thodg/libgit2

diff --git a/include/git2/checkout.h b/include/git2/checkout.h
index 844f0a9..3793a4f 100644
--- a/include/git2/checkout.h
+++ b/include/git2/checkout.h
@@ -131,6 +131,13 @@ typedef enum {
 	/** Don't refresh index/config/etc before doing checkout */
 	GIT_CHECKOUT_NO_REFRESH = (1u << 9),
 
+	/** Allow checkout to skip unmerged files */
+	GIT_CHECKOUT_SKIP_UNMERGED = (1u << 10),
+	/** For unmerged files, checkout stage 2 from index */
+	GIT_CHECKOUT_USE_OURS = (1u << 11),
+	/** For unmerged files, checkout stage 3 from index */
+	GIT_CHECKOUT_USE_THEIRS = (1u << 12),
+
 	/** Treat pathspec as simple list of exact match file paths */
 	GIT_CHECKOUT_DISABLE_PATHSPEC_MATCH = (1u << 13),
 
@@ -141,13 +148,6 @@ typedef enum {
 	 * THE FOLLOWING OPTIONS ARE NOT YET IMPLEMENTED
 	 */
 
-	/** Allow checkout to skip unmerged files (NOT IMPLEMENTED) */
-	GIT_CHECKOUT_SKIP_UNMERGED = (1u << 10),
-	/** For unmerged files, checkout stage 2 from index (NOT IMPLEMENTED) */
-	GIT_CHECKOUT_USE_OURS = (1u << 11),
-	/** For unmerged files, checkout stage 3 from index (NOT IMPLEMENTED) */
-	GIT_CHECKOUT_USE_THEIRS = (1u << 12),
-
 	/** Recursively checkout submodules with same options (NOT IMPLEMENTED) */
 	GIT_CHECKOUT_UPDATE_SUBMODULES = (1u << 16),
 	/** Recursively checkout submodules if HEAD moved in super repo (NOT IMPLEMENTED) */
@@ -238,6 +238,9 @@ typedef struct git_checkout_opts {
 	git_tree *baseline; /** expected content of workdir, defaults to HEAD */
 
 	const char *target_directory; /** alternative checkout path to workdir */
+
+	const char *our_label; /** the name of the "our" side of conflicts */
+	const char *their_label; /** the name of the "their" side of conflicts */
 } git_checkout_opts;
 
 #define GIT_CHECKOUT_OPTS_VERSION 1
diff --git a/src/checkout.c b/src/checkout.c
index d3f673d..fa0609f 100644
--- a/src/checkout.c
+++ b/src/checkout.c
@@ -41,24 +41,6 @@ enum {
 		(CHECKOUT_ACTION__UPDATE_BLOB | CHECKOUT_ACTION__REMOVE),
 };
 
-typedef struct {
-	git_repository *repo;
-	git_diff_list *diff;
-	git_checkout_opts opts;
-	bool opts_free_baseline;
-	char *pfx;
-	git_index *index;
-	git_pool pool;
-	git_vector removes;
-	git_buf path;
-	size_t workdir_len;
-	unsigned int strategy;
-	int can_symlink;
-	bool reload_submodules;
-	size_t total_steps;
-	size_t completed_steps;
-} checkout_data;
-
 static int checkout_notify(
 	checkout_data *data,
 	git_checkout_notify_t why,
@@ -707,6 +689,7 @@ static int blob_content_to_file(
 	struct stat *st,
 	git_blob *blob,
 	const char *path,
+	const char * hint_path,
 	mode_t entry_filemode,
 	git_checkout_opts *opts)
 {
@@ -715,9 +698,12 @@ static int blob_content_to_file(
 	git_buf out = GIT_BUF_INIT;
 	git_filter_list *fl = NULL;
 
+	if (hint_path == NULL)
+		hint_path = path;
+
 	if (!opts->disable_filters)
 		error = git_filter_list_load(
-			&fl, git_blob_owner(blob), blob, path, GIT_FILTER_TO_WORKTREE);
+			&fl, git_blob_owner(blob), blob, hint_path, GIT_FILTER_TO_WORKTREE);
 
 	if (!error)
 		error = git_filter_list_apply_to_blob(&out, fl, blob);
@@ -886,34 +872,26 @@ static int checkout_safe_for_update_only(const char *path, mode_t expected_mode)
 	return 0;
 }
 
-static int checkout_blob(
+int git_checkout__write_content(
 	checkout_data *data,
-	const git_diff_file *file)
+	const git_oid *oid,
+	const char *full_path,
+	const char *hint_path,
+	unsigned int mode,
+	struct stat *st)
 {
 	int error = 0;
 	git_blob *blob;
-	struct stat st;
-
-	git_buf_truncate(&data->path, data->workdir_len);
-	if (git_buf_puts(&data->path, file->path) < 0)
-		return -1;
-
-	if ((data->strategy & GIT_CHECKOUT_UPDATE_ONLY) != 0) {
-		int rval = checkout_safe_for_update_only(
-			git_buf_cstr(&data->path), file->mode);
-		if (rval <= 0)
-			return rval;
-	}
 
-	if ((error = git_blob_lookup(&blob, data->repo, &file->oid)) < 0)
+	if ((error = git_blob_lookup(&blob, data->repo, oid)) < 0)
 		return error;
 
-	if (S_ISLNK(file->mode))
+	if (S_ISLNK(mode))
 		error = blob_content_to_link(
-			&st, blob, git_buf_cstr(&data->path), data->opts.dir_mode, data->can_symlink);
+			st, blob, full_path, data->opts.dir_mode, data->can_symlink);
 	else
 		error = blob_content_to_file(
-			&st, blob, git_buf_cstr(&data->path), file->mode, &data->opts);
+			st, blob, full_path, hint_path, mode, &data->opts);
 
 	git_blob_free(blob);
 
@@ -928,6 +906,30 @@ static int checkout_blob(
 		error = 0;
 	}
 
+	return error;
+}
+
+static int checkout_blob(
+	checkout_data *data,
+	const git_diff_file *file)
+{
+	int error = 0;
+	struct stat st;
+
+	git_buf_truncate(&data->path, data->workdir_len);
+	if (git_buf_puts(&data->path, file->path) < 0)
+		return -1;
+
+	if ((data->strategy & GIT_CHECKOUT_UPDATE_ONLY) != 0) {
+		int rval = checkout_safe_for_update_only(
+			git_buf_cstr(&data->path), file->mode);
+		if (rval <= 0)
+			return rval;
+	}
+
+	error = git_checkout__write_content(
+		data, &file->oid, git_buf_cstr(&data->path), NULL, file->mode, &st);
+
 	/* update the index unless prevented */
 	if (!error && (data->strategy & GIT_CHECKOUT_DONT_UPDATE_INDEX) == 0)
 		error = checkout_update_index(data, file, &st);
@@ -1172,7 +1174,17 @@ static int checkout_data_init(
 				(error = git_index_read(data->index)) < 0)
 				goto cleanup;
 
-			/* clear the REUC when doing a tree or commit checkout */
+			/* cannot checkout if unresolved conflicts exist */
+			if ((data->opts.checkout_strategy & GIT_CHECKOUT_FORCE) == 0 &&
+				git_index_has_conflicts(data->index)) {
+				error = GIT_EMERGECONFLICT;
+				giterr_set(GITERR_CHECKOUT,
+					"unresolved conflicts exist in the index");
+				goto cleanup;
+			}
+
+			/* clean conflict data when doing a tree or commit checkout */
+			git_index_name_clear(data->index);
 			git_index_reuc_clear(data->index);
 		}
 	}
@@ -1312,6 +1324,9 @@ int git_checkout_iterator(
 
 	assert(data.completed_steps == data.total_steps);
 
+	/* Write conflict data to disk */
+	error = git_checkout__conflicts(&data);
+
 cleanup:
 	if (error == GIT_EUSER)
 		giterr_clear();
diff --git a/src/checkout.h b/src/checkout.h
index 6d71868..27e682f 100644
--- a/src/checkout.h
+++ b/src/checkout.h
@@ -9,9 +9,28 @@
 
 #include "git2/checkout.h"
 #include "iterator.h"
+#include "pool.h"
 
 #define GIT_CHECKOUT__NOTIFY_CONFLICT_TREE (1u << 12)
 
+typedef struct {
+	git_repository *repo;
+	git_diff_list *diff;
+	git_checkout_opts opts;
+	bool opts_free_baseline;
+	char *pfx;
+	git_index *index;
+	git_pool pool;
+	git_vector removes;
+	git_buf path;
+	size_t workdir_len;
+	unsigned int strategy;
+	int can_symlink;
+	bool reload_submodules;
+	size_t total_steps;
+	size_t completed_steps;
+} checkout_data;
+
 /**
  * Update the working directory to match the target iterator.  The
  * expected baseline value can be passed in via the checkout options
@@ -21,4 +40,14 @@ extern int git_checkout_iterator(
 	git_iterator *target,
 	const git_checkout_opts *opts);
 
+int git_checkout__write_content(
+	checkout_data *data,
+	const git_oid *oid,
+	const char *path,
+	const char *hint_path,
+	unsigned int mode,
+	struct stat *st);
+
+int git_checkout__conflicts(checkout_data *data);
+
 #endif
diff --git a/src/checkout_conflicts.c b/src/checkout_conflicts.c
new file mode 100644
index 0000000..0c9c768
--- /dev/null
+++ b/src/checkout_conflicts.c
@@ -0,0 +1,593 @@
+/*
+ * Copyright (C) the libgit2 contributors. All rights reserved.
+ *
+ * This file is part of libgit2, distributed under the GNU GPL v2 with
+ * a Linking Exception. For full terms see the included COPYING file.
+ */
+
+#include <assert.h>
+
+#include "checkout.h"
+
+#include "vector.h"
+#include "index.h"
+#include "merge_file.h"
+#include "git2/repository.h"
+#include "git2/types.h"
+#include "git2/index.h"
+#include "git2/sys/index.h"
+
+typedef struct {
+	const git_index_entry *ancestor;
+	const git_index_entry *ours;
+	const git_index_entry *theirs;
+
+	int name_collision:1,
+		directoryfile:1;
+} checkout_conflictdata;
+
+GIT_INLINE(int) checkout_idxentry_cmp(
+	const git_index_entry *a,
+	const git_index_entry *b)
+{
+	if (!a && !b)
+		return 0;
+	else if (!a && b)
+		return -1;
+	else if(a && !b)
+		return 1;
+	else
+		return strcmp(a->path, b->path);
+}
+
+static int checkout_conflictdata_cmp(const void *a, const void *b)
+{
+	const checkout_conflictdata *ca = a;
+	const checkout_conflictdata *cb = b;
+	int diff;
+
+	if ((diff = checkout_idxentry_cmp(ca->ancestor, cb->ancestor)) == 0 &&
+		(diff = checkout_idxentry_cmp(ca->ours, cb->theirs)) == 0)
+		diff = checkout_idxentry_cmp(ca->theirs, cb->theirs);
+
+	return diff;
+}
+
+int checkout_conflictdata_empty(const git_vector *conflicts, size_t idx)
+{
+	const checkout_conflictdata *conflict;
+
+	if ((conflict = git_vector_get(conflicts, idx)) == NULL)
+		return -1;
+
+	return (conflict->ancestor == NULL &&
+		conflict->ours == NULL &&
+		conflict->theirs == NULL);
+}
+
+static int checkout_conflicts_load(checkout_data *data, git_vector *conflicts)
+{
+	git_index_conflict_iterator *iterator = NULL;
+	const git_index_entry *ancestor, *ours, *theirs;
+	checkout_conflictdata *conflict;
+	int error = 0;
+
+	if ((error = git_index_conflict_iterator_new(&iterator, data->index)) < 0)
+		goto done;
+
+	conflicts->_cmp = checkout_conflictdata_cmp;
+
+	/* Collect the conflicts */
+	while ((error = git_index_conflict_next(
+		&ancestor, &ours, &theirs, iterator)) == 0) {
+
+		conflict = git__calloc(1, sizeof(checkout_conflictdata));
+		GITERR_CHECK_ALLOC(conflict);
+
+		conflict->ancestor = ancestor;
+		conflict->ours = ours;
+		conflict->theirs = theirs;
+
+		git_vector_insert(conflicts, conflict);
+	}
+
+	if (error == GIT_ITEROVER)
+		error = 0;
+
+done:
+	git_index_conflict_iterator_free(iterator);
+
+	return error;
+}
+
+GIT_INLINE(int) checkout_conflicts_cmp_entry(
+	const char *path,
+	const git_index_entry *entry)
+{
+	/* TODO: is strcmp right here?  should we use index->strcomp ? */
+	return strcmp((const char *)path, entry->path);
+}
+
+static int checkout_conflicts_cmp_ancestor(const void *p, const void *c)
+{
+	const char *path = p;
+	const checkout_conflictdata *conflict = c;
+
+	if (!conflict->ancestor)
+		return 1;
+
+	return checkout_conflicts_cmp_entry(path, conflict->ancestor);
+}
+
+static checkout_conflictdata *checkout_conflicts_search_ancestor(
+	git_vector *conflicts,
+	const char *path)
+{
+	size_t pos;
+
+	if (git_vector_bsearch2(&pos, conflicts, checkout_conflicts_cmp_ancestor, path) < 0)
+		return NULL;
+
+	return git_vector_get(conflicts, pos);
+}
+
+static checkout_conflictdata *checkout_conflicts_search_branch(
+	git_vector *conflicts,
+	const char *path)
+{
+	checkout_conflictdata *conflict;
+	size_t i;
+
+	git_vector_foreach(conflicts, i, conflict) {
+		int cmp = -1;
+
+		if (conflict->ancestor)
+			break;
+
+		if (conflict->ours)
+			cmp = checkout_conflicts_cmp_entry(path, conflict->ours);
+		else if (conflict->theirs)
+			cmp = checkout_conflicts_cmp_entry(path, conflict->theirs);
+
+		if (cmp == 0)
+			return conflict;
+	}
+
+	return NULL;
+}
+
+static int checkout_conflicts_load_byname_entry(
+	checkout_conflictdata **ancestor_out,
+	checkout_conflictdata **ours_out,
+	checkout_conflictdata **theirs_out,
+	git_vector *conflicts,
+	const git_index_name_entry *name_entry)
+{
+	checkout_conflictdata *ancestor, *ours = NULL, *theirs = NULL;
+	int error = 0;
+
+	*ancestor_out = NULL;
+	*ours_out = NULL;
+	*theirs_out = NULL;
+
+	if (!name_entry->ancestor) {
+		giterr_set(GITERR_INDEX, "A NAME entry exists without an ancestor");
+		error = -1;
+		goto done;
+	}
+
+	if (!name_entry->ours && !name_entry->theirs) {
+		giterr_set(GITERR_INDEX, "A NAME entry exists without an ours or theirs");
+		error = -1;
+		goto done;
+	}
+
+	if ((ancestor = checkout_conflicts_search_ancestor(conflicts,
+		name_entry->ancestor)) == NULL) {
+		giterr_set(GITERR_INDEX,
+			"A NAME entry referenced ancestor entry '%s' which does not exist in the main index",
+			name_entry->ancestor);
+		error = -1;
+		goto done;
+	}
+
+	if (name_entry->ours) {
+		if (strcmp(name_entry->ancestor, name_entry->ours) == 0)
+			ours = ancestor;
+		else if ((ours = checkout_conflicts_search_branch(conflicts, name_entry->ours)) == NULL ||
+			ours->ours == NULL) {
+			giterr_set(GITERR_INDEX,
+				"A NAME entry referenced our entry '%s' which does not exist in the main index",
+				name_entry->ours);
+			error = -1;
+			goto done;
+		}
+	}
+
+	if (name_entry->theirs) {
+		if (strcmp(name_entry->ancestor, name_entry->theirs) == 0)
+			theirs = ancestor;
+		else if ((theirs = checkout_conflicts_search_branch(conflicts, name_entry->theirs)) == NULL ||
+			theirs->theirs == NULL) {
+			giterr_set(GITERR_INDEX,
+				"A NAME entry referenced their entry '%s' which does not exist in the main index",
+				name_entry->theirs);
+			error = -1;
+			goto done;
+		}
+	}
+
+	*ancestor_out = ancestor;
+	*ours_out = ours;
+	*theirs_out = theirs;
+
+done:
+	return error;
+}
+
+static int checkout_conflicts_coalesce_renames(
+	checkout_data *data,
+	git_vector *conflicts)
+{
+	const git_index_name_entry *name_entry;
+	checkout_conflictdata *ancestor_conflict, *our_conflict, *their_conflict;
+	size_t i, names;
+	int error = 0;
+
+	/* Juggle entries based on renames */
+	for (i = 0, names = git_index_name_entrycount(data->index);
+		i < names;
+		i++) {
+
+		name_entry = git_index_name_get_byindex(data->index, i);
+
+		if ((error = checkout_conflicts_load_byname_entry(
+			&ancestor_conflict, &our_conflict, &their_conflict,
+			conflicts, name_entry)) < 0)
+			goto done;
+
+		if (our_conflict && our_conflict != ancestor_conflict) {
+			ancestor_conflict->ours = our_conflict->ours;
+			our_conflict->ours = NULL;
+
+			if (our_conflict->theirs)
+				our_conflict->name_collision = 1;
+
+			if (our_conflict->name_collision)
+				ancestor_conflict->name_collision = 1;
+		}
+
+		if (their_conflict && their_conflict != ancestor_conflict) {
+			ancestor_conflict->theirs = their_conflict->theirs;
+			their_conflict->theirs = NULL;
+
+			if (their_conflict->ours)
+				their_conflict->name_collision = 1;
+
+			if (their_conflict->name_collision)
+				ancestor_conflict->name_collision = 1;
+		}
+	}
+
+	git_vector_remove_matching(conflicts, checkout_conflictdata_empty);
+
+done:
+	return error;
+}
+
+/* TODO: does this exist elsewhere? */
+GIT_INLINE(void) path_equal_or_prefixed(
+	bool *path_eq,
+	bool *path_prefixed,
+	const char *parent,
+	const char *child)
+{
+	size_t child_len = strlen(child);
+	size_t parent_len = strlen(parent);
+
+	if (child_len == parent_len) {
+		*path_eq = (strcmp(parent, child) == 0);
+		*path_prefixed = 0;
+		return;
+	}
+	
+	*path_eq = 0;
+
+	if (child_len < parent_len ||
+		strncmp(parent, child, parent_len) != 0)
+		*path_prefixed = 0;
+	else
+		*path_prefixed = (child[parent_len] == '/');
+}
+
+static int checkout_conflicts_mark_directoryfile(
+	checkout_data *data,
+	git_vector *conflicts)
+{
+	checkout_conflictdata *conflict;
+	const git_index_entry *entry;
+	size_t i, j, len;
+	const char *path;
+	bool eq, prefixed;
+	int error = 0;
+
+	len = git_index_entrycount(data->index);
+
+	/* Find d/f conflicts */
+	git_vector_foreach(conflicts, i, conflict) {
+		if ((conflict->ours && conflict->theirs) ||
+			(!conflict->ours && !conflict->theirs))
+			continue;
+
+		path = conflict->ours ?
+			conflict->ours->path : conflict->theirs->path;
+
+		if ((error = git_index_find(&j, data->index, path)) < 0) {
+			if (error == GIT_ENOTFOUND)
+				giterr_set(GITERR_MERGE,
+					"Index inconsistency, could not find entry for expected conflict '%s'", path);
+
+			goto done;
+		}
+
+		for (; j < len; j++) {
+			if ((entry = git_index_get_byindex(data->index, j)) == NULL) {
+				giterr_set(GITERR_MERGE,
+					"Index inconsistency, truncated index while loading expected conflict '%s'", path);
+				error = -1;
+				goto done;
+			}
+
+			path_equal_or_prefixed(&eq, &prefixed, path, entry->path);
+
+			if (eq)
+				continue;
+
+			if (prefixed)
+				conflict->directoryfile = 1;
+
+			break;
+		}
+	}
+
+done:
+	return error;
+}
+
+static int conflict_entry_name(
+	git_buf *out,
+	const char *side_name,
+	const char *filename)
+{
+	if (git_buf_puts(out, side_name) < 0 ||
+		git_buf_putc(out, ':') < 0 ||
+		git_buf_puts(out, filename) < 0)
+		return -1;
+
+	return 0;
+}
+
+static int conflict_path_suffixed(
+	git_buf *out,
+	const char *path,
+	const char *side_name)
+{
+	if (git_buf_puts(out, path) < 0 ||
+		git_buf_putc(out, '~') < 0 ||
+		git_buf_puts(out, side_name) < 0)
+		return -1;
+
+	return 0;
+}
+
+static int checkout_write_entry(
+	checkout_data *data,
+	checkout_conflictdata *conflict,
+	const git_index_entry *side)
+{
+	const char *hint_path = NULL, *side_label;
+	struct stat st;
+
+	assert (side == conflict->ours ||
+		side == conflict->theirs);
+
+	git_buf_truncate(&data->path, data->workdir_len);
+	if (git_buf_puts(&data->path, side->path) < 0)
+		return -1;
+
+	if (conflict->name_collision || conflict->directoryfile) {
+		if (side == conflict->ours)
+			side_label = data->opts.our_label ? data->opts.our_label :
+				"ours";
+		else if (side == conflict->theirs)
+			side_label = data->opts.their_label ? data->opts.their_label :
+				"theirs";
+
+		if (git_buf_putc(&data->path, '~') < 0 ||
+			git_buf_puts(&data->path, side_label) < 0)
+			return -1;
+
+		hint_path = side->path;
+	}
+
+	return git_checkout__write_content(data,
+		&side->oid, git_buf_cstr(&data->path), hint_path, side->mode, &st);
+}
+
+static int checkout_write_entries(
+	checkout_data *data,
+	checkout_conflictdata *conflict)
+{
+	int error = 0;
+
+	if ((error = checkout_write_entry(data, conflict, conflict->ours)) >= 0)
+		error = checkout_write_entry(data, conflict, conflict->theirs);
+
+	return error;
+}
+
+static int checkout_write_merge(
+	checkout_data *data,
+	checkout_conflictdata *conflict)
+{
+	git_buf our_label = GIT_BUF_INIT, their_label = GIT_BUF_INIT,
+		path_suffixed = GIT_BUF_INIT, path_workdir = GIT_BUF_INIT;
+	git_merge_file_input ancestor = GIT_MERGE_FILE_INPUT_INIT,
+		ours = GIT_MERGE_FILE_INPUT_INIT,
+		theirs = GIT_MERGE_FILE_INPUT_INIT;
+	git_merge_file_result result = GIT_MERGE_FILE_RESULT_INIT;
+	git_filebuf output = GIT_FILEBUF_INIT;
+	const char *our_label_raw, *their_label_raw, *path;
+	int error = 0;
+
+	if ((conflict->ancestor &&
+		(error = git_merge_file_input_from_index_entry(
+		&ancestor, data->repo, conflict->ancestor)) < 0) ||
+		(error = git_merge_file_input_from_index_entry(
+		&ours, data->repo, conflict->ours)) < 0 ||
+		(error = git_merge_file_input_from_index_entry(
+		&theirs, data->repo, conflict->theirs)) < 0)
+		goto done;
+
+	ancestor.label = NULL;
+	ours.label = our_label_raw = data->opts.our_label ? data->opts.our_label : "ours";
+	theirs.label = their_label_raw = data->opts.their_label ? data->opts.their_label : "theirs";
+
+	/* If all the paths are identical, decorate the diff3 file with the branch
+	 * names.  Otherwise, append branch_name:path.
+	 */
+	if (conflict->ours && conflict->theirs &&
+		strcmp(conflict->ours->path, conflict->theirs->path) != 0) {
+
+		if ((error = conflict_entry_name(
+			&our_label, ours.label, conflict->ours->path)) < 0 ||
+			(error = conflict_entry_name(
+			&their_label, theirs.label, conflict->theirs->path)) < 0)
+			goto done;
+
+		ours.label = git_buf_cstr(&our_label);
+		theirs.label = git_buf_cstr(&their_label);
+	}
+
+	if ((error = git_merge_files(&result, &ancestor, &ours, &theirs, 0)) < 0)
+		goto done;
+
+	if (result.path == NULL || result.mode == 0) {
+		giterr_set(GITERR_CHECKOUT, "Could not merge contents of file");
+		error = GIT_EMERGECONFLICT;
+		goto done;
+	}
+
+	/* Rename 2->1 conflicts need the branch name appended */
+	if (conflict->name_collision) {
+		/* TODO: strcmp? */
+		if ((error = conflict_path_suffixed(&path_suffixed, result.path,
+			(strcmp(result.path, conflict->ours->path) == 0 ?
+			our_label_raw : their_label_raw))) < 0)
+			goto done;
+		
+		path = git_buf_cstr(&path_suffixed);
+	} else
+		path = result.path;
+
+	if ((error = git_buf_joinpath(&path_workdir, git_repository_workdir(data->repo), path)) < 0 ||
+		(error = git_futils_mkpath2file(path_workdir.ptr, 0755) < 0) ||
+		(error = git_filebuf_open(&output, path_workdir.ptr, GIT_FILEBUF_DO_NOT_BUFFER)) < 0 ||
+		(error = git_filebuf_write(&output, result.data, result.len)) < 0 ||
+		(error = git_filebuf_commit(&output, result.mode)) < 0)
+		goto done;
+
+done:
+	git_buf_free(&our_label);
+	git_buf_free(&their_label);
+
+	git_merge_file_input_free(&ancestor);
+	git_merge_file_input_free(&ours);
+	git_merge_file_input_free(&theirs);
+	git_merge_file_result_free(&result);
+	git_buf_free(&path_workdir);
+	git_buf_free(&path_suffixed);
+
+	return error;
+}
+
+GIT_INLINE(bool) conflict_is_1_to_2(checkout_conflictdata *conflict)
+{
+	/* TODO: can't we detect these when we coalesce? */
+	return conflict->ancestor && conflict->ours && conflict->theirs &&
+		(strcmp(conflict->ancestor->path, conflict->ours->path) != 0 &&
+		strcmp(conflict->ancestor->path, conflict->theirs->path) != 0 &&
+		strcmp(conflict->ours->path, conflict->theirs->path) != 0);
+}
+
+int git_checkout__conflicts(checkout_data *data)
+{
+	git_vector conflicts = GIT_VECTOR_INIT;
+	checkout_conflictdata *conflict;
+	size_t i;
+	int error = 0;
+
+	if (data->strategy & GIT_CHECKOUT_SKIP_UNMERGED)
+		return 0;
+
+	if ((error = checkout_conflicts_load(data, &conflicts)) < 0 ||
+		(error = checkout_conflicts_coalesce_renames(data, &conflicts)) < 0 ||
+		(error = checkout_conflicts_mark_directoryfile(data, &conflicts)) < 0)
+		goto done;
+
+	git_vector_foreach(&conflicts, i, conflict) {
+		/* Both deleted: nothing to do */
+		if (conflict->ours == NULL && conflict->theirs == NULL)
+			error = 0;
+
+		else if ((data->strategy & GIT_CHECKOUT_USE_OURS) &&
+			conflict->ours)
+			error = checkout_write_entry(data, conflict, conflict->ours);
+		else if ((data->strategy & GIT_CHECKOUT_USE_THEIRS) &&
+			conflict->theirs)
+			error = checkout_write_entry(data, conflict, conflict->theirs);
+
+		/* Ignore the other side of name collisions. */
+		else if ((data->strategy & GIT_CHECKOUT_USE_OURS) &&
+			!conflict->ours && conflict->name_collision)
+			error = 0;
+		else if ((data->strategy & GIT_CHECKOUT_USE_THEIRS) &&
+			!conflict->theirs && conflict->name_collision)
+			error = 0;
+
+		/* For modify/delete, name collisions and d/f conflicts, write
+		 * the file (potentially with the name mangled.
+		 */
+		else if (conflict->ours != NULL && conflict->theirs == NULL)
+			error = checkout_write_entry(data, conflict, conflict->ours);
+		else if (conflict->ours == NULL && conflict->theirs != NULL)
+			error = checkout_write_entry(data, conflict, conflict->theirs);
+
+		/* Add/add conflicts and rename 1->2 conflicts, write the
+		 * ours/theirs sides (potentially name mangled).
+		 */
+		else if (conflict_is_1_to_2(conflict))
+			error = checkout_write_entries(data, conflict);
+
+		/* If all sides are links, write the ours side */
+		else if (S_ISLNK(conflict->ours->mode) &&
+			S_ISLNK(conflict->theirs->mode))
+			error = checkout_write_entry(data, conflict, conflict->ours);
+		/* Link/file conflicts, write the file side */
+		else if (S_ISLNK(conflict->ours->mode))
+			error = checkout_write_entry(data, conflict, conflict->theirs);
+		else if (S_ISLNK(conflict->theirs->mode))
+			error = checkout_write_entry(data, conflict, conflict->ours);
+
+		else
+			error = checkout_write_merge(data, conflict);
+	}
+
+done:
+	git_vector_foreach(&conflicts, i, conflict)
+		git__free(conflict);
+
+	git_vector_free(&conflicts);
+
+	return error;
+}
diff --git a/src/merge_file.c b/src/merge_file.c
index c3477cc..48fc46e 100644
--- a/src/merge_file.c
+++ b/src/merge_file.c
@@ -47,7 +47,7 @@ GIT_INLINE(int) merge_file_best_mode(
 	 * assume executable.  Otherwise, if any mode changed from the ancestor,
 	 * use that one.
 	 */
-	if (GIT_MERGE_FILE_SIDE_EXISTS(ancestor)) {
+	if (!GIT_MERGE_FILE_SIDE_EXISTS(ancestor)) {
 		if (ours->mode == GIT_FILEMODE_BLOB_EXECUTABLE ||
 			theirs->mode == GIT_FILEMODE_BLOB_EXECUTABLE)
 			return GIT_FILEMODE_BLOB_EXECUTABLE;
diff --git a/src/reset.c b/src/reset.c
index cea212a..87dc45a 100644
--- a/src/reset.c
+++ b/src/reset.c
@@ -135,7 +135,7 @@ int git_reset(
 
 	if (reset_type == GIT_RESET_HARD) {
 		/* overwrite working directory with HEAD */
-		opts.checkout_strategy = GIT_CHECKOUT_FORCE;
+		opts.checkout_strategy = GIT_CHECKOUT_FORCE | GIT_CHECKOUT_SKIP_UNMERGED;
 
 		if ((error = git_checkout_tree(repo, (git_object *)tree, &opts)) < 0)
 			goto cleanup;