	git_tree_free(head_tree);
+	git_index_free(index_repo);
 	git_diff_free(wd_diff_list);
 
 	return error;
@@ -2400,7 +2397,7 @@ int git_merge__indexes(git_repository *repo, git_index *index_new)
 
 	/* Remove removed items from the index */
 	git_vector_foreach(&paths, i, path) {
-		if ((e = git_index_get_bypath(index_new, path, 0)) == NULL) {
+		if (git_index_get_bypath(index_new, path, 0) == NULL) {
 			if ((error = git_index_remove(index_repo, path, 0)) < 0 &&
 				error != GIT_ENOTFOUND)
 				goto done;
diff --git a/tests/merge/workdir/dirty.c b/tests/merge/workdir/dirty.c
new file mode 100644
index 0000000..625d3d0
--- /dev/null
+++ b/tests/merge/workdir/dirty.c
@@ -0,0 +1,322 @@
+#include "clar_libgit2.h"
+#include "git2/merge.h"
+#include "buffer.h"
+#include "merge.h"
+#include "../merge_helpers.h"
+#include "posix.h"
+
+#define TEST_REPO_PATH "merge-resolve"
+#define MERGE_BRANCH_OID "7cb63eed597130ba4abb87b3e544b85021905520"
+
+#define AUTOMERGEABLE_MERGED_FILE \
+	"this file is changed in master\n" \
+	"this file is automergeable\n" \
+	"this file is automergeable\n" \
+	"this file is automergeable\n" \
+	"this file is automergeable\n" \
+	"this file is automergeable\n" \
+	"this file is automergeable\n" \
+	"this file is automergeable\n" \
+	"this file is changed in branch\n"
+
+#define CHANGED_IN_BRANCH_FILE \
+	"changed in branch\n"
+
+static git_repository *repo;
+static git_index *repo_index;
+
+static char *unaffected[][4] = {
+	{ "added-in-master.txt", NULL },
+	{ "changed-in-master.txt", NULL },
+	{ "unchanged.txt", NULL },
+	{ "added-in-master.txt", "changed-in-master.txt", NULL },
+	{ "added-in-master.txt", "unchanged.txt", NULL },
+	{ "changed-in-master.txt", "unchanged.txt", NULL },
+	{ "added-in-master.txt", "changed-in-master.txt", "unchanged.txt", NULL },
+	{ "new_file.txt", NULL },
+	{ "new_file.txt", "unchanged.txt", NULL },
+	{ NULL },
+};
+
+static char *affected[][5] = {
+	{ "automergeable.txt", NULL },
+	{ "changed-in-branch.txt", NULL },
+	{ "conflicting.txt", NULL },
+	{ "removed-in-branch.txt", NULL },
+	{ "automergeable.txt", "changed-in-branch.txt", NULL },
+	{ "automergeable.txt", "conflicting.txt", NULL },
+	{ "automergeable.txt", "removed-in-branch.txt", NULL },
+	{ "changed-in-branch.txt", "conflicting.txt", NULL },
+	{ "changed-in-branch.txt", "removed-in-branch.txt", NULL },
+	{ "conflicting.txt", "removed-in-branch.txt", NULL },
+	{ "automergeable.txt", "changed-in-branch.txt", "conflicting.txt", NULL },
+	{ "automergeable.txt", "changed-in-branch.txt", "removed-in-branch.txt", NULL },
+	{ "automergeable.txt", "conflicting.txt", "removed-in-branch.txt", NULL },
+	{ "changed-in-branch.txt", "conflicting.txt", "removed-in-branch.txt", NULL },
+	{ "automergeable.txt", "changed-in-branch.txt", "conflicting.txt", "removed-in-branch.txt", NULL },
+	{ NULL },
+};
+
+static char *result_contents[4][6] = {
+	{ "automergeable.txt", AUTOMERGEABLE_MERGED_FILE, NULL, NULL },
+	{ "changed-in-branch.txt", CHANGED_IN_BRANCH_FILE, NULL, NULL },
+	{ "automergeable.txt", AUTOMERGEABLE_MERGED_FILE, "changed-in-branch.txt", CHANGED_IN_BRANCH_FILE, NULL, NULL },
+	{ NULL }
+};
+
+void test_merge_workdir_dirty__initialize(void)
+{
+	repo = cl_git_sandbox_init(TEST_REPO_PATH);
+	git_repository_index(&repo_index, repo);
+}
+
+void test_merge_workdir_dirty__cleanup(void)
+{
+	git_index_free(repo_index);
+	cl_git_sandbox_cleanup();
+}
+
+static void set_core_autocrlf_to(git_repository *repo, bool value)
+{
+	git_config *cfg;
+
+	cl_git_pass(git_repository_config(&cfg, repo));
+	cl_git_pass(git_config_set_bool(cfg, "core.autocrlf", value));
+
+	git_config_free(cfg);
+}
+
+static int merge_branch(git_merge_result **result, int merge_file_favor, int checkout_strategy)
+{
+	git_oid their_oids[1];
+	git_merge_head *their_heads[1];
+	git_merge_opts opts = GIT_MERGE_OPTS_INIT;
+	int error;
+
+	cl_git_pass(git_oid_fromstr(&their_oids[0], MERGE_BRANCH_OID));
+	cl_git_pass(git_merge_head_from_id(&their_heads[0], repo, &their_oids[0]));
+
+	opts.merge_tree_opts.file_favor = merge_file_favor;
+	opts.checkout_opts.checkout_strategy = checkout_strategy;
+	error = git_merge(result, repo, (const git_merge_head **)their_heads, 1, &opts);
+
+	git_merge_head_free(their_heads[0]);
+
+	return error;
+}
+
+static void write_files(char *files[])
+{
+	char *filename;
+	git_buf path = GIT_BUF_INIT, content = GIT_BUF_INIT;
+	size_t i;
+
+	for (i = 0, filename = files[i]; filename; filename = files[++i]) {
+		git_buf_clear(&path);
+		git_buf_clear(&content);
+
+		git_buf_printf(&path, "%s/%s", TEST_REPO_PATH, filename);
+		git_buf_printf(&content, "This is a dirty file in the working directory!\n\n"
+			"It will not be staged!  Its filename is %s.\n", filename);
+
+		cl_git_mkfile(path.ptr, content.ptr);
+	}
+
+	git_buf_free(&path);
+	git_buf_free(&content);
+}
+
+static void hack_index(char *files[])
+{
+	char *filename;
+	struct stat statbuf;
+	git_buf path = GIT_BUF_INIT;
+	git_index_entry *entry;
+	size_t i;
+
+	/* Update the index to suggest that checkout placed these files on
+	 * disk, keeping the object id but updating the cache, which will
+	 * emulate a Git implementation's different filter.
+	 */
+	for (i = 0, filename = files[i]; filename; filename = files[++i]) {
+		git_buf_clear(&path);
+
+		cl_assert(entry = (git_index_entry *)
+			git_index_get_bypath(repo_index, filename, 0));
+
+		cl_git_pass(git_buf_printf(&path, "%s/%s", TEST_REPO_PATH, filename));
+		cl_git_pass(p_stat(path.ptr, &statbuf));
+
+		entry->ctime.seconds = (git_time_t)statbuf.st_ctime;
+		entry->ctime.nanoseconds = 0;
+		entry->mtime.seconds = (git_time_t)statbuf.st_mtime;
+		entry->mtime.nanoseconds = 0;
+		entry->dev = statbuf.st_dev;
+		entry->ino = statbuf.st_ino;
+		entry->uid  = statbuf.st_uid;
+		entry->gid  = statbuf.st_gid;
+		entry->file_size = statbuf.st_size;
+	}
+
+	git_buf_free(&path);
+}
+
+static void stage_random_files(char *files[])
+{
+	char *filename;
+	size_t i;
+
+	write_files(files);
+
+	for (i = 0, filename = files[i]; filename; filename = files[++i])
+		cl_git_pass(git_index_add_bypath(repo_index, filename));
+}
+
+static void stage_content(char *content[])
+{
+	git_reference *head;
+	git_object *head_object;
+	git_merge_result *result = NULL;
+	git_buf path = GIT_BUF_INIT;
+	char *filename, *text;
+	size_t i;
+
+	cl_git_pass(git_repository_head(&head, repo));
+	cl_git_pass(git_reference_peel(&head_object, head, GIT_OBJ_COMMIT));
+	cl_git_pass(git_reset(repo, head_object, GIT_RESET_HARD));
+
+	for (i = 0, filename = content[i], text = content[++i];
+		filename && text;
+		filename = content[++i], text = content[++i]) {
+
+		git_buf_clear(&path);
+
+		cl_git_pass(git_buf_printf(&path, "%s/%s", TEST_REPO_PATH, filename));
+
+		cl_git_mkfile(path.ptr, text);
+		cl_git_pass(git_index_add_bypath(repo_index, filename));
+	}
+
+	git_merge_result_free(result);
+	git_object_free(head_object);
+	git_reference_free(head);
+	git_buf_free(&path);
+}
+
+static int merge_dirty_files(char *dirty_files[])
+{
+	git_reference *head;
+	git_object *head_object;
+	git_merge_result *result = NULL;
+	int error;
+
+	cl_git_pass(git_repository_head(&head, repo));
+	cl_git_pass(git_reference_peel(&head_object, head, GIT_OBJ_COMMIT));
+	cl_git_pass(git_reset(repo, head_object, GIT_RESET_HARD));
+
+	write_files(dirty_files);
+
+	error = merge_branch(&result, 0, 0);
+
+	git_merge_result_free(result);
+	git_object_free(head_object);
+	git_reference_free(head);
+
+	return error;
+}
+
+static int merge_differently_filtered_files(char *files[])
+{
+	git_reference *head;
+	git_object *head_object;
+	git_merge_result *result = NULL;
+	int error;
+
+	cl_git_pass(git_repository_head(&head, repo));
+	cl_git_pass(git_reference_peel(&head_object, head, GIT_OBJ_COMMIT));
+	cl_git_pass(git_reset(repo, head_object, GIT_RESET_HARD));
+
+	write_files(files);
+	hack_index(files);
+
+	cl_git_pass(git_index_write(repo_index));
+
+	error = merge_branch(&result, 0, 0);
+
+	git_merge_result_free(result);
+	git_object_free(head_object);
+	git_reference_free(head);
+
+	return error;
+}
+
+static int merge_staged_files(char *staged_files[])
+{
+	git_merge_result *result = NULL;
+	int error;
+	
+	stage_random_files(staged_files);
+
+	error = merge_branch(&result, 0, 0);
+
+	git_merge_result_free(result);
+
+	return error;
+}
+
+void test_merge_workdir_dirty__unaffected_dirty_files_allowed(void)
+{
+	char **files;
+	size_t i;
+
+	for (i = 0, files = unaffected[i]; files[0]; files = unaffected[++i])
+		cl_git_pass(merge_dirty_files(files));
+}
+
+void test_merge_workdir_dirty__affected_dirty_files_disallowed(void)
+{
+	char **files;
+	size_t i;
+
+	for (i = 0, files = affected[i]; files[0]; files = affected[++i])
+		cl_git_fail(merge_dirty_files(files));
+}
+
+void test_merge_workdir_dirty__staged_files_in_index_disallowed(void)
+{
+	char **files;
+	size_t i;
+
+	for (i = 0, files = unaffected[i]; files[0]; files = unaffected[++i])
+		cl_git_fail(merge_staged_files(files));
+
+	for (i = 0, files = affected[i]; files[0]; files = affected[++i])
+		cl_git_fail(merge_staged_files(files));
+}
+
+void test_merge_workdir_dirty__identical_staged_files_allowed(void)
+{
+	git_merge_result *result;
+	char **content;
+	size_t i;
+
+	set_core_autocrlf_to(repo, false);
+	
+	for (i = 0, content = result_contents[i]; content[0]; content = result_contents[++i]) {
+		stage_content(content);
+
+		git_index_write(repo_index);
+		cl_git_pass(merge_branch(&result, 0, 0));
+
+		git_merge_result_free(result);
+	}
+}
+
+void test_merge_workdir_dirty__honors_cache(void)
+{
+	char **files;
+	size_t i;
+
+	for (i = 0, files = affected[i]; files[0]; files = affected[++i])
+		cl_git_pass(merge_differently_filtered_files(files));
+}