rugged 0.19.0 → 0.28.0

data/vendor/libgit2/src/checkout.c

@@ -5,10 +5,10 @@
  * a Linking Exception. For full terms see the included COPYING file.
  */
 
-#include <assert.h>
-
 #include "checkout.h"
 
+#include <assert.h>
+
 #include "git2/repository.h"
 #include "git2/refs.h"
 #include "git2/tree.h"
@@ -17,6 +17,8 @@
 #include "git2/diff.h"
 #include "git2/submodule.h"
 #include "git2/sys/index.h"
+#include "git2/sys/filter.h"
+#include "git2/merge.h"
 
 #include "refs.h"
 #include "repository.h"
@@ -24,8 +26,14 @@
 #include "filter.h"
 #include "blob.h"
 #include "diff.h"
+#include "diff_generate.h"
 #include "pathspec.h"
 #include "buf_text.h"
+#include "diff_xdiff.h"
+#include "path.h"
+#include "attr.h"
+#include "pool.h"
+#include "strmap.h"
 
 /* See docs/checkout-internals.md for more information */
 
@@ -35,30 +43,54 @@ enum {
 	CHECKOUT_ACTION__UPDATE_BLOB = 2,
 	CHECKOUT_ACTION__UPDATE_SUBMODULE = 4,
 	CHECKOUT_ACTION__CONFLICT = 8,
-	CHECKOUT_ACTION__MAX = 8,
-	CHECKOUT_ACTION__DEFER_REMOVE = 16,
+	CHECKOUT_ACTION__REMOVE_CONFLICT = 16,
+	CHECKOUT_ACTION__UPDATE_CONFLICT = 32,
+	CHECKOUT_ACTION__MAX = 32,
+	CHECKOUT_ACTION__DEFER_REMOVE = 64,
 	CHECKOUT_ACTION__REMOVE_AND_UPDATE =
 		(CHECKOUT_ACTION__UPDATE_BLOB | CHECKOUT_ACTION__REMOVE),
 };
 
 typedef struct {
 	git_repository *repo;
-	git_diff_list *diff;
-	git_checkout_opts opts;
+	git_iterator *target;
+	git_diff *diff;
+	git_checkout_options opts;
 	bool opts_free_baseline;
 	char *pfx;
 	git_index *index;
 	git_pool pool;
 	git_vector removes;
-	git_buf path;
-	size_t workdir_len;
+	git_vector remove_conflicts;
+	git_vector update_conflicts;
+	git_vector *update_reuc;
+	git_vector *update_names;
+	git_buf target_path;
+	size_t target_len;
+	git_buf tmp;
 	unsigned int strategy;
 	int can_symlink;
+	int respect_filemode;
 	bool reload_submodules;
 	size_t total_steps;
 	size_t completed_steps;
+	git_checkout_perfdata perfdata;
+	git_strmap *mkdir_map;
+	git_attr_session attr_session;
 } checkout_data;
 
+typedef struct {
+	const git_index_entry *ancestor;
+	const git_index_entry *ours;
+	const git_index_entry *theirs;
+
+	int name_collision:1,
+		directoryfile:1,
+		one_to_two:1,
+		binary:1,
+		submodule:1;
+} checkout_conflictdata;
+
 static int checkout_notify(
 	checkout_data *data,
 	git_checkout_notify_t why,
@@ -69,19 +101,17 @@ static int checkout_notify(
 	const git_diff_file *baseline = NULL, *target = NULL, *workdir = NULL;
 	const char *path = NULL;
 
-	if (!data->opts.notify_cb)
-		return 0;
-
-	if ((why & data->opts.notify_flags) == 0)
+	if (!data->opts.notify_cb ||
+		(why & data->opts.notify_flags) == 0)
 		return 0;
 
 	if (wditem) {
 		memset(&wdfile, 0, sizeof(wdfile));
 
-		git_oid_cpy(&wdfile.oid, &wditem->oid);
+		git_oid_cpy(&wdfile.id, &wditem->id);
 		wdfile.path = wditem->path;
 		wdfile.size = wditem->file_size;
-		wdfile.flags = GIT_DIFF_FLAG_VALID_OID;
+		wdfile.flags = GIT_DIFF_FLAG_VALID_ID;
 		wdfile.mode = wditem->mode;
 
 		workdir = &wdfile;
@@ -101,6 +131,7 @@ static int checkout_notify(
 		case GIT_DELTA_ADDED:
 		case GIT_DELTA_IGNORED:
 		case GIT_DELTA_UNTRACKED:
+		case GIT_DELTA_UNREADABLE:
 			target = &delta->new_file;
 			break;
 		case GIT_DELTA_DELETED:
@@ -111,13 +142,44 @@ static int checkout_notify(
 		path = delta->old_file.path;
 	}
 
-	return data->opts.notify_cb(
-		why, path, baseline, target, workdir, data->opts.notify_payload);
+	{
+		int error = data->opts.notify_cb(
+			why, path, baseline, target, workdir, data->opts.notify_payload);
+
+		return git_error_set_after_callback_function(
+			error, "git_checkout notification");
+	}
+}
+
+GIT_INLINE(bool) is_workdir_base_or_new(
+	const git_oid *workdir_id,
+	const git_diff_file *baseitem,
+	const git_diff_file *newitem)
+{
+	return (git_oid__cmp(&baseitem->id, workdir_id) == 0 ||
+		git_oid__cmp(&newitem->id, workdir_id) == 0);
+}
+
+GIT_INLINE(bool) is_filemode_changed(git_filemode_t a, git_filemode_t b, int respect_filemode)
+{
+	/* If core.filemode = false, ignore links in the repository and executable bit changes */
+	if (!respect_filemode) {
+		if (a == S_IFLNK)
+			a = GIT_FILEMODE_BLOB;
+		if (b == S_IFLNK)
+			b = GIT_FILEMODE_BLOB;
+
+		a &= ~0111;
+		b &= ~0111;
+	}
+
+	return (a != b);
 }
 
 static bool checkout_is_workdir_modified(
 	checkout_data *data,
 	const git_diff_file *baseitem,
+	const git_diff_file *newitem,
 	const git_index_entry *wditem)
 {
 	git_oid oid;
@@ -128,30 +190,42 @@ static bool checkout_is_workdir_modified(
 		git_submodule *sm;
 		unsigned int sm_status = 0;
 		const git_oid *sm_oid = NULL;
+		bool rval = false;
 
-		if (git_submodule_lookup(&sm, data->repo, wditem->path) < 0 ||
-			git_submodule_status(&sm_status, sm) < 0)
-			return true;
-
-		if (GIT_SUBMODULE_STATUS_IS_WD_DIRTY(sm_status))
+		if (git_submodule_lookup(&sm, data->repo, wditem->path) < 0) {
+			git_error_clear();
 			return true;
+		}
 
-		sm_oid = git_submodule_wd_id(sm);
-		if (!sm_oid)
-			return false;
+		if (git_submodule_status(&sm_status, data->repo, wditem->path, GIT_SUBMODULE_IGNORE_UNSPECIFIED) < 0 ||
+			GIT_SUBMODULE_STATUS_IS_WD_DIRTY(sm_status))
+			rval = true;
+		else if ((sm_oid = git_submodule_wd_id(sm)) == NULL)
+			rval = false;
+		else
+			rval = (git_oid__cmp(&baseitem->id, sm_oid) != 0);
 
-		return (git_oid__cmp(&baseitem->oid, sm_oid) != 0);
+		git_submodule_free(sm);
+		return rval;
 	}
 
-	/* Look at the cache to decide if the workdir is modified.  If not,
-	 * we can simply compare the oid in the cache to the baseitem instead
-	 * of hashing the file.
+	/*
+	 * Look at the cache to decide if the workdir is modified: if the
+	 * cache contents match the workdir contents, then we do not need
+	 * to examine the working directory directly, instead we can
+	 * examine the cache to see if _it_ has been modified.  This allows
+	 * us to avoid touching the disk.
 	 */
-	if ((ie = git_index_get_bypath(data->index, wditem->path, 0)) != NULL) {
-		if (wditem->mtime.seconds == ie->mtime.seconds &&
-			wditem->mtime.nanoseconds == ie->mtime.nanoseconds &&
-			wditem->file_size == ie->file_size)
-			return (git_oid__cmp(&baseitem->oid, &ie->oid) != 0);
+	ie = git_index_get_bypath(data->index, wditem->path, 0);
+
+	if (ie != NULL &&
+		git_index_time_eq(&wditem->mtime, &ie->mtime) &&
+		wditem->file_size == ie->file_size &&
+		!is_filemode_changed(wditem->mode, ie->mode, data->respect_filemode)) {
+
+		/* The workdir is modified iff the index entry is modified */
+		return !is_workdir_base_or_new(&ie->id, baseitem, newitem) ||
+			is_filemode_changed(baseitem->mode, ie->mode, data->respect_filemode);
 	}
 
 	/* depending on where base is coming from, we may or may not know
@@ -160,145 +234,220 @@ static bool checkout_is_workdir_modified(
 	if (baseitem->size && wditem->file_size != baseitem->size)
 		return true;
 
-	if (git_diff__oid_for_file(
-			data->repo, wditem->path, wditem->mode,
-			wditem->file_size, &oid) < 0)
+	/* if the workdir item is a directory, it cannot be a modified file */
+	if (S_ISDIR(wditem->mode))
+		return false;
+
+	if (is_filemode_changed(baseitem->mode, wditem->mode, data->respect_filemode))
+		return true;
+
+	if (git_diff__oid_for_entry(&oid, data->diff, wditem, wditem->mode, NULL) < 0)
 		return false;
 
-	return (git_oid__cmp(&baseitem->oid, &oid) != 0);
+	/* Allow the checkout if the workdir is not modified *or* if the checkout
+	 * target's contents are already in the working directory.
+	 */
+	return !is_workdir_base_or_new(&oid, baseitem, newitem);
 }
 
 #define CHECKOUT_ACTION_IF(FLAG,YES,NO) \
 	((data->strategy & GIT_CHECKOUT_##FLAG) ? CHECKOUT_ACTION__##YES : CHECKOUT_ACTION__##NO)
 
 static int checkout_action_common(
+	int *action,
 	checkout_data *data,
-	int action,
 	const git_diff_delta *delta,
 	const git_index_entry *wd)
 {
 	git_checkout_notify_t notify = GIT_CHECKOUT_NOTIFY_NONE;
 
-	if (action <= 0)
-		return action;
-
 	if ((data->strategy & GIT_CHECKOUT_UPDATE_ONLY) != 0)
-		action = (action & ~CHECKOUT_ACTION__REMOVE);
+		*action = (*action & ~CHECKOUT_ACTION__REMOVE);
 
-	if ((action & CHECKOUT_ACTION__UPDATE_BLOB) != 0) {
+	if ((*action & CHECKOUT_ACTION__UPDATE_BLOB) != 0) {
 		if (S_ISGITLINK(delta->new_file.mode))
-			action = (action & ~CHECKOUT_ACTION__UPDATE_BLOB) |
+			*action = (*action & ~CHECKOUT_ACTION__UPDATE_BLOB) |
 				CHECKOUT_ACTION__UPDATE_SUBMODULE;
 
 		/* to "update" a symlink, we must remove the old one first */
 		if (delta->new_file.mode == GIT_FILEMODE_LINK && wd != NULL)
-			action |= CHECKOUT_ACTION__REMOVE;
+			*action |= CHECKOUT_ACTION__REMOVE;
+
+		/* if the file is on disk and doesn't match our mode, force update */
+		if (wd &&
+			GIT_PERMS_IS_EXEC(wd->mode) !=
+			GIT_PERMS_IS_EXEC(delta->new_file.mode))
+				*action |= CHECKOUT_ACTION__REMOVE;
 
 		notify = GIT_CHECKOUT_NOTIFY_UPDATED;
 	}
 
-	if ((action & CHECKOUT_ACTION__CONFLICT) != 0)
+	if ((*action & CHECKOUT_ACTION__CONFLICT) != 0)
 		notify = GIT_CHECKOUT_NOTIFY_CONFLICT;
 
-	if (notify != GIT_CHECKOUT_NOTIFY_NONE &&
-		checkout_notify(data, notify, delta, wd) != 0)
-		return GIT_EUSER;
-
-	return action;
+	return checkout_notify(data, notify, delta, wd);
 }
 
 static int checkout_action_no_wd(
+	int *action,
 	checkout_data *data,
 	const git_diff_delta *delta)
 {
-	int action = CHECKOUT_ACTION__NONE;
+	int error = 0;
+
+	*action = CHECKOUT_ACTION__NONE;
 
 	switch (delta->status) {
 	case GIT_DELTA_UNMODIFIED: /* case 12 */
-		if (checkout_notify(data, GIT_CHECKOUT_NOTIFY_DIRTY, delta, NULL))
-			return GIT_EUSER;
-		action = CHECKOUT_ACTION_IF(SAFE_CREATE, UPDATE_BLOB, NONE);
+		error = checkout_notify(data, GIT_CHECKOUT_NOTIFY_DIRTY, delta, NULL);
+		if (error)
+			return error;
+		*action = CHECKOUT_ACTION_IF(RECREATE_MISSING, UPDATE_BLOB, NONE);
 		break;
 	case GIT_DELTA_ADDED:    /* case 2 or 28 (and 5 but not really) */
-		action = CHECKOUT_ACTION_IF(SAFE, UPDATE_BLOB, NONE);
+		*action = CHECKOUT_ACTION_IF(SAFE, UPDATE_BLOB, NONE);
 		break;
 	case GIT_DELTA_MODIFIED: /* case 13 (and 35 but not really) */
-		action = CHECKOUT_ACTION_IF(SAFE_CREATE, UPDATE_BLOB, CONFLICT);
+		*action = CHECKOUT_ACTION_IF(RECREATE_MISSING, UPDATE_BLOB, CONFLICT);
 		break;
 	case GIT_DELTA_TYPECHANGE: /* case 21 (B->T) and 28 (T->B)*/
 		if (delta->new_file.mode == GIT_FILEMODE_TREE)
-			action = CHECKOUT_ACTION_IF(SAFE, UPDATE_BLOB, NONE);
+			*action = CHECKOUT_ACTION_IF(SAFE, UPDATE_BLOB, NONE);
 		break;
 	case GIT_DELTA_DELETED: /* case 8 or 25 */
+		*action = CHECKOUT_ACTION_IF(SAFE, REMOVE, NONE);
+		break;
 	default: /* impossible */
 		break;
 	}
 
-	return checkout_action_common(data, action, delta, NULL);
+	return checkout_action_common(action, data, delta, NULL);
+}
+
+static int checkout_target_fullpath(
+	git_buf **out, checkout_data *data, const char *path)
+{
+	git_buf_truncate(&data->target_path, data->target_len);
+
+	if (path && git_buf_puts(&data->target_path, path) < 0)
+		return -1;
+
+	*out = &data->target_path;
+
+	return 0;
+}
+
+static bool wd_item_is_removable(
+	checkout_data *data, const git_index_entry *wd)
+{
+	git_buf *full;
+
+	if (wd->mode != GIT_FILEMODE_TREE)
+		return true;
+
+	if (checkout_target_fullpath(&full, data, wd->path) < 0)
+		return false;
+
+	return !full || !git_path_contains(full, DOT_GIT);
 }
 
+static int checkout_queue_remove(checkout_data *data, const char *path)
+{
+	char *copy = git_pool_strdup(&data->pool, path);
+	GIT_ERROR_CHECK_ALLOC(copy);
+	return git_vector_insert(&data->removes, copy);
+}
+
+/* note that this advances the iterator over the wd item */
 static int checkout_action_wd_only(
 	checkout_data *data,
 	git_iterator *workdir,
-	const git_index_entry *wd,
+	const git_index_entry **wditem,
 	git_vector *pathspec)
 {
+	int error = 0;
 	bool remove = false;
 	git_checkout_notify_t notify = GIT_CHECKOUT_NOTIFY_NONE;
+	const git_index_entry *wd = *wditem;
 
-	if (!git_pathspec_match_path(
+	if (!git_pathspec__match(
 			pathspec, wd->path,
 			(data->strategy & GIT_CHECKOUT_DISABLE_PATHSPEC_MATCH) != 0,
-			git_iterator_ignore_case(workdir), NULL))
-		return 0;
+			git_iterator_ignore_case(workdir), NULL, NULL))
+		return git_iterator_advance(wditem, workdir);
 
 	/* check if item is tracked in the index but not in the checkout diff */
 	if (data->index != NULL) {
-		if (wd->mode != GIT_FILEMODE_TREE) {
-			int error;
+		size_t pos;
+
+		error = git_index__find_pos(
+			&pos, data->index, wd->path, 0, GIT_INDEX_STAGE_ANY);
 
-			if ((error = git_index_find(NULL, data->index, wd->path)) == 0) {
+		if (wd->mode != GIT_FILEMODE_TREE) {
+			if (!error) { /* found by git_index__find_pos call */
 				notify = GIT_CHECKOUT_NOTIFY_DIRTY;
 				remove = ((data->strategy & GIT_CHECKOUT_FORCE) != 0);
 			} else if (error != GIT_ENOTFOUND)
 				return error;
+			else
+				error = 0; /* git_index__find_pos does not set error msg */
 		} else {
 			/* for tree entries, we have to see if there are any index
 			 * entries that are contained inside that tree
 			 */
-			size_t pos = git_index__prefix_position(data->index, wd->path);
 			const git_index_entry *e = git_index_get_byindex(data->index, pos);
 
-			if (e != NULL && data->diff->pfxcomp(e->path, wd->path) == 0) {
-				notify = GIT_CHECKOUT_NOTIFY_DIRTY;
-				remove = ((data->strategy & GIT_CHECKOUT_FORCE) != 0);
-			}
+			if (e != NULL && data->diff->pfxcomp(e->path, wd->path) == 0)
+				return git_iterator_advance_into(wditem, workdir);
 		}
 	}
 
-	if (notify != GIT_CHECKOUT_NOTIFY_NONE)
-		/* found in index */;
-	else if (git_iterator_current_is_ignored(workdir)) {
-		notify = GIT_CHECKOUT_NOTIFY_IGNORED;
-		remove = ((data->strategy & GIT_CHECKOUT_REMOVE_IGNORED) != 0);
-	}
-	else {
-		notify = GIT_CHECKOUT_NOTIFY_UNTRACKED;
-		remove = ((data->strategy & GIT_CHECKOUT_REMOVE_UNTRACKED) != 0);
-	}
+	if (notify != GIT_CHECKOUT_NOTIFY_NONE) {
+		/* if we found something in the index, notify and advance */
+		if ((error = checkout_notify(data, notify, NULL, wd)) != 0)
+			return error;
 
-	if (checkout_notify(data, notify, NULL, wd))
-		return GIT_EUSER;
+		if (remove && wd_item_is_removable(data, wd))
+			error = checkout_queue_remove(data, wd->path);
 
-	if (remove) {
-		char *path = git_pool_strdup(&data->pool, wd->path);
-		GITERR_CHECK_ALLOC(path);
+		if (!error)
+			error = git_iterator_advance(wditem, workdir);
+	} else {
+		/* untracked or ignored - can't know which until we advance through */
+		bool over = false, removable = wd_item_is_removable(data, wd);
+		git_iterator_status_t untracked_state;
+
+		/* copy the entry for issuing notification callback later */
+		git_index_entry saved_wd = *wd;
+		git_buf_sets(&data->tmp, wd->path);
+		saved_wd.path = data->tmp.ptr;
+
+		error = git_iterator_advance_over(
+			wditem, &untracked_state, workdir);
+		if (error == GIT_ITEROVER)
+			over = true;
+		else if (error < 0)
+			return error;
 
-		if (git_vector_insert(&data->removes, path) < 0)
-			return -1;
+		if (untracked_state == GIT_ITERATOR_STATUS_IGNORED) {
+			notify = GIT_CHECKOUT_NOTIFY_IGNORED;
+			remove = ((data->strategy & GIT_CHECKOUT_REMOVE_IGNORED) != 0);
+		} else {
+			notify = GIT_CHECKOUT_NOTIFY_UNTRACKED;
+			remove = ((data->strategy & GIT_CHECKOUT_REMOVE_UNTRACKED) != 0);
+		}
+
+		if ((error = checkout_notify(data, notify, NULL, &saved_wd)) != 0)
+			return error;
+
+		if (remove && removable)
+			error = checkout_queue_remove(data, saved_wd.path);
+
+		if (!error && over) /* restore ITEROVER if needed */
+			error = GIT_ITEROVER;
 	}
 
-	return 0;
+	return error;
 }
 
 static bool submodule_is_config_only(
@@ -307,45 +456,65 @@ static bool submodule_is_config_only(
 {
 	git_submodule *sm = NULL;
 	unsigned int sm_loc = 0;
+	bool rval = false;
 
-	if (git_submodule_lookup(&sm, data->repo, path) < 0 ||
-		git_submodule_location(&sm_loc, sm) < 0 ||
-		sm_loc == GIT_SUBMODULE_STATUS_IN_CONFIG)
+	if (git_submodule_lookup(&sm, data->repo, path) < 0)
 		return true;
 
-	return false;
+	if (git_submodule_location(&sm_loc, sm) < 0 ||
+		sm_loc == GIT_SUBMODULE_STATUS_IN_CONFIG)
+		rval = true;
+
+	git_submodule_free(sm);
+
+	return rval;
+}
+
+static bool checkout_is_empty_dir(checkout_data *data, const char *path)
+{
+	git_buf *fullpath;
+
+	if (checkout_target_fullpath(&fullpath, data, path) < 0)
+		return false;
+
+	return git_path_is_empty_dir(fullpath->ptr);
 }
 
 static int checkout_action_with_wd(
+	int *action,
 	checkout_data *data,
 	const git_diff_delta *delta,
+	git_iterator *workdir,
 	const git_index_entry *wd)
 {
-	int action = CHECKOUT_ACTION__NONE;
+	*action = CHECKOUT_ACTION__NONE;
 
 	switch (delta->status) {
 	case GIT_DELTA_UNMODIFIED: /* case 14/15 or 33 */
-		if (checkout_is_workdir_modified(data, &delta->old_file, wd)) {
-			if (checkout_notify(
-					data, GIT_CHECKOUT_NOTIFY_DIRTY, delta, wd))
-				return GIT_EUSER;
-			action = CHECKOUT_ACTION_IF(FORCE, UPDATE_BLOB, NONE);
+		if (checkout_is_workdir_modified(data, &delta->old_file, &delta->new_file, wd)) {
+			GIT_ERROR_CHECK_ERROR(
+				checkout_notify(data, GIT_CHECKOUT_NOTIFY_DIRTY, delta, wd) );
+			*action = CHECKOUT_ACTION_IF(FORCE, UPDATE_BLOB, NONE);
 		}
 		break;
 	case GIT_DELTA_ADDED: /* case 3, 4 or 6 */
-		action = CHECKOUT_ACTION_IF(FORCE, UPDATE_BLOB, CONFLICT);
+		if (git_iterator_current_is_ignored(workdir))
+			*action = CHECKOUT_ACTION_IF(DONT_OVERWRITE_IGNORED, CONFLICT, UPDATE_BLOB);
+		else
+			*action = CHECKOUT_ACTION_IF(FORCE, UPDATE_BLOB, CONFLICT);
 		break;
 	case GIT_DELTA_DELETED: /* case 9 or 10 (or 26 but not really) */
-		if (checkout_is_workdir_modified(data, &delta->old_file, wd))
-			action = CHECKOUT_ACTION_IF(FORCE, REMOVE, CONFLICT);
+		if (checkout_is_workdir_modified(data, &delta->old_file, &delta->new_file, wd))
+			*action = CHECKOUT_ACTION_IF(FORCE, REMOVE, CONFLICT);
 		else
-			action = CHECKOUT_ACTION_IF(SAFE, REMOVE, NONE);
+			*action = CHECKOUT_ACTION_IF(SAFE, REMOVE, NONE);
 		break;
 	case GIT_DELTA_MODIFIED: /* case 16, 17, 18 (or 36 but not really) */
-		if (checkout_is_workdir_modified(data, &delta->old_file, wd))
-			action = CHECKOUT_ACTION_IF(FORCE, UPDATE_BLOB, CONFLICT);
+		if (wd->mode != GIT_FILEMODE_COMMIT &&
+			checkout_is_workdir_modified(data, &delta->old_file, &delta->new_file, wd))
+			*action = CHECKOUT_ACTION_IF(FORCE, UPDATE_BLOB, CONFLICT);
 		else
-			action = CHECKOUT_ACTION_IF(SAFE, UPDATE_BLOB, NONE);
+			*action = CHECKOUT_ACTION_IF(SAFE, UPDATE_BLOB, NONE);
 		break;
 	case GIT_DELTA_TYPECHANGE: /* case 22, 23, 29, 30 */
 		if (delta->old_file.mode == GIT_FILEMODE_TREE) {
@@ -353,92 +522,97 @@ static int checkout_action_with_wd(
 				/* either deleting items in old tree will delete the wd dir,
 				 * or we'll get a conflict when we attempt blob update...
 				 */
-				action = CHECKOUT_ACTION_IF(SAFE, UPDATE_BLOB, NONE);
+				*action = CHECKOUT_ACTION_IF(SAFE, UPDATE_BLOB, NONE);
 			else if (wd->mode == GIT_FILEMODE_COMMIT) {
 				/* workdir is possibly a "phantom" submodule - treat as a
 				 * tree if the only submodule info came from the config
 				 */
 				if (submodule_is_config_only(data, wd->path))
-					action = CHECKOUT_ACTION_IF(SAFE, UPDATE_BLOB, NONE);
+					*action = CHECKOUT_ACTION_IF(SAFE, UPDATE_BLOB, NONE);
 				else
-					action = CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, CONFLICT);
+					*action = CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, CONFLICT);
 			} else
-				action = CHECKOUT_ACTION_IF(FORCE, REMOVE, CONFLICT);
+				*action = CHECKOUT_ACTION_IF(FORCE, REMOVE, CONFLICT);
 		}
-		else if (checkout_is_workdir_modified(data, &delta->old_file, wd))
-			action = CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, CONFLICT);
+		else if (checkout_is_workdir_modified(data, &delta->old_file, &delta->new_file, wd))
+			*action = CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, CONFLICT);
 		else
-			action = CHECKOUT_ACTION_IF(SAFE, REMOVE_AND_UPDATE, NONE);
+			*action = CHECKOUT_ACTION_IF(SAFE, REMOVE_AND_UPDATE, NONE);
 
 		/* don't update if the typechange is to a tree */
 		if (delta->new_file.mode == GIT_FILEMODE_TREE)
-			action = (action & ~CHECKOUT_ACTION__UPDATE_BLOB);
+			*action = (*action & ~CHECKOUT_ACTION__UPDATE_BLOB);
 		break;
 	default: /* impossible */
 		break;
 	}
 
-	return checkout_action_common(data, action, delta, wd);
+	return checkout_action_common(action, data, delta, wd);
 }
 
 static int checkout_action_with_wd_blocker(
+	int *action,
 	checkout_data *data,
 	const git_diff_delta *delta,
 	const git_index_entry *wd)
 {
-	int action = CHECKOUT_ACTION__NONE;
+	*action = CHECKOUT_ACTION__NONE;
 
 	switch (delta->status) {
 	case GIT_DELTA_UNMODIFIED:
 		/* should show delta as dirty / deleted */
-		if (checkout_notify(data, GIT_CHECKOUT_NOTIFY_DIRTY, delta, wd))
-			return GIT_EUSER;
-		action = CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, NONE);
+		GIT_ERROR_CHECK_ERROR(
+			checkout_notify(data, GIT_CHECKOUT_NOTIFY_DIRTY, delta, wd) );
+		*action = CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, NONE);
 		break;
 	case GIT_DELTA_ADDED:
 	case GIT_DELTA_MODIFIED:
-		action = CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, CONFLICT);
+		*action = CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, CONFLICT);
 		break;
 	case GIT_DELTA_DELETED:
-		action = CHECKOUT_ACTION_IF(FORCE, REMOVE, CONFLICT);
+		*action = CHECKOUT_ACTION_IF(FORCE, REMOVE, CONFLICT);
 		break;
 	case GIT_DELTA_TYPECHANGE:
 		/* not 100% certain about this... */
-		action = CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, CONFLICT);
+		*action = CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, CONFLICT);
 		break;
 	default: /* impossible */
 		break;
 	}
 
-	return checkout_action_common(data, action, delta, wd);
+	return checkout_action_common(action, data, delta, wd);
 }
 
 static int checkout_action_with_wd_dir(
+	int *action,
 	checkout_data *data,
 	const git_diff_delta *delta,
+	git_iterator *workdir,
 	const git_index_entry *wd)
 {
-	int action = CHECKOUT_ACTION__NONE;
+	*action = CHECKOUT_ACTION__NONE;
 
 	switch (delta->status) {
 	case GIT_DELTA_UNMODIFIED: /* case 19 or 24 (or 34 but not really) */
-		if (checkout_notify(data, GIT_CHECKOUT_NOTIFY_DIRTY, delta, NULL) ||
-			checkout_notify(
-				data, GIT_CHECKOUT_NOTIFY_UNTRACKED, NULL, wd))
-			return GIT_EUSER;
+		GIT_ERROR_CHECK_ERROR(
+			checkout_notify(data, GIT_CHECKOUT_NOTIFY_DIRTY, delta, NULL));
+		GIT_ERROR_CHECK_ERROR(
+			checkout_notify(data, GIT_CHECKOUT_NOTIFY_UNTRACKED, NULL, wd));
+		*action = CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, NONE);
 		break;
 	case GIT_DELTA_ADDED:/* case 4 (and 7 for dir) */
 	case GIT_DELTA_MODIFIED: /* case 20 (or 37 but not really) */
 		if (delta->old_file.mode == GIT_FILEMODE_COMMIT)
 			/* expected submodule (and maybe found one) */;
 		else if (delta->new_file.mode != GIT_FILEMODE_TREE)
-			action = CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, CONFLICT);
+			*action = git_iterator_current_is_ignored(workdir) ?
+				CHECKOUT_ACTION_IF(DONT_OVERWRITE_IGNORED, CONFLICT, REMOVE_AND_UPDATE) :
+				CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, CONFLICT);
 		break;
 	case GIT_DELTA_DELETED: /* case 11 (and 27 for dir) */
-		if (delta->old_file.mode != GIT_FILEMODE_TREE &&
-			checkout_notify(
-				data, GIT_CHECKOUT_NOTIFY_UNTRACKED, NULL, wd))
-			return GIT_EUSER;
+		if (delta->old_file.mode != GIT_FILEMODE_TREE)
+			GIT_ERROR_CHECK_ERROR(
+				checkout_notify(data, GIT_CHECKOUT_NOTIFY_UNTRACKED, NULL, wd));
 		break;
 	case GIT_DELTA_TYPECHANGE: /* case 24 or 31 */
 		if (delta->old_file.mode == GIT_FILEMODE_TREE) {
@@ -448,39 +622,53 @@ static int checkout_action_with_wd_dir(
 			 * directory if is it left empty, so we can defer removing the
 			 * dir and it will succeed if no children are left.
 			 */
-			action = CHECKOUT_ACTION_IF(SAFE, UPDATE_BLOB, NONE);
-			if (action != CHECKOUT_ACTION__NONE)
-				action |= CHECKOUT_ACTION__DEFER_REMOVE;
+			*action = CHECKOUT_ACTION_IF(SAFE, UPDATE_BLOB, NONE);
 		}
 		else if (delta->new_file.mode != GIT_FILEMODE_TREE)
 			/* For typechange to dir, dir is already created so no action */
-			action = CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, CONFLICT);
+			*action = CHECKOUT_ACTION_IF(FORCE, REMOVE_AND_UPDATE, CONFLICT);
 		break;
 	default: /* impossible */
 		break;
 	}
 
-	return checkout_action_common(data, action, delta, wd);
+	return checkout_action_common(action, data, delta, wd);
+}
+
+static int checkout_action_with_wd_dir_empty(
+	int *action,
+	checkout_data *data,
+	const git_diff_delta *delta)
+{
+	int error = checkout_action_no_wd(action, data, delta);
+
+	/* We can always safely remove an empty directory. */
+	if (error == 0 && *action != CHECKOUT_ACTION__NONE)
+		*action |= CHECKOUT_ACTION__REMOVE;
+
+	return error;
 }
 
 static int checkout_action(
+	int *action,
 	checkout_data *data,
 	git_diff_delta *delta,
 	git_iterator *workdir,
-	const git_index_entry **wditem_ptr,
+	const git_index_entry **wditem,
 	git_vector *pathspec)
 {
-	const git_index_entry *wd = *wditem_ptr;
-	int cmp = -1, act;
+	int cmp = -1, error;
 	int (*strcomp)(const char *, const char *) = data->diff->strcomp;
 	int (*pfxcomp)(const char *str, const char *pfx) = data->diff->pfxcomp;
-	int error;
+	int (*advance)(const git_index_entry **, git_iterator *) = NULL;
 
 	/* move workdir iterator to follow along with deltas */
 
 	while (1) {
+		const git_index_entry *wd = *wditem;
+
 		if (!wd)
-			return checkout_action_no_wd(data, delta);
+			return checkout_action_no_wd(action, data, delta);
 
 		cmp = strcomp(wd->path, delta->old_file.path);
 
@@ -498,79 +686,76 @@ static int checkout_action(
 			if (cmp == 0) {
 				if (wd->mode == GIT_FILEMODE_TREE) {
 					/* case 2 - entry prefixed by workdir tree */
-					error = git_iterator_advance_into_or_over(&wd, workdir);
-					if (error && error != GIT_ITEROVER)
-						goto fail;
-					*wditem_ptr = wd;
+					error = git_iterator_advance_into(wditem, workdir);
+					if (error < 0 && error != GIT_ITEROVER)
+						goto done;
 					continue;
 				}
 
 				/* case 3 maybe - wd contains non-dir where dir expected */
 				if (delta->old_file.path[strlen(wd->path)] == '/') {
-					act = checkout_action_with_wd_blocker(data, delta, wd);
-					*wditem_ptr =
-						git_iterator_advance(&wd, workdir) ? NULL : wd;
-					return act;
+					error = checkout_action_with_wd_blocker(
+						action, data, delta, wd);
+					advance = git_iterator_advance;
+					goto done;
 				}
 			}
 
 			/* case 1 - handle wd item (if it matches pathspec) */
-			if (checkout_action_wd_only(data, workdir, wd, pathspec) < 0)
-				goto fail;
-			if ((error = git_iterator_advance(&wd, workdir)) < 0 &&
-				error != GIT_ITEROVER)
-				goto fail;
-
-			*wditem_ptr = wd;
+			error = checkout_action_wd_only(data, workdir, wditem, pathspec);
+			if (error && error != GIT_ITEROVER)
+				goto done;
 			continue;
 		}
 
 		if (cmp == 0) {
 			/* case 4 */
-			act = checkout_action_with_wd(data, delta, wd);
-			*wditem_ptr = git_iterator_advance(&wd, workdir) ? NULL : wd;
-			return act;
+			error = checkout_action_with_wd(action, data, delta, workdir, wd);
+			advance = git_iterator_advance;
+			goto done;
 		}
 
 		cmp = pfxcomp(wd->path, delta->old_file.path);
 
 		if (cmp == 0) { /* case 5 */
 			if (wd->path[strlen(delta->old_file.path)] != '/')
-				return checkout_action_no_wd(data, delta);
+				return checkout_action_no_wd(action, data, delta);
 
 			if (delta->status == GIT_DELTA_TYPECHANGE) {
 				if (delta->old_file.mode == GIT_FILEMODE_TREE) {
-					act = checkout_action_with_wd(data, delta, wd);
-					if ((error = git_iterator_advance_into(&wd, workdir)) < 0 &&
-						error != GIT_ENOTFOUND)
-						goto fail;
-					*wditem_ptr = wd;
-					return act;
+					error = checkout_action_with_wd(action, data, delta, workdir, wd);
+					advance = git_iterator_advance_into;
+					goto done;
 				}
 
 				if (delta->new_file.mode == GIT_FILEMODE_TREE ||
 					delta->new_file.mode == GIT_FILEMODE_COMMIT ||
 					delta->old_file.mode == GIT_FILEMODE_COMMIT)
 				{
-					act = checkout_action_with_wd(data, delta, wd);
-					if ((error = git_iterator_advance(&wd, workdir)) < 0 &&
-						error != GIT_ITEROVER)
-						goto fail;
-					*wditem_ptr = wd;
-					return act;
+					error = checkout_action_with_wd(action, data, delta, workdir, wd);
+					advance = git_iterator_advance;
+					goto done;
 				}
 			}
 
-			return checkout_action_with_wd_dir(data, delta, wd);
+			return checkout_is_empty_dir(data, wd->path) ?
+				checkout_action_with_wd_dir_empty(action, data, delta) :
+				checkout_action_with_wd_dir(action, data, delta, workdir, wd);
 		}
 
 		/* case 6 - wd is after delta */
-		return checkout_action_no_wd(data, delta);
+		return checkout_action_no_wd(action, data, delta);
 	}
 
-fail:
-	*wditem_ptr = NULL;
-	return -1;
+done:
+	if (!error && advance != NULL &&
+		(error = advance(wditem, workdir)) < 0) {
+		*wditem = NULL;
+		if (error == GIT_ITEROVER)
+			error = 0;
+	}
+
+	return error;
 }
 
 static int checkout_remaining_wd_items(
@@ -581,10 +766,8 @@ static int checkout_remaining_wd_items(
 {
 	int error = 0;
 
-	while (wd && !error) {
-		if (!(error = checkout_action_wd_only(data, workdir, wd, spec)))
-			error = git_iterator_advance(&wd, workdir);
-	}
+	while (wd && !error)
+		error = checkout_action_wd_only(data, workdir, &wd, spec);
 
 	if (error == GIT_ITEROVER)
 		error = 0;
@@ -592,219 +775,842 @@ static int checkout_remaining_wd_items(
 	return error;
 }
 
-static int checkout_get_actions(
-	uint32_t **actions_ptr,
-	size_t **counts_ptr,
-	checkout_data *data,
-	git_iterator *workdir)
+GIT_INLINE(int) checkout_idxentry_cmp(
+	const git_index_entry *a,
+	const git_index_entry *b)
 {
-	int error = 0;
-	const git_index_entry *wditem;
-	git_vector pathspec = GIT_VECTOR_INIT, *deltas;
-	git_pool pathpool = GIT_POOL_INIT_STRINGPOOL;
-	git_diff_delta *delta;
-	size_t i, *counts = NULL;
-	uint32_t *actions = NULL;
+	if (!a && !b)
+		return 0;
+	else if (!a && b)
+		return -1;
+	else if(a && !b)
+		return 1;
+	else
+		return strcmp(a->path, b->path);
+}
 
-	if (data->opts.paths.count > 0 &&
-		git_pathspec_init(&pathspec, &data->opts.paths, &pathpool) < 0)
+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, void *payload)
+{
+	checkout_conflictdata *conflict;
+
+	GIT_UNUSED(payload);
+
+	if ((conflict = git_vector_get(conflicts, idx)) == NULL)
 		return -1;
 
-	if ((error = git_iterator_current(&wditem, workdir)) < 0 &&
-		error != GIT_ITEROVER)
-		goto fail;
+	if (conflict->ancestor || conflict->ours || conflict->theirs)
+		return 0;
 
-	deltas = &data->diff->deltas;
+	git__free(conflict);
+	return 1;
+}
 
-	*counts_ptr = counts = git__calloc(CHECKOUT_ACTION__MAX+1, sizeof(size_t));
-	*actions_ptr = actions = git__calloc(
-		deltas->length ? deltas->length : 1, sizeof(uint32_t));
-	if (!counts || !actions) {
-		error = -1;
-		goto fail;
-	}
+GIT_INLINE(bool) conflict_pathspec_match(
+	checkout_data *data,
+	git_iterator *workdir,
+	git_vector *pathspec,
+	const git_index_entry *ancestor,
+	const git_index_entry *ours,
+	const git_index_entry *theirs)
+{
+	/* if the pathspec matches ours *or* theirs, proceed */
+	if (ours && git_pathspec__match(pathspec, ours->path,
+		(data->strategy & GIT_CHECKOUT_DISABLE_PATHSPEC_MATCH) != 0,
+		git_iterator_ignore_case(workdir), NULL, NULL))
+		return true;
 
-	git_vector_foreach(deltas, i, delta) {
-		int act = checkout_action(data, delta, workdir, &wditem, &pathspec);
+	if (theirs && git_pathspec__match(pathspec, theirs->path,
+		(data->strategy & GIT_CHECKOUT_DISABLE_PATHSPEC_MATCH) != 0,
+		git_iterator_ignore_case(workdir), NULL, NULL))
+		return true;
 
-		if (act < 0) {
-			error = act;
-			goto fail;
-		}
+	if (ancestor && git_pathspec__match(pathspec, ancestor->path,
+		(data->strategy & GIT_CHECKOUT_DISABLE_PATHSPEC_MATCH) != 0,
+		git_iterator_ignore_case(workdir), NULL, NULL))
+		return true;
 
-		actions[i] = act;
+	return false;
+}
 
-		if (act & CHECKOUT_ACTION__REMOVE)
-			counts[CHECKOUT_ACTION__REMOVE]++;
-		if (act & CHECKOUT_ACTION__UPDATE_BLOB)
-			counts[CHECKOUT_ACTION__UPDATE_BLOB]++;
-		if (act & CHECKOUT_ACTION__UPDATE_SUBMODULE)
-			counts[CHECKOUT_ACTION__UPDATE_SUBMODULE]++;
-		if (act & CHECKOUT_ACTION__CONFLICT)
-			counts[CHECKOUT_ACTION__CONFLICT]++;
-	}
+GIT_INLINE(int) checkout_conflict_detect_submodule(checkout_conflictdata *conflict)
+{
+	conflict->submodule = ((conflict->ancestor && S_ISGITLINK(conflict->ancestor->mode)) ||
+		(conflict->ours && S_ISGITLINK(conflict->ours->mode)) ||
+		(conflict->theirs && S_ISGITLINK(conflict->theirs->mode)));
+	return 0;
+}
 
-	error = checkout_remaining_wd_items(data, workdir, wditem, &pathspec);
-	if (error < 0)
-		goto fail;
+GIT_INLINE(int) checkout_conflict_detect_binary(git_repository *repo, checkout_conflictdata *conflict)
+{
+	git_blob *ancestor_blob = NULL, *our_blob = NULL, *their_blob = NULL;
+	int error = 0;
 
-	counts[CHECKOUT_ACTION__REMOVE] += data->removes.length;
+	if (conflict->submodule)
+		return 0;
 
-	if (counts[CHECKOUT_ACTION__CONFLICT] > 0 &&
-		(data->strategy & GIT_CHECKOUT_ALLOW_CONFLICTS) == 0)
-	{
-		giterr_set(GITERR_CHECKOUT, "%d conflicts prevent checkout",
-			(int)counts[CHECKOUT_ACTION__CONFLICT]);
-		error = GIT_EMERGECONFLICT;
-		goto fail;
+	if (conflict->ancestor) {
+		if ((error = git_blob_lookup(&ancestor_blob, repo, &conflict->ancestor->id)) < 0)
+			goto done;
+
+		conflict->binary = git_blob_is_binary(ancestor_blob);
 	}
 
-	git_pathspec_free(&pathspec);
-	git_pool_clear(&pathpool);
+	if (!conflict->binary && conflict->ours) {
+		if ((error = git_blob_lookup(&our_blob, repo, &conflict->ours->id)) < 0)
+			goto done;
 
-	return 0;
+		conflict->binary = git_blob_is_binary(our_blob);
+	}
 
-fail:
-	*counts_ptr = NULL;
-	git__free(counts);
-	*actions_ptr = NULL;
-	git__free(actions);
+	if (!conflict->binary && conflict->theirs) {
+		if ((error = git_blob_lookup(&their_blob, repo, &conflict->theirs->id)) < 0)
+			goto done;
 
-	git_pathspec_free(&pathspec);
-	git_pool_clear(&pathpool);
+		conflict->binary = git_blob_is_binary(their_blob);
+	}
+
+done:
+	git_blob_free(ancestor_blob);
+	git_blob_free(our_blob);
+	git_blob_free(their_blob);
 
 	return error;
 }
 
-static int buffer_to_file(
-	struct stat *st,
-	git_buf *buffer,
-	const char *path,
-	mode_t dir_mode,
-	int file_open_flags,
-	mode_t file_mode)
+static int checkout_conflict_append_update(
+	const git_index_entry *ancestor,
+	const git_index_entry *ours,
+	const git_index_entry *theirs,
+	void *payload)
 {
+	checkout_data *data = payload;
+	checkout_conflictdata *conflict;
 	int error;
 
-	if ((error = git_futils_mkpath2file(path, dir_mode)) < 0)
-		return error;
+	conflict = git__calloc(1, sizeof(checkout_conflictdata));
+	GIT_ERROR_CHECK_ALLOC(conflict);
 
-	if ((error = git_futils_writebuffer(
-			buffer, path, file_open_flags, file_mode)) < 0)
-		return error;
+	conflict->ancestor = ancestor;
+	conflict->ours = ours;
+	conflict->theirs = theirs;
 
-	if (st != NULL && (error = p_stat(path, st)) < 0) {
-		giterr_set(GITERR_OS, "Error while statting '%s'", path);
+	if ((error = checkout_conflict_detect_submodule(conflict)) < 0 ||
+		(error = checkout_conflict_detect_binary(data->repo, conflict)) < 0)
+	{
+		git__free(conflict);
 		return error;
 	}
 
-	if ((file_mode & 0100) != 0 && (error = p_chmod(path, file_mode)) < 0) {
-		giterr_set(GITERR_OS, "Failed to set permissions on '%s'", path);
-		return error;
-	}
+	if (git_vector_insert(&data->update_conflicts, conflict))
+		return -1;
 
 	return 0;
 }
 
-static int blob_content_to_file(
-	struct stat *st,
-	git_blob *blob,
-	const char *path,
-	mode_t entry_filemode,
-	git_checkout_opts *opts)
-{
-	int error = -1, nb_filters = 0;
-	mode_t file_mode = opts->file_mode;
-	bool dont_free_filtered;
-	git_buf unfiltered = GIT_BUF_INIT, filtered = GIT_BUF_INIT;
-	git_vector filters = GIT_VECTOR_INIT;
-
-	/* Create a fake git_buf from the blob raw data... */
-	filtered.ptr  = (void *)git_blob_rawcontent(blob);
-	filtered.size = (size_t)git_blob_rawsize(blob);
-	/* ... and make sure it doesn't get unexpectedly freed */
-	dont_free_filtered = true;
-
-	if (!opts->disable_filters &&
-		!git_buf_text_is_binary(&filtered) &&
-		(nb_filters = git_filters_load(
-			&filters,
-			git_object_owner((git_object *)blob),
-			path,
-			GIT_FILTER_TO_WORKTREE)) > 0)
-	{
-		/* reset 'filtered' so it can be a filter target */
-		git_buf_init(&filtered, 0);
-		dont_free_filtered = false;
-	}
+static int checkout_conflicts_foreach(
+	checkout_data *data,
+	git_index *index,
+	git_iterator *workdir,
+	git_vector *pathspec,
+	int (*cb)(const git_index_entry *, const git_index_entry *, const git_index_entry *, void *),
+	void *payload)
+{
+	git_index_conflict_iterator *iterator = NULL;
+	const git_index_entry *ancestor, *ours, *theirs;
+	int error = 0;
 
-	if (nb_filters < 0)
-		return nb_filters;
+	if ((error = git_index_conflict_iterator_new(&iterator, index)) < 0)
+		goto done;
 
-	if (nb_filters > 0)	 {
-		if ((error = git_blob__getbuf(&unfiltered, blob)) < 0)
-			goto cleanup;
+	/* Collect the conflicts */
+	while ((error = git_index_conflict_next(&ancestor, &ours, &theirs, iterator)) == 0) {
+		if (!conflict_pathspec_match(data, workdir, pathspec, ancestor, ours, theirs))
+			continue;
 
-		if ((error = git_filters_apply(&filtered, &unfiltered, &filters)) < 0)
-			goto cleanup;
+		if ((error = cb(ancestor, ours, theirs, payload)) < 0)
+			goto done;
 	}
 
-	/* Allow overriding of file mode */
-	if (!file_mode)
-		file_mode = entry_filemode;
-
-	error = buffer_to_file(
-		st, &filtered, path, opts->dir_mode, opts->file_open_flags, file_mode);
-
-	if (!error)
-		st->st_mode = entry_filemode;
+	if (error == GIT_ITEROVER)
+		error = 0;
 
-cleanup:
-	git_filters_free(&filters);
-	git_buf_free(&unfiltered);
-	if (!dont_free_filtered)
-		git_buf_free(&filtered);
+done:
+	git_index_conflict_iterator_free(iterator);
 
 	return error;
 }
 
-static int blob_content_to_link(
-	struct stat *st,
-	git_blob *blob,
-	const char *path,
-	mode_t dir_mode,
-	int can_symlink)
+static int checkout_conflicts_load(checkout_data *data, git_iterator *workdir, git_vector *pathspec)
 {
-	git_buf linktarget = GIT_BUF_INIT;
-	int error;
-
-	if ((error = git_futils_mkpath2file(path, dir_mode)) < 0)
-		return error;
+	git_index *index;
 
-	if ((error = git_blob__getbuf(&linktarget, blob)) < 0)
-		return error;
+	/* Only write conficts from sources that have them: indexes. */
+	if ((index = git_iterator_index(data->target)) == NULL)
+		return 0;
 
-	if (can_symlink) {
-		if ((error = p_symlink(git_buf_cstr(&linktarget), path)) < 0)
-			giterr_set(GITERR_OS, "Could not create symlink %s\n", path);
-	} else {
-		error = git_futils_fake_symlink(git_buf_cstr(&linktarget), path);
-	}
+	data->update_conflicts._cmp = checkout_conflictdata_cmp;
 
-	if (!error) {
-		if ((error = p_lstat(path, st)) < 0)
-			giterr_set(GITERR_CHECKOUT, "Could not stat symlink %s", path);
+	if (checkout_conflicts_foreach(data, index, workdir, pathspec, checkout_conflict_append_update, data) < 0)
+		return -1;
 
-		st->st_mode = GIT_FILEMODE_LINK;
-	}
+	/* Collect the REUC and NAME entries */
+	data->update_reuc = &index->reuc;
+	data->update_names = &index->names;
 
-	git_buf_free(&linktarget);
+	return 0;
+}
 
-	return error;
+GIT_INLINE(int) checkout_conflicts_cmp_entry(
+	const char *path,
+	const git_index_entry *entry)
+{
+	return strcmp((const char *)path, entry->path);
 }
 
-static int checkout_update_index(
-	checkout_data *data,
+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(
+	checkout_data *data,
+	const char *path)
+{
+	size_t pos;
+
+	if (git_vector_bsearch2(&pos, &data->update_conflicts, checkout_conflicts_cmp_ancestor, path) < 0)
+		return NULL;
+
+	return git_vector_get(&data->update_conflicts, pos);
+}
+
+static checkout_conflictdata *checkout_conflicts_search_branch(
+	checkout_data *data,
+	const char *path)
+{
+	checkout_conflictdata *conflict;
+	size_t i;
+
+	git_vector_foreach(&data->update_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,
+	checkout_data *data,
+	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) {
+		git_error_set(GIT_ERROR_INDEX, "a NAME entry exists without an ancestor");
+		error = -1;
+		goto done;
+	}
+
+	if (!name_entry->ours && !name_entry->theirs) {
+		git_error_set(GIT_ERROR_INDEX, "a NAME entry exists without an ours or theirs");
+		error = -1;
+		goto done;
+	}
+
+	if ((ancestor = checkout_conflicts_search_ancestor(data,
+		name_entry->ancestor)) == NULL) {
+		git_error_set(GIT_ERROR_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(data, name_entry->ours)) == NULL ||
+			ours->ours == NULL) {
+			git_error_set(GIT_ERROR_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 (name_entry->ours && strcmp(name_entry->ours, name_entry->theirs) == 0)
+			theirs = ours;
+		else if ((theirs = checkout_conflicts_search_branch(data, name_entry->theirs)) == NULL ||
+			theirs->theirs == NULL) {
+			git_error_set(GIT_ERROR_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_index *index;
+	const git_index_name_entry *name_entry;
+	checkout_conflictdata *ancestor_conflict, *our_conflict, *their_conflict;
+	size_t i, names;
+	int error = 0;
+
+	if ((index = git_iterator_index(data->target)) == NULL)
+		return 0;
+
+	/* Juggle entries based on renames */
+	names = git_index_name_entrycount(index);
+
+	for (i = 0; i < names; i++) {
+		name_entry = git_index_name_get_byindex(index, i);
+
+		if ((error = checkout_conflicts_load_byname_entry(
+			&ancestor_conflict, &our_conflict, &their_conflict,
+			data, 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;
+		}
+
+		if (our_conflict && our_conflict != ancestor_conflict &&
+			their_conflict && their_conflict != ancestor_conflict)
+			ancestor_conflict->one_to_two = 1;
+	}
+
+	git_vector_remove_matching(
+		&data->update_conflicts, checkout_conflictdata_empty, NULL);
+
+done:
+	return error;
+}
+
+static int checkout_conflicts_mark_directoryfile(
+	checkout_data *data)
+{
+	git_index *index;
+	checkout_conflictdata *conflict;
+	const git_index_entry *entry;
+	size_t i, j, len;
+	const char *path;
+	int prefixed, error = 0;
+
+	if ((index = git_iterator_index(data->target)) == NULL)
+		return 0;
+
+	len = git_index_entrycount(index);
+
+	/* Find d/f conflicts */
+	git_vector_foreach(&data->update_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, index, path)) < 0) {
+			if (error == GIT_ENOTFOUND)
+				git_error_set(GIT_ERROR_INDEX,
+					"index inconsistency, could not find entry for expected conflict '%s'", path);
+
+			goto done;
+		}
+
+		for (; j < len; j++) {
+			if ((entry = git_index_get_byindex(index, j)) == NULL) {
+				git_error_set(GIT_ERROR_INDEX,
+					"index inconsistency, truncated index while loading expected conflict '%s'", path);
+				error = -1;
+				goto done;
+			}
+
+			prefixed = git_path_equal_or_prefixed(path, entry->path, NULL);
+
+			if (prefixed == GIT_PATH_EQUAL)
+				continue;
+
+			if (prefixed == GIT_PATH_PREFIX)
+				conflict->directoryfile = 1;
+
+			break;
+		}
+	}
+
+done:
+	return error;
+}
+
+static int checkout_get_update_conflicts(
+	checkout_data *data,
+	git_iterator *workdir,
+	git_vector *pathspec)
+{
+	int error = 0;
+
+	if (data->strategy & GIT_CHECKOUT_SKIP_UNMERGED)
+		return 0;
+
+	if ((error = checkout_conflicts_load(data, workdir, pathspec)) < 0 ||
+		(error = checkout_conflicts_coalesce_renames(data)) < 0 ||
+		(error = checkout_conflicts_mark_directoryfile(data)) < 0)
+		goto done;
+
+done:
+	return error;
+}
+
+static int checkout_conflict_append_remove(
+	const git_index_entry *ancestor,
+	const git_index_entry *ours,
+	const git_index_entry *theirs,
+	void *payload)
+{
+	checkout_data *data = payload;
+	const char *name;
+
+	assert(ancestor || ours || theirs);
+
+	if (ancestor)
+		name = git__strdup(ancestor->path);
+	else if (ours)
+		name = git__strdup(ours->path);
+	else if (theirs)
+		name = git__strdup(theirs->path);
+	else
+		abort();
+
+	GIT_ERROR_CHECK_ALLOC(name);
+
+	return git_vector_insert(&data->remove_conflicts, (char *)name);
+}
+
+static int checkout_get_remove_conflicts(
+	checkout_data *data,
+	git_iterator *workdir,
+	git_vector *pathspec)
+{
+	if ((data->strategy & GIT_CHECKOUT_DONT_UPDATE_INDEX) != 0)
+		return 0;
+
+	return checkout_conflicts_foreach(data, data->index, workdir, pathspec, checkout_conflict_append_remove, data);
+}
+
+static int checkout_verify_paths(
+	git_repository *repo,
+	int action,
+	git_diff_delta *delta)
+{
+	unsigned int flags = GIT_PATH_REJECT_WORKDIR_DEFAULTS;
+
+	if (action & CHECKOUT_ACTION__REMOVE) {
+		if (!git_path_isvalid(repo, delta->old_file.path, delta->old_file.mode, flags)) {
+			git_error_set(GIT_ERROR_CHECKOUT, "cannot remove invalid path '%s'", delta->old_file.path);
+			return -1;
+		}
+	}
+
+	if (action & ~CHECKOUT_ACTION__REMOVE) {
+		if (!git_path_isvalid(repo, delta->new_file.path, delta->new_file.mode, flags)) {
+			git_error_set(GIT_ERROR_CHECKOUT, "cannot checkout to invalid path '%s'", delta->new_file.path);
+			return -1;
+		}
+	}
+
+	return 0;
+}
+
+static int checkout_get_actions(
+	uint32_t **actions_ptr,
+	size_t **counts_ptr,
+	checkout_data *data,
+	git_iterator *workdir)
+{
+	int error = 0, act;
+	const git_index_entry *wditem;
+	git_vector pathspec = GIT_VECTOR_INIT, *deltas;
+	git_pool pathpool;
+	git_diff_delta *delta;
+	size_t i, *counts = NULL;
+	uint32_t *actions = NULL;
+
+	git_pool_init(&pathpool, 1);
+
+	if (data->opts.paths.count > 0 &&
+		git_pathspec__vinit(&pathspec, &data->opts.paths, &pathpool) < 0)
+		return -1;
+
+	if ((error = git_iterator_current(&wditem, workdir)) < 0 &&
+		error != GIT_ITEROVER)
+		goto fail;
+
+	deltas = &data->diff->deltas;
+
+	*counts_ptr = counts = git__calloc(CHECKOUT_ACTION__MAX+1, sizeof(size_t));
+	*actions_ptr = actions = git__calloc(
+		deltas->length ? deltas->length : 1, sizeof(uint32_t));
+	if (!counts || !actions) {
+		error = -1;
+		goto fail;
+	}
+
+	git_vector_foreach(deltas, i, delta) {
+		if ((error = checkout_action(&act, data, delta, workdir, &wditem, &pathspec)) == 0)
+			error = checkout_verify_paths(data->repo, act, delta);
+
+		if (error != 0)
+			goto fail;
+
+		actions[i] = act;
+
+		if (act & CHECKOUT_ACTION__REMOVE)
+			counts[CHECKOUT_ACTION__REMOVE]++;
+		if (act & CHECKOUT_ACTION__UPDATE_BLOB)
+			counts[CHECKOUT_ACTION__UPDATE_BLOB]++;
+		if (act & CHECKOUT_ACTION__UPDATE_SUBMODULE)
+			counts[CHECKOUT_ACTION__UPDATE_SUBMODULE]++;
+		if (act & CHECKOUT_ACTION__CONFLICT)
+			counts[CHECKOUT_ACTION__CONFLICT]++;
+	}
+
+	error = checkout_remaining_wd_items(data, workdir, wditem, &pathspec);
+	if (error)
+		goto fail;
+
+	counts[CHECKOUT_ACTION__REMOVE] += data->removes.length;
+
+	if (counts[CHECKOUT_ACTION__CONFLICT] > 0 &&
+		(data->strategy & GIT_CHECKOUT_ALLOW_CONFLICTS) == 0)
+	{
+		git_error_set(GIT_ERROR_CHECKOUT, "%"PRIuZ" %s checkout",
+			counts[CHECKOUT_ACTION__CONFLICT],
+			counts[CHECKOUT_ACTION__CONFLICT] == 1 ?
+			"conflict prevents" : "conflicts prevent");
+		error = GIT_ECONFLICT;
+		goto fail;
+	}
+
+
+	if ((error = checkout_get_remove_conflicts(data, workdir, &pathspec)) < 0 ||
+		(error = checkout_get_update_conflicts(data, workdir, &pathspec)) < 0)
+		goto fail;
+
+	counts[CHECKOUT_ACTION__REMOVE_CONFLICT] = git_vector_length(&data->remove_conflicts);
+	counts[CHECKOUT_ACTION__UPDATE_CONFLICT] = git_vector_length(&data->update_conflicts);
+
+	git_pathspec__vfree(&pathspec);
+	git_pool_clear(&pathpool);
+
+	return 0;
+
+fail:
+	*counts_ptr = NULL;
+	git__free(counts);
+	*actions_ptr = NULL;
+	git__free(actions);
+
+	git_pathspec__vfree(&pathspec);
+	git_pool_clear(&pathpool);
+
+	return error;
+}
+
+static bool should_remove_existing(checkout_data *data)
+{
+	int ignorecase;
+
+	if (git_repository__cvar(&ignorecase, data->repo, GIT_CVAR_IGNORECASE) < 0) {
+		ignorecase = 0;
+	}
+
+	return (ignorecase &&
+		(data->strategy & GIT_CHECKOUT_DONT_REMOVE_EXISTING) == 0);
+}
+
+#define MKDIR_NORMAL \
+	GIT_MKDIR_PATH | GIT_MKDIR_VERIFY_DIR
+#define MKDIR_REMOVE_EXISTING \
+	MKDIR_NORMAL | GIT_MKDIR_REMOVE_FILES | GIT_MKDIR_REMOVE_SYMLINKS
+
+static int checkout_mkdir(
+	checkout_data *data,
+	const char *path,
+	const char *base,
+	mode_t mode,
+	unsigned int flags)
+{
+	struct git_futils_mkdir_options mkdir_opts = {0};
+	int error;
+
+	mkdir_opts.dir_map = data->mkdir_map;
+	mkdir_opts.pool = &data->pool;
+
+	error = git_futils_mkdir_relative(
+		path, base, mode, flags, &mkdir_opts);
+
+	data->perfdata.mkdir_calls += mkdir_opts.perfdata.mkdir_calls;
+	data->perfdata.stat_calls += mkdir_opts.perfdata.stat_calls;
+	data->perfdata.chmod_calls += mkdir_opts.perfdata.chmod_calls;
+
+	return error;
+}
+
+static int mkpath2file(
+	checkout_data *data, const char *path, unsigned int mode)
+{
+	struct stat st;
+	bool remove_existing = should_remove_existing(data);
+	unsigned int flags =
+		(remove_existing ? MKDIR_REMOVE_EXISTING : MKDIR_NORMAL) |
+		GIT_MKDIR_SKIP_LAST;
+	int error;
+
+	if ((error = checkout_mkdir(
+			data, path, data->opts.target_directory, mode, flags)) < 0)
+		return error;
+
+	if (remove_existing) {
+		data->perfdata.stat_calls++;
+
+		if (p_lstat(path, &st) == 0) {
+
+			/* Some file, symlink or folder already exists at this name.
+			 * We would have removed it in remove_the_old unless we're on
+			 * a case inensitive filesystem (or the user has asked us not
+			 * to).  Remove the similarly named file to write the new.
+			 */
+			error = git_futils_rmdir_r(path, NULL, GIT_RMDIR_REMOVE_FILES);
+		} else if (errno != ENOENT) {
+			git_error_set(GIT_ERROR_OS, "failed to stat '%s'", path);
+			return GIT_EEXISTS;
+		} else {
+			git_error_clear();
+		}
+	}
+
+	return error;
+}
+
+struct checkout_stream {
+	git_writestream base;
+	const char *path;
+	int fd;
+	int open;
+};
+
+static int checkout_stream_write(
+	git_writestream *s, const char *buffer, size_t len)
+{
+	struct checkout_stream *stream = (struct checkout_stream *)s;
+	int ret;
+
+	if ((ret = p_write(stream->fd, buffer, len)) < 0)
+		git_error_set(GIT_ERROR_OS, "could not write to '%s'", stream->path);
+
+	return ret;
+}
+
+static int checkout_stream_close(git_writestream *s)
+{
+	struct checkout_stream *stream = (struct checkout_stream *)s;
+	assert(stream && stream->open);
+
+	stream->open = 0;
+	return p_close(stream->fd);
+}
+
+static void checkout_stream_free(git_writestream *s)
+{
+	GIT_UNUSED(s);
+}
+
+static int blob_content_to_file(
+	checkout_data *data,
+	struct stat *st,
+	git_blob *blob,
+	const char *path,
+	const char *hint_path,
+	mode_t entry_filemode)
+{
+	int flags = data->opts.file_open_flags;
+	mode_t file_mode = data->opts.file_mode ?
+		data->opts.file_mode : entry_filemode;
+	git_filter_options filter_opts = GIT_FILTER_OPTIONS_INIT;
+	struct checkout_stream writer;
+	mode_t mode;
+	git_filter_list *fl = NULL;
+	int fd;
+	int error = 0;
+
+	if (hint_path == NULL)
+		hint_path = path;
+
+	if ((error = mkpath2file(data, path, data->opts.dir_mode)) < 0)
+		return error;
+
+	if (flags <= 0)
+		flags = O_CREAT | O_TRUNC | O_WRONLY;
+	if (!(mode = file_mode))
+		mode = GIT_FILEMODE_BLOB;
+
+	if ((fd = p_open(path, flags, mode)) < 0) {
+		git_error_set(GIT_ERROR_OS, "could not open '%s' for writing", path);
+		return fd;
+	}
+
+	filter_opts.attr_session = &data->attr_session;
+	filter_opts.temp_buf = &data->tmp;
+
+	if (!data->opts.disable_filters &&
+		(error = git_filter_list__load_ext(
+			&fl, data->repo, blob, hint_path,
+			GIT_FILTER_TO_WORKTREE, &filter_opts))) {
+		p_close(fd);
+		return error;
+	}
+
+	/* setup the writer */
+	memset(&writer, 0, sizeof(struct checkout_stream));
+	writer.base.write = checkout_stream_write;
+	writer.base.close = checkout_stream_close;
+	writer.base.free = checkout_stream_free;
+	writer.path = path;
+	writer.fd = fd;
+	writer.open = 1;
+
+	error = git_filter_list_stream_blob(fl, blob, &writer.base);
+
+	assert(writer.open == 0);
+
+	git_filter_list_free(fl);
+
+	if (error < 0)
+		return error;
+
+	if (st) {
+		data->perfdata.stat_calls++;
+
+		if ((error = p_stat(path, st)) < 0) {
+			git_error_set(GIT_ERROR_OS, "failed to stat '%s'", path);
+			return error;
+		}
+
+		st->st_mode = entry_filemode;
+	}
+
+	return 0;
+}
+
+static int blob_content_to_link(
+	checkout_data *data,
+	struct stat *st,
+	git_blob *blob,
+	const char *path)
+{
+	git_buf linktarget = GIT_BUF_INIT;
+	int error;
+
+	if ((error = mkpath2file(data, path, data->opts.dir_mode)) < 0)
+		return error;
+
+	if ((error = git_blob__getbuf(&linktarget, blob)) < 0)
+		return error;
+
+	if (data->can_symlink) {
+		if ((error = p_symlink(git_buf_cstr(&linktarget), path)) < 0)
+			git_error_set(GIT_ERROR_OS, "could not create symlink %s", path);
+	} else {
+		error = git_futils_fake_symlink(git_buf_cstr(&linktarget), path);
+	}
+
+	if (!error) {
+		data->perfdata.stat_calls++;
+
+		if ((error = p_lstat(path, st)) < 0)
+			git_error_set(GIT_ERROR_CHECKOUT, "could not stat symlink %s", path);
+
+		st->st_mode = GIT_FILEMODE_LINK;
+	}
+
+	git_buf_dispose(&linktarget);
+
+	return error;
+}
+
+static int checkout_update_index(
+	checkout_data *data,
 	const git_diff_file *file,
 	struct stat *st)
 {
@@ -815,8 +1621,8 @@ static int checkout_update_index(
 
 	memset(&entry, 0, sizeof(entry));
 	entry.path = (char *)file->path; /* cast to prevent warning */
-	git_index_entry__init_from_stat(&entry, st);
-	git_oid_cpy(&entry.oid, &file->oid);
+	git_index_entry__init_from_stat(&entry, st, true);
+	git_oid_cpy(&entry.id, &file->id);
 
 	return git_index_add(data->index, &entry);
 }
@@ -825,19 +1631,20 @@ static int checkout_submodule_update_index(
 	checkout_data *data,
 	const git_diff_file *file)
 {
+	git_buf *fullpath;
 	struct stat st;
 
 	/* update the index unless prevented */
 	if ((data->strategy & GIT_CHECKOUT_DONT_UPDATE_INDEX) != 0)
 		return 0;
 
-	git_buf_truncate(&data->path, data->workdir_len);
-	if (git_buf_puts(&data->path, file->path) < 0)
+	if (checkout_target_fullpath(&fullpath, data, file->path) < 0)
 		return -1;
 
-	if (p_stat(git_buf_cstr(&data->path), &st) < 0) {
-		giterr_set(
-			GITERR_CHECKOUT, "Could not stat submodule %s\n", file->path);
+	data->perfdata.stat_calls++;
+	if (p_stat(fullpath->ptr, &st) < 0) {
+		git_error_set(
+			GIT_ERROR_CHECKOUT, "could not stat submodule %s\n", file->path);
 		return GIT_ENOTFOUND;
 	}
 
@@ -850,24 +1657,25 @@ static int checkout_submodule(
 	checkout_data *data,
 	const git_diff_file *file)
 {
+	bool remove_existing = should_remove_existing(data);
 	int error = 0;
-	git_submodule *sm;
 
 	/* Until submodules are supported, UPDATE_ONLY means do nothing here */
 	if ((data->strategy & GIT_CHECKOUT_UPDATE_ONLY) != 0)
 		return 0;
 
-	if ((error = git_futils_mkdir(
-			file->path, data->opts.target_directory,
-			data->opts.dir_mode, GIT_MKDIR_PATH)) < 0)
+	if ((error = checkout_mkdir(
+			data,
+			file->path, data->opts.target_directory, data->opts.dir_mode,
+			remove_existing ? MKDIR_REMOVE_EXISTING : MKDIR_NORMAL)) < 0)
 		return error;
 
-	if ((error = git_submodule_lookup(&sm, data->repo, file->path)) < 0) {
+	if ((error = git_submodule_lookup(NULL, data->repo, file->path)) < 0) {
 		/* I've observed repos with submodules in the tree that do not
 		 * have a .gitmodules - core Git just makes an empty directory
 		 */
 		if (error == GIT_ENOTFOUND) {
-			giterr_clear();
+			git_error_clear();
 			return checkout_submodule_update_index(data, file);
 		}
 
@@ -896,17 +1704,20 @@ static void report_progress(
 			data->opts.progress_payload);
 }
 
-static int checkout_safe_for_update_only(const char *path, mode_t expected_mode)
+static int checkout_safe_for_update_only(
+	checkout_data *data, const char *path, mode_t expected_mode)
 {
 	struct stat st;
 
+	data->perfdata.stat_calls++;
+
 	if (p_lstat(path, &st) < 0) {
 		/* if doesn't exist, then no error and no update */
 		if (errno == ENOENT || errno == ENOTDIR)
 			return 0;
 
 		/* otherwise, stat error and no update */
-		giterr_set(GITERR_OS, "Failed to stat file '%s'", path);
+		git_error_set(GIT_ERROR_OS, "failed to stat '%s'", path);
 		return -1;
 	}
 
@@ -917,47 +1728,62 @@ static int checkout_safe_for_update_only(const char *path, mode_t expected_mode)
 	return 0;
 }
 
-static int checkout_blob(
+static int 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;
+
+	if ((error = git_blob_lookup(&blob, data->repo, oid)) < 0)
+		return error;
+
+	if (S_ISLNK(mode))
+		error = blob_content_to_link(data, st, blob, full_path);
+	else
+		error = blob_content_to_file(data, st, blob, full_path, hint_path, mode);
+
+	git_blob_free(blob);
+
+	/* if we try to create the blob and an existing directory blocks it from
+	 * being written, then there must have been a typechange conflict in a
+	 * parent directory - suppress the error and try to continue.
+	 */
+	if ((data->strategy & GIT_CHECKOUT_ALLOW_CONFLICTS) != 0 &&
+		(error == GIT_ENOTFOUND || error == GIT_EEXISTS))
+	{
+		git_error_clear();
+		error = 0;
+	}
+
+	return error;
+}
+
+static int checkout_blob(
+	checkout_data *data,
+	const git_diff_file *file)
+{
+	git_buf *fullpath;
 	struct stat st;
+	int error = 0;
 
-	git_buf_truncate(&data->path, data->workdir_len);
-	if (git_buf_puts(&data->path, file->path) < 0)
+	if (checkout_target_fullpath(&fullpath, data, 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);
+			data, fullpath->ptr, file->mode);
+
 		if (rval <= 0)
 			return rval;
 	}
 
-	if ((error = git_blob_lookup(&blob, data->repo, &file->oid)) < 0)
-		return error;
-
-	if (S_ISLNK(file->mode))
-		error = blob_content_to_link(
-			&st, blob, git_buf_cstr(&data->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);
-
-	git_blob_free(blob);
-
-	/* if we try to create the blob and an existing directory blocks it from
-	 * being written, then there must have been a typechange conflict in a
-	 * parent directory - suppress the error and try to continue.
-	 */
-	if ((data->strategy & GIT_CHECKOUT_ALLOW_CONFLICTS) != 0 &&
-		(error == GIT_ENOTFOUND || error == GIT_EEXISTS))
-	{
-		giterr_clear();
-		error = 0;
-	}
+	error = checkout_write_content(
+		data, &file->id, fullpath->ptr, NULL, file->mode, &st);
 
 	/* update the index unless prevented */
 	if (!error && (data->strategy & GIT_CHECKOUT_DONT_UPDATE_INDEX) == 0)
@@ -978,18 +1804,21 @@ static int checkout_remove_the_old(
 	git_diff_delta *delta;
 	const char *str;
 	size_t i;
-	const char *workdir = git_buf_cstr(&data->path);
+	git_buf *fullpath;
 	uint32_t flg = GIT_RMDIR_EMPTY_PARENTS |
 		GIT_RMDIR_REMOVE_FILES | GIT_RMDIR_REMOVE_BLOCKERS;
 
 	if (data->opts.checkout_strategy & GIT_CHECKOUT_SKIP_LOCKED_DIRECTORIES)
 		flg |= GIT_RMDIR_SKIP_NONEMPTY;
 
-	git_buf_truncate(&data->path, data->workdir_len);
+	if (checkout_target_fullpath(&fullpath, data, NULL) < 0)
+		return -1;
 
 	git_vector_foreach(&data->diff->deltas, i, delta) {
 		if (actions[i] & CHECKOUT_ACTION__REMOVE) {
-			error = git_futils_rmdir_r(delta->old_file.path, workdir, flg);
+			error = git_futils_rmdir_r(
+				delta->old_file.path, fullpath->ptr, flg);
+
 			if (error < 0)
 				return error;
 
@@ -1006,7 +1835,7 @@ static int checkout_remove_the_old(
 	}
 
 	git_vector_foreach(&data->removes, i, str) {
-		error = git_futils_rmdir_r(str, workdir, flg);
+		error = git_futils_rmdir_r(str, fullpath->ptr, flg);
 		if (error < 0)
 			return error;
 
@@ -1034,7 +1863,7 @@ static int checkout_deferred_remove(git_repository *repo, const char *path)
 
 	if (error == GIT_ENOTFOUND) {
 		error = 0;
-		giterr_clear();
+		git_error_clear();
 	}
 
 	return error;
@@ -1085,11 +1914,6 @@ static int checkout_create_submodules(
 	git_diff_delta *delta;
 	size_t i;
 
-	/* initial reload of submodules if .gitmodules was changed */
-	if (data->reload_submodules &&
-		(error = git_submodule_reload_all(data->repo)) < 0)
-		return error;
-
 	git_vector_foreach(&data->diff->deltas, i, delta) {
 		if (actions[i] & CHECKOUT_ACTION__DEFER_REMOVE) {
 			/* this has a blocker directory that should only be removed iff
@@ -1110,8 +1934,7 @@ static int checkout_create_submodules(
 		}
 	}
 
-	/* final reload once submodules have been updated */
-	return git_submodule_reload_all(data->repo);
+	return 0;
 }
 
 static int checkout_lookup_head_tree(git_tree **out, git_repository *repo)
@@ -1121,7 +1944,7 @@ static int checkout_lookup_head_tree(git_tree **out, git_repository *repo)
 	git_object *head;
 
 	if (!(error = git_repository_head(&ref, repo)) &&
-		!(error = git_reference_peel(&head, ref, GIT_OBJ_TREE)))
+		!(error = git_reference_peel(&head, ref, GIT_OBJECT_TREE)))
 		*out = (git_tree *)head;
 
 	git_reference_free(ref);
@@ -1129,6 +1952,385 @@ static int checkout_lookup_head_tree(git_tree **out, git_repository *repo)
 	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 checkout_path_suffixed(git_buf *path, const char *suffix)
+{
+	size_t path_len;
+	int i = 0, error = 0;
+
+	if ((error = git_buf_putc(path, '~')) < 0 || (error = git_buf_puts(path, suffix)) < 0)
+		return -1;
+
+	path_len = git_buf_len(path);
+
+	while (git_path_exists(git_buf_cstr(path)) && i < INT_MAX) {
+		git_buf_truncate(path, path_len);
+
+		if ((error = git_buf_putc(path, '_')) < 0 ||
+			(error = git_buf_printf(path, "%d", i)) < 0)
+			return error;
+
+		i++;
+	}
+
+	if (i == INT_MAX) {
+		git_buf_truncate(path, path_len);
+
+		git_error_set(GIT_ERROR_CHECKOUT, "could not write '%s': working directory file exists", path->ptr);
+		return GIT_EEXISTS;
+	}
+
+	return 0;
+}
+
+static int checkout_write_entry(
+	checkout_data *data,
+	checkout_conflictdata *conflict,
+	const git_index_entry *side)
+{
+	const char *hint_path = NULL, *suffix;
+	git_buf *fullpath;
+	struct stat st;
+	int error;
+
+	assert (side == conflict->ours || side == conflict->theirs);
+
+	if (checkout_target_fullpath(&fullpath, data, side->path) < 0)
+		return -1;
+
+	if ((conflict->name_collision || conflict->directoryfile) &&
+		(data->strategy & GIT_CHECKOUT_USE_OURS) == 0 &&
+		(data->strategy & GIT_CHECKOUT_USE_THEIRS) == 0) {
+
+		if (side == conflict->ours)
+			suffix = data->opts.our_label ? data->opts.our_label :
+				"ours";
+		else
+			suffix = data->opts.their_label ? data->opts.their_label :
+				"theirs";
+
+		if (checkout_path_suffixed(fullpath, suffix) < 0)
+			return -1;
+
+		hint_path = side->path;
+	}
+
+	if ((data->strategy & GIT_CHECKOUT_UPDATE_ONLY) != 0 &&
+		(error = checkout_safe_for_update_only(data, fullpath->ptr, side->mode)) <= 0)
+		return error;
+
+	if (!S_ISGITLINK(side->mode))
+		return checkout_write_content(data,
+					      &side->id, fullpath->ptr, hint_path, side->mode, &st);
+
+	return 0;
+}
+
+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_merge_path(
+	git_buf *out,
+	checkout_data *data,
+	checkout_conflictdata *conflict,
+	git_merge_file_result *result)
+{
+	const char *our_label_raw, *their_label_raw, *suffix;
+	int error = 0;
+
+	if ((error = git_buf_joinpath(out, git_repository_workdir(data->repo), result->path)) < 0)
+		return error;
+
+	/* Most conflicts simply use the filename in the index */
+	if (!conflict->name_collision)
+		return 0;
+
+	/* Rename 2->1 conflicts need the branch name appended */
+	our_label_raw = data->opts.our_label ? data->opts.our_label : "ours";
+	their_label_raw = data->opts.their_label ? data->opts.their_label : "theirs";
+	suffix = strcmp(result->path, conflict->ours->path) == 0 ? our_label_raw : their_label_raw;
+
+	if ((error = checkout_path_suffixed(out, suffix)) < 0)
+		return error;
+
+	return 0;
+}
+
+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,
+		in_data = GIT_BUF_INIT, out_data = GIT_BUF_INIT;
+	git_merge_file_options opts = GIT_MERGE_FILE_OPTIONS_INIT;
+	git_merge_file_result result = {0};
+	git_filebuf output = GIT_FILEBUF_INIT;
+	git_filter_list *fl = NULL;
+	git_filter_options filter_opts = GIT_FILTER_OPTIONS_INIT;
+	int error = 0;
+
+	if (data->opts.checkout_strategy & GIT_CHECKOUT_CONFLICT_STYLE_DIFF3)
+		opts.flags |= GIT_MERGE_FILE_STYLE_DIFF3;
+
+	opts.ancestor_label = data->opts.ancestor_label ?
+		data->opts.ancestor_label : "ancestor";
+	opts.our_label = data->opts.our_label ?
+		data->opts.our_label : "ours";
+	opts.their_label = 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, opts.our_label, conflict->ours->path)) < 0 ||
+			(error = conflict_entry_name(
+			&their_label, opts.their_label, conflict->theirs->path)) < 0)
+			goto done;
+
+		opts.our_label = git_buf_cstr(&our_label);
+		opts.their_label = git_buf_cstr(&their_label);
+	}
+
+	if ((error = git_merge_file_from_index(&result, data->repo,
+		conflict->ancestor, conflict->ours, conflict->theirs, &opts)) < 0)
+		goto done;
+
+	if (result.path == NULL || result.mode == 0) {
+		git_error_set(GIT_ERROR_CHECKOUT, "could not merge contents of file");
+		error = GIT_ECONFLICT;
+		goto done;
+	}
+
+	if ((error = checkout_merge_path(&path_workdir, data, conflict, &result)) < 0)
+		goto done;
+
+	if ((data->strategy & GIT_CHECKOUT_UPDATE_ONLY) != 0 &&
+		(error = checkout_safe_for_update_only(data, git_buf_cstr(&path_workdir), result.mode)) <= 0)
+		goto done;
+
+	if (!data->opts.disable_filters) {
+		in_data.ptr = (char *)result.ptr;
+		in_data.size = result.len;
+
+		filter_opts.attr_session = &data->attr_session;
+		filter_opts.temp_buf = &data->tmp;
+
+		if ((error = git_filter_list__load_ext(
+				&fl, data->repo, NULL, git_buf_cstr(&path_workdir),
+				GIT_FILTER_TO_WORKTREE, &filter_opts)) < 0 ||
+			(error = git_filter_list_apply_to_data(&out_data, fl, &in_data)) < 0)
+			goto done;
+	} else {
+		out_data.ptr = (char *)result.ptr;
+		out_data.size = result.len;
+	}
+
+	if ((error = mkpath2file(data, path_workdir.ptr, data->opts.dir_mode)) < 0 ||
+		(error = git_filebuf_open(&output, git_buf_cstr(&path_workdir), GIT_FILEBUF_DO_NOT_BUFFER, result.mode)) < 0 ||
+		(error = git_filebuf_write(&output, out_data.ptr, out_data.size)) < 0 ||
+		(error = git_filebuf_commit(&output)) < 0)
+		goto done;
+
+done:
+	git_filter_list_free(fl);
+
+	git_buf_dispose(&out_data);
+	git_buf_dispose(&our_label);
+	git_buf_dispose(&their_label);
+
+	git_merge_file_result_free(&result);
+	git_buf_dispose(&path_workdir);
+	git_buf_dispose(&path_suffixed);
+
+	return error;
+}
+
+static int checkout_conflict_add(
+	checkout_data *data,
+	const git_index_entry *conflict)
+{
+	int error = git_index_remove(data->index, conflict->path, 0);
+
+	if (error == GIT_ENOTFOUND)
+		git_error_clear();
+	else if (error < 0)
+		return error;
+
+	return git_index_add(data->index, conflict);
+}
+
+static int checkout_conflict_update_index(
+	checkout_data *data,
+	checkout_conflictdata *conflict)
+{
+	int error = 0;
+
+	if (conflict->ancestor)
+		error = checkout_conflict_add(data, conflict->ancestor);
+
+	if (!error && conflict->ours)
+		error = checkout_conflict_add(data, conflict->ours);
+
+	if (!error && conflict->theirs)
+		error = checkout_conflict_add(data, conflict->theirs);
+
+	return error;
+}
+
+static int checkout_create_conflicts(checkout_data *data)
+{
+	checkout_conflictdata *conflict;
+	size_t i;
+	int error = 0;
+
+	git_vector_foreach(&data->update_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->one_to_two)
+			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);
+
+		/* If any side is a gitlink, do nothing. */
+		else if (conflict->submodule)
+			error = 0;
+
+		/* If any side is binary, write the ours side */
+		else if (conflict->binary)
+			error = checkout_write_entry(data, conflict, conflict->ours);
+
+		else if (!error)
+			error = checkout_write_merge(data, conflict);
+
+		/* Update the index extensions (REUC and NAME) if we're checking
+		 * out a different index. (Otherwise just leave them there.)
+		 */
+		if (!error && (data->strategy & GIT_CHECKOUT_DONT_UPDATE_INDEX) == 0)
+			error = checkout_conflict_update_index(data, conflict);
+
+		if (error)
+			break;
+
+		data->completed_steps++;
+		report_progress(data,
+			conflict->ours ? conflict->ours->path :
+			(conflict->theirs ? conflict->theirs->path : conflict->ancestor->path));
+	}
+
+	return error;
+}
+
+static int checkout_remove_conflicts(checkout_data *data)
+{
+	const char *conflict;
+	size_t i;
+
+	git_vector_foreach(&data->remove_conflicts, i, conflict) {
+		if (git_index_conflict_remove(data->index, conflict) < 0)
+			return -1;
+
+		data->completed_steps++;
+	}
+
+	return 0;
+}
+
+static int checkout_extensions_update_index(checkout_data *data)
+{
+	const git_index_reuc_entry *reuc_entry;
+	const git_index_name_entry *name_entry;
+	size_t i;
+	int error = 0;
+
+	if ((data->strategy & GIT_CHECKOUT_UPDATE_ONLY) != 0)
+		return 0;
+
+	if (data->update_reuc) {
+		git_vector_foreach(data->update_reuc, i, reuc_entry) {
+			if ((error = git_index_reuc_add(data->index, reuc_entry->path,
+				reuc_entry->mode[0], &reuc_entry->oid[0],
+				reuc_entry->mode[1], &reuc_entry->oid[1],
+				reuc_entry->mode[2], &reuc_entry->oid[2])) < 0)
+				goto done;
+		}
+	}
+
+	if (data->update_names) {
+		git_vector_foreach(data->update_names, i, name_entry) {
+			if ((error = git_index_name_add(data->index, name_entry->ancestor,
+				name_entry->ours, name_entry->theirs)) < 0)
+				goto done;
+		}
+	}
+
+done:
+	return error;
+}
+
 static void checkout_data_clear(checkout_data *data)
 {
 	if (data->opts_free_baseline) {
@@ -1139,19 +2341,28 @@ static void checkout_data_clear(checkout_data *data)
 	git_vector_free(&data->removes);
 	git_pool_clear(&data->pool);
 
+	git_vector_free_deep(&data->remove_conflicts);
+	git_vector_free_deep(&data->update_conflicts);
+
 	git__free(data->pfx);
 	data->pfx = NULL;
 
-	git_buf_free(&data->path);
+	git_buf_dispose(&data->target_path);
+	git_buf_dispose(&data->tmp);
 
 	git_index_free(data->index);
 	data->index = NULL;
+
+	git_strmap_free(data->mkdir_map);
+	data->mkdir_map = NULL;
+
+	git_attr_session__free(&data->attr_session);
 }
 
 static int checkout_data_init(
 	checkout_data *data,
 	git_iterator *target,
-	git_checkout_opts *proposed)
+	const git_checkout_options *proposed)
 {
 	int error = 0;
 	git_repository *repo = git_iterator_owner(target);
@@ -1159,7 +2370,7 @@ static int checkout_data_init(
 	memset(data, 0, sizeof(*data));
 
 	if (!repo) {
-		giterr_set(GITERR_CHECKOUT, "Cannot checkout nothing");
+		git_error_set(GIT_ERROR_CHECKOUT, "cannot checkout nothing");
 		return -1;
 	}
 
@@ -1168,51 +2379,77 @@ static int checkout_data_init(
 		return error;
 
 	data->repo = repo;
+	data->target = target;
 
-	GITERR_CHECK_VERSION(
-		proposed, GIT_CHECKOUT_OPTS_VERSION, "git_checkout_opts");
+	GIT_ERROR_CHECK_VERSION(
+		proposed, GIT_CHECKOUT_OPTIONS_VERSION, "git_checkout_options");
 
 	if (!proposed)
-		GIT_INIT_STRUCTURE(&data->opts, GIT_CHECKOUT_OPTS_VERSION);
+		GIT_INIT_STRUCTURE(&data->opts, GIT_CHECKOUT_OPTIONS_VERSION);
 	else
-		memmove(&data->opts, proposed, sizeof(git_checkout_opts));
+		memmove(&data->opts, proposed, sizeof(git_checkout_options));
 
 	if (!data->opts.target_directory)
 		data->opts.target_directory = git_repository_workdir(repo);
 	else if (!git_path_isdir(data->opts.target_directory) &&
-			 (error = git_futils_mkdir(data->opts.target_directory, NULL,
-					GIT_DIR_MODE, GIT_MKDIR_VERIFY_DIR)) < 0)
+			 (error = checkout_mkdir(data,
+				data->opts.target_directory, NULL,
+				GIT_DIR_MODE, GIT_MKDIR_VERIFY_DIR)) < 0)
+		goto cleanup;
+
+	if ((error = git_repository_index(&data->index, data->repo)) < 0)
 		goto cleanup;
 
 	/* refresh config and index content unless NO_REFRESH is given */
 	if ((data->opts.checkout_strategy & GIT_CHECKOUT_NO_REFRESH) == 0) {
 		git_config *cfg;
 
-		if ((error = git_repository_config__weakptr(&cfg, repo)) < 0 ||
-			(error = git_config_refresh(cfg)) < 0)
+		if ((error = git_repository_config__weakptr(&cfg, repo)) < 0)
 			goto cleanup;
 
-		/* if we are checking out the index, don't reload,
-		 * otherwise get index and force reload
+		/* Reload the repository index (unless we're checking out the
+		 * index; then it has the changes we're trying to check out
+		 * and those should not be overwritten.)
 		 */
-		if ((data->index = git_iterator_get_index(target)) != NULL) {
-			GIT_REFCOUNT_INC(data->index);
-		} else {
-			/* otherwise, grab and reload the index */
-			if ((error = git_repository_index(&data->index, data->repo)) < 0 ||
-				(error = git_index_read(data->index)) < 0)
-				goto cleanup;
+		if (data->index != git_iterator_index(target)) {
+			if (data->opts.checkout_strategy & GIT_CHECKOUT_FORCE) {
+				/* When forcing, we can blindly re-read the index */
+				if ((error = git_index_read(data->index, false)) < 0)
+					goto cleanup;
+			} else {
+				/*
+				 * When not being forced, we need to check for unresolved
+				 * conflicts and unsaved changes in the index before
+				 * proceeding.
+				 */
+				if (git_index_has_conflicts(data->index)) {
+					error = GIT_ECONFLICT;
+					git_error_set(GIT_ERROR_CHECKOUT,
+						"unresolved conflicts exist in the index");
+					goto cleanup;
+				}
 
-			/* clear the REUC when doing a tree or commit checkout */
+				if ((error = git_index_read_safely(data->index)) < 0)
+					goto cleanup;
+			}
+
+			/* clean conflict data in the current index */
+			git_index_name_clear(data->index);
 			git_index_reuc_clear(data->index);
 		}
 	}
 
-	/* if you are forcing, definitely allow safe updates */
+	/* if you are forcing, allow all safe updates, plus recreate missing */
 	if ((data->opts.checkout_strategy & GIT_CHECKOUT_FORCE) != 0)
-		data->opts.checkout_strategy |= GIT_CHECKOUT_SAFE_CREATE;
-	if ((data->opts.checkout_strategy & GIT_CHECKOUT_SAFE_CREATE) != 0)
-		data->opts.checkout_strategy |= GIT_CHECKOUT_SAFE;
+		data->opts.checkout_strategy |= GIT_CHECKOUT_SAFE |
+			GIT_CHECKOUT_RECREATE_MISSING;
+
+	/* if the repository does not actually have an index file, then this
+	 * is an initial checkout (perhaps from clone), so we allow safe updates
+	 */
+	if (!data->index->on_disk &&
+		(data->opts.checkout_strategy & GIT_CHECKOUT_SAFE) != 0)
+		data->opts.checkout_strategy |= GIT_CHECKOUT_RECREATE_MISSING;
 
 	data->strategy = data->opts.checkout_strategy;
 
@@ -1230,27 +2467,67 @@ static int checkout_data_init(
 			 &data->can_symlink, repo, GIT_CVAR_SYMLINKS)) < 0)
 		goto cleanup;
 
-	if (!data->opts.baseline) {
+	if ((error = git_repository__cvar(
+			 &data->respect_filemode, repo, GIT_CVAR_FILEMODE)) < 0)
+		goto cleanup;
+
+	if (!data->opts.baseline && !data->opts.baseline_index) {
 		data->opts_free_baseline = true;
+		error = 0;
 
-		error = checkout_lookup_head_tree(&data->opts.baseline, repo);
+		/* if we don't have an index, this is an initial checkout and
+		 * should be against an empty baseline
+		 */
+		if (data->index->on_disk)
+			error = checkout_lookup_head_tree(&data->opts.baseline, repo);
 
-		if (error == GIT_EORPHANEDHEAD) {
+		if (error == GIT_EUNBORNBRANCH) {
 			error = 0;
-			giterr_clear();
+			git_error_clear();
 		}
 
 		if (error < 0)
 			goto cleanup;
 	}
 
+	if ((data->opts.checkout_strategy &
+		(GIT_CHECKOUT_CONFLICT_STYLE_MERGE | GIT_CHECKOUT_CONFLICT_STYLE_DIFF3)) == 0) {
+		git_config_entry *conflict_style = NULL;
+		git_config *cfg = NULL;
+
+		if ((error = git_repository_config__weakptr(&cfg, repo)) < 0 ||
+			(error = git_config_get_entry(&conflict_style, cfg, "merge.conflictstyle")) < 0 ||
+			error == GIT_ENOTFOUND)
+			;
+		else if (error)
+			goto cleanup;
+		else if (strcmp(conflict_style->value, "merge") == 0)
+			data->opts.checkout_strategy |= GIT_CHECKOUT_CONFLICT_STYLE_MERGE;
+		else if (strcmp(conflict_style->value, "diff3") == 0)
+			data->opts.checkout_strategy |= GIT_CHECKOUT_CONFLICT_STYLE_DIFF3;
+		else {
+			git_error_set(GIT_ERROR_CHECKOUT, "unknown style '%s' given for 'merge.conflictstyle'",
+				conflict_style->value);
+			error = -1;
+			git_config_entry_free(conflict_style);
+			goto cleanup;
+		}
+		git_config_entry_free(conflict_style);
+	}
+
+	git_pool_init(&data->pool, 1);
+
 	if ((error = git_vector_init(&data->removes, 0, git__strcmp_cb)) < 0 ||
-		(error = git_pool_init(&data->pool, 1, 0)) < 0 ||
-		(error = git_buf_puts(&data->path, data->opts.target_directory)) < 0 ||
-		(error = git_path_to_dir(&data->path)) < 0)
+		(error = git_vector_init(&data->remove_conflicts, 0, NULL)) < 0 ||
+		(error = git_vector_init(&data->update_conflicts, 0, NULL)) < 0 ||
+		(error = git_buf_puts(&data->target_path, data->opts.target_directory)) < 0 ||
+		(error = git_path_to_dir(&data->target_path)) < 0 ||
+		(error = git_strmap_alloc(&data->mkdir_map)) < 0)
 		goto cleanup;
 
-	data->workdir_len = git_buf_len(&data->path);
+	data->target_len = git_buf_len(&data->target_path);
+
+	git_attr_session__init(&data->attr_session, data->repo);
 
 cleanup:
 	if (error < 0)
@@ -1259,17 +2536,22 @@ cleanup:
 	return error;
 }
 
+#define CHECKOUT_INDEX_DONT_WRITE_MASK \
+	(GIT_CHECKOUT_DONT_UPDATE_INDEX | GIT_CHECKOUT_DONT_WRITE_INDEX)
+
 int git_checkout_iterator(
 	git_iterator *target,
-	git_checkout_opts *opts)
+	git_index *index,
+	const git_checkout_options *opts)
 {
 	int error = 0;
 	git_iterator *baseline = NULL, *workdir = NULL;
+	git_iterator_options baseline_opts = GIT_ITERATOR_OPTIONS_INIT,
+		workdir_opts = GIT_ITERATOR_OPTIONS_INIT;
 	checkout_data data = {0};
 	git_diff_options diff_opts = GIT_DIFF_OPTIONS_INIT;
 	uint32_t *actions = NULL;
 	size_t *counts = NULL;
-	git_iterator_flag_t iterflags = 0;
 
 	/* initialize structures and options */
 	error = checkout_data_init(&data, target, opts);
@@ -1278,12 +2560,14 @@ int git_checkout_iterator(
 
 	diff_opts.flags =
 		GIT_DIFF_INCLUDE_UNMODIFIED |
+		GIT_DIFF_INCLUDE_UNREADABLE |
 		GIT_DIFF_INCLUDE_UNTRACKED |
 		GIT_DIFF_RECURSE_UNTRACKED_DIRS | /* needed to match baseline */
 		GIT_DIFF_INCLUDE_IGNORED |
 		GIT_DIFF_INCLUDE_TYPECHANGE |
 		GIT_DIFF_INCLUDE_TYPECHANGE_TREES |
-		GIT_DIFF_SKIP_BINARY_CHECK;
+		GIT_DIFF_SKIP_BINARY_CHECK |
+		GIT_DIFF_INCLUDE_CASECHANGE;
 	if (data.opts.checkout_strategy & GIT_CHECKOUT_DISABLE_PATHSPEC_MATCH)
 		diff_opts.flags |= GIT_DIFF_DISABLE_PATHSPEC_MATCH;
 	if (data.opts.paths.count > 0)
@@ -1291,19 +2575,38 @@ int git_checkout_iterator(
 
 	/* set up iterators */
 
-	iterflags = git_iterator_ignore_case(target) ?
+	workdir_opts.flags = git_iterator_ignore_case(target) ?
 		GIT_ITERATOR_IGNORE_CASE : GIT_ITERATOR_DONT_IGNORE_CASE;
+	workdir_opts.flags |= GIT_ITERATOR_DONT_AUTOEXPAND;
+	workdir_opts.start = data.pfx;
+	workdir_opts.end = data.pfx;
 
-	if ((error = git_iterator_reset(target, data.pfx, data.pfx)) < 0 ||
+	if ((error = git_iterator_reset_range(target, data.pfx, data.pfx)) < 0 ||
 		(error = git_iterator_for_workdir_ext(
-			&workdir, data.repo, data.opts.target_directory,
-			iterflags | GIT_ITERATOR_DONT_AUTOEXPAND,
-			data.pfx, data.pfx)) < 0 ||
-		(error = git_iterator_for_tree(
-			&baseline, data.opts.baseline,
-			iterflags, data.pfx, data.pfx)) < 0)
+			&workdir, data.repo, data.opts.target_directory, index, NULL,
+			&workdir_opts)) < 0)
 		goto cleanup;
 
+	baseline_opts.flags = git_iterator_ignore_case(target) ?
+		GIT_ITERATOR_IGNORE_CASE : GIT_ITERATOR_DONT_IGNORE_CASE;
+	baseline_opts.start = data.pfx;
+	baseline_opts.end = data.pfx;
+	if (opts && (opts->checkout_strategy & GIT_CHECKOUT_DISABLE_PATHSPEC_MATCH)) {
+		baseline_opts.pathlist.count = opts->paths.count;
+		baseline_opts.pathlist.strings = opts->paths.strings;
+	}
+
+	if (data.opts.baseline_index) {
+		if ((error = git_iterator_for_index(
+				&baseline, git_index_owner(data.opts.baseline_index),
+				data.opts.baseline_index, &baseline_opts)) < 0)
+			goto cleanup;
+	} else {
+		if ((error = git_iterator_for_tree(
+				&baseline, data.opts.baseline, &baseline_opts)) < 0)
+			goto cleanup;
+	}
+
 	/* Should not have case insensitivity mismatch */
 	assert(git_iterator_ignore_case(workdir) == git_iterator_ignore_case(baseline));
 
@@ -1315,14 +2618,17 @@ int git_checkout_iterator(
 		goto cleanup;
 
 	/* Loop through diff (and working directory iterator) building a list of
-	 * actions to be taken, plus look for conflicts and send notifications.
+	 * actions to be taken, plus look for conflicts and send notifications,
+	 * then loop through conflicts.
 	 */
-	if ((error = checkout_get_actions(&actions, &counts, &data, workdir)) < 0)
+	if ((error = checkout_get_actions(&actions, &counts, &data, workdir)) != 0)
 		goto cleanup;
 
 	data.total_steps = counts[CHECKOUT_ACTION__REMOVE] +
+		counts[CHECKOUT_ACTION__REMOVE_CONFLICT] +
 		counts[CHECKOUT_ACTION__UPDATE_BLOB] +
-		counts[CHECKOUT_ACTION__UPDATE_SUBMODULE];
+		counts[CHECKOUT_ACTION__UPDATE_SUBMODULE] +
+		counts[CHECKOUT_ACTION__UPDATE_CONFLICT];
 
 	report_progress(&data, NULL); /* establish 0 baseline */
 
@@ -1333,6 +2639,10 @@ int git_checkout_iterator(
 		(error = checkout_remove_the_old(actions, &data)) < 0)
 		goto cleanup;
 
+	if (counts[CHECKOUT_ACTION__REMOVE_CONFLICT] > 0 &&
+		(error = checkout_remove_conflicts(&data)) < 0)
+		goto cleanup;
+
 	if (counts[CHECKOUT_ACTION__UPDATE_BLOB] > 0 &&
 		(error = checkout_create_the_new(actions, &data)) < 0)
 		goto cleanup;
@@ -1341,17 +2651,25 @@ int git_checkout_iterator(
 		(error = checkout_create_submodules(actions, &data)) < 0)
 		goto cleanup;
 
+	if (counts[CHECKOUT_ACTION__UPDATE_CONFLICT] > 0 &&
+		(error = checkout_create_conflicts(&data)) < 0)
+		goto cleanup;
+
+	if (data.index != git_iterator_index(target) &&
+		(error = checkout_extensions_update_index(&data)) < 0)
+		goto cleanup;
+
 	assert(data.completed_steps == data.total_steps);
 
-cleanup:
-	if (error == GIT_EUSER)
-		giterr_clear();
+	if (data.opts.perfdata_cb)
+		data.opts.perfdata_cb(&data.perfdata, data.opts.perfdata_payload);
 
+cleanup:
 	if (!error && data.index != NULL &&
-		(data.strategy & GIT_CHECKOUT_DONT_UPDATE_INDEX) == 0)
+		(data.strategy & CHECKOUT_INDEX_DONT_WRITE_MASK) == 0)
 		error = git_index_write(data.index);
 
-	git_diff_list_free(data.diff);
+	git_diff_free(data.diff);
 	git_iterator_free(workdir);
 	git_iterator_free(baseline);
 	git__free(actions);
@@ -1364,20 +2682,26 @@ cleanup:
 int git_checkout_index(
 	git_repository *repo,
 	git_index *index,
-	git_checkout_opts *opts)
+	const git_checkout_options *opts)
 {
-	int error;
+	int error, owned = 0;
 	git_iterator *index_i;
 
 	if (!index && !repo) {
-		giterr_set(GITERR_CHECKOUT,
-			"Must provide either repository or index to checkout");
+		git_error_set(GIT_ERROR_CHECKOUT,
+			"must provide either repository or index to checkout");
 		return -1;
 	}
-	if (index && repo && git_index_owner(index) != repo) {
-		giterr_set(GITERR_CHECKOUT,
-			"Index to checkout does not match repository");
+
+	if (index && repo &&
+		git_index_owner(index) &&
+		git_index_owner(index) != repo) {
+		git_error_set(GIT_ERROR_CHECKOUT,
+			"index to checkout does not match repository");
 		return -1;
+	} else if(index && repo && !git_index_owner(index)) {
+		GIT_REFCOUNT_OWN(index, repo);
+		owned = 1;
 	}
 
 	if (!repo)
@@ -1387,8 +2711,11 @@ int git_checkout_index(
 		return error;
 	GIT_REFCOUNT_INC(index);
 
-	if (!(error = git_iterator_for_index(&index_i, index, 0, NULL, NULL)))
-		error = git_checkout_iterator(index_i, opts);
+	if (!(error = git_iterator_for_index(&index_i, repo, index, NULL)))
+		error = git_checkout_iterator(index_i, index, opts);
+
+	if (owned)
+		GIT_REFCOUNT_OWN(index, NULL);
 
 	git_iterator_free(index_i);
 	git_index_free(index);
@@ -1399,36 +2726,58 @@ int git_checkout_index(
 int git_checkout_tree(
 	git_repository *repo,
 	const git_object *treeish,
-	git_checkout_opts *opts)
+	const git_checkout_options *opts)
 {
 	int error;
+	git_index *index;
 	git_tree *tree = NULL;
 	git_iterator *tree_i = NULL;
+	git_iterator_options iter_opts = GIT_ITERATOR_OPTIONS_INIT;
 
 	if (!treeish && !repo) {
-		giterr_set(GITERR_CHECKOUT,
-			"Must provide either repository or tree to checkout");
+		git_error_set(GIT_ERROR_CHECKOUT,
+			"must provide either repository or tree to checkout");
 		return -1;
 	}
 	if (treeish && repo && git_object_owner(treeish) != repo) {
-		giterr_set(GITERR_CHECKOUT,
-			"Object to checkout does not match repository");
+		git_error_set(GIT_ERROR_CHECKOUT,
+			"object to checkout does not match repository");
 		return -1;
 	}
 
 	if (!repo)
 		repo = git_object_owner(treeish);
 
-	if (git_object_peel((git_object **)&tree, treeish, GIT_OBJ_TREE) < 0) {
-		giterr_set(
-			GITERR_CHECKOUT, "Provided object cannot be peeled to a tree");
-		return -1;
+	if (treeish) {
+		if (git_object_peel((git_object **)&tree, treeish, GIT_OBJECT_TREE) < 0) {
+			git_error_set(
+				GIT_ERROR_CHECKOUT, "provided object cannot be peeled to a tree");
+			return -1;
+		}
+	}
+	else {
+		if ((error = checkout_lookup_head_tree(&tree, repo)) < 0) {
+			if (error != GIT_EUNBORNBRANCH)
+				git_error_set(
+					GIT_ERROR_CHECKOUT,
+					"HEAD could not be peeled to a tree and no treeish given");
+			return error;
+		}
+	}
+
+	if ((error = git_repository_index(&index, repo)) < 0)
+		return error;
+
+	if (opts && (opts->checkout_strategy & GIT_CHECKOUT_DISABLE_PATHSPEC_MATCH)) {
+		iter_opts.pathlist.count = opts->paths.count;
+		iter_opts.pathlist.strings = opts->paths.strings;
 	}
 
-	if (!(error = git_iterator_for_tree(&tree_i, tree, 0, NULL, NULL)))
-		error = git_checkout_iterator(tree_i, opts);
+	if (!(error = git_iterator_for_tree(&tree_i, tree, &iter_opts)))
+		error = git_checkout_iterator(tree_i, index, opts);
 
 	git_iterator_free(tree_i);
+	git_index_free(index);
 	git_tree_free(tree);
 
 	return error;
@@ -1436,20 +2785,15 @@ int git_checkout_tree(
 
 int git_checkout_head(
 	git_repository *repo,
-	git_checkout_opts *opts)
+	const git_checkout_options *opts)
 {
-	int error;
-	git_tree *head = NULL;
-	git_iterator *head_i = NULL;
-
 	assert(repo);
+	return git_checkout_tree(repo, NULL, opts);
+}
 
-	if (!(error = checkout_lookup_head_tree(&head, repo)) &&
-		!(error = git_iterator_for_tree(&head_i, head, 0, NULL, NULL)))
-		error = git_checkout_iterator(head_i, opts);
-
-	git_iterator_free(head_i);
-	git_tree_free(head);
-
-	return error;
+int git_checkout_init_options(git_checkout_options *opts, unsigned int version)
+{
+	GIT_INIT_STRUCTURE_FROM_TEMPLATE(
+		opts, version, git_checkout_options, GIT_CHECKOUT_OPTIONS_INIT);
+	return 0;
 }