Declare merge-ort ready for general usage

index 7f5750ce6ab0..60270feadc54 100644
@@ -1562,18 +1562,7 @@ static void get_provisional_directory_renames(struct merge_options *opt,
 				 "no destination getting a majority of the "
 				 "files."),
 			       source_dir);
-			/*
-			 * We should mark this as unclean IF something attempts
-			 * to use this rename.  We do not yet have the logic
-			 * in place to detect if this directory rename is being
-			 * used, and optimizations that reduce the number of
-			 * renames cause this to falsely trigger.  For now,
-			 * just disable it, causing t6423 testcase 2a to break.
-			 * We'll later fix the detection, and when we do we
-			 * will re-enable setting *clean to 0 (and thereby fix
-			 * t6423 testcase 2a).
-			 */
-			/*   *clean = 0;   */
+			*clean = 0;
 		} else {
 			strmap_put(&renames->dir_renames[side],
 				   source_dir, (void*)best);

index 7f5750ce6ab0..34a91c435737 100644
@@ -2405,7 +2405,7 @@ static int detect_and_process_renames(struct merge_options *opt,
 	clean &= collect_renames(opt, &combined, MERGE_SIDE2,
 				 &renames->dir_renames[1],
 				 &renames->dir_renames[2]);
-	QSORT(combined.queue, combined.nr, compare_pairs);
+	STABLE_QSORT(combined.queue, combined.nr, compare_pairs);
 	trace2_region_leave("merge", "directory renames", opt->repo);
 
 	trace2_region_enter("merge", "process renames", opt->repo);

@@ -2550,6 +2550,7 @@ static void write_tree(struct object_id *result_oid,
 	 */
 	relevant_entries.items = versions->items + offset;
 	relevant_entries.nr = versions->nr - offset;
+	/* No need for STABLE_QSORT -- filenames must be unique */
 	QSORT(relevant_entries.items, relevant_entries.nr, tree_entry_order);
 
 	/* Pre-allocate some space in buf */

@@ -3325,6 +3326,11 @@ static int record_conflicted_index_entries(struct merge_options *opt,
 	 * entries we added to the end into their right locations.
 	 */
 	remove_marked_cache_entries(index, 1);
+	/*
+	 * No need for STABLE_QSORT -- cmp_cache_name_compare sorts primarily
+	 * on filename and secondarily on stage, and (name, stage #) are a
+	 * unique tuple.
+	 */
 	QSORT(index->cache, index->cache_nr, cmp_cache_name_compare);
 
 	return errs;

index 34a91c435737..3c606fa7e4b3 100644
@@ -18,6 +18,7 @@
 #include "merge-ort.h"
 
 #include "alloc.h"
+#include "attr.h"
 #include "blob.h"
 #include "cache-tree.h"
 #include "commit.h"

@@ -220,6 +221,16 @@ struct merge_options_internal {
 	 */
 	struct rename_info renames;
 
+	/*
+	 * attr_index: hacky minimal index used for renormalization
+	 *
+	 * renormalization code _requires_ an index, though it only needs to
+	 * find a .gitattributes file within the index.  So, when
+	 * renormalization is important, we create a special index with just
+	 * that one file.
+	 */
+	struct index_state attr_index;
+
 	/*
 	 * current_dir_name, toplevel_dir: temporary vars
 	 *

@@ -399,6 +410,9 @@ static void clear_or_reinit_internal_opts(struct merge_options_internal *opti,
 	string_list_clear(&opti->paths_to_free, 0);
 	opti->paths_to_free.strdup_strings = 0;
 
+	if (opti->attr_index.cache_nr)
+		discard_index(&opti->attr_index);
+
 	/* Free memory used by various renames maps */
 	for (i = MERGE_SIDE1; i <= MERGE_SIDE2; ++i) {
 		strintmap_func(&renames->dirs_removed[i]);

@@ -3407,6 +3421,8 @@ void merge_finalize(struct merge_options *opt,
 {
 	struct merge_options_internal *opti = result->priv;
 
+	if (opt->renormalize)
+		git_attr_set_direction(GIT_ATTR_CHECKIN);
 	assert(opt->priv == NULL);
 
 	clear_or_reinit_internal_opts(opti, 0);

@@ -3482,6 +3498,10 @@ static void merge_start(struct merge_options *opt, struct merge_result *result)
 	/* Default to histogram diff.  Actually, just hardcode it...for now. */
 	opt->xdl_opts = DIFF_WITH_ALG(opt, HISTOGRAM_DIFF);
 
+	/* Handle attr direction stuff for renormalization */
+	if (opt->renormalize)
+		git_attr_set_direction(GIT_ATTR_CHECKOUT);
+
 	/* Initialization of opt->priv, our internal merge data */
 	trace2_region_enter("merge", "allocate/init", opt->repo);
 	if (opt->priv) {

index 3c606fa7e4b3..cdc1e2fe7a24 100644
@@ -410,7 +410,7 @@ static void clear_or_reinit_internal_opts(struct merge_options_internal *opti,
 	string_list_clear(&opti->paths_to_free, 0);
 	opti->paths_to_free.strdup_strings = 0;
 
-	if (opti->attr_index.cache_nr)
+	if (opti->attr_index.cache_nr) /* true iff opt->renormalize */
 		discard_index(&opti->attr_index);
 
 	/* Free memory used by various renames maps */

@@ -1201,6 +1201,63 @@ static int merge_submodule(struct merge_options *opt,
 	return 0;
 }
 
+static void initialize_attr_index(struct merge_options *opt)
+{
+	/*
+	 * The renormalize_buffer() functions require attributes, and
+	 * annoyingly those can only be read from the working tree or from
+	 * an index_state.  merge-ort doesn't have an index_state, so we
+	 * generate a fake one containing only attribute information.
+	 */
+	struct merged_info *mi;
+	struct index_state *attr_index = &opt->priv->attr_index;
+	struct cache_entry *ce;
+
+	attr_index->initialized = 1;
+
+	if (!opt->renormalize)
+		return;
+
+	mi = strmap_get(&opt->priv->paths, GITATTRIBUTES_FILE);
+	if (!mi)
+		return;
+
+	if (mi->clean) {
+		int len = strlen(GITATTRIBUTES_FILE);
+		ce = make_empty_cache_entry(attr_index, len);
+		ce->ce_mode = create_ce_mode(mi->result.mode);
+		ce->ce_flags = create_ce_flags(0);
+		ce->ce_namelen = len;
+		oidcpy(&ce->oid, &mi->result.oid);
+		memcpy(ce->name, GITATTRIBUTES_FILE, len);
+		add_index_entry(attr_index, ce,
+				ADD_CACHE_OK_TO_ADD | ADD_CACHE_OK_TO_REPLACE);
+		get_stream_filter(attr_index, GITATTRIBUTES_FILE, &ce->oid);
+	} else {
+		int stage, len;
+		struct conflict_info *ci;
+
+		ASSIGN_AND_VERIFY_CI(ci, mi);
+		for (stage = 0; stage < 3; stage++) {
+			unsigned stage_mask = (1 << stage);
+
+			if (!(ci->filemask & stage_mask))
+				continue;
+			len = strlen(GITATTRIBUTES_FILE);
+			ce = make_empty_cache_entry(attr_index, len);
+			ce->ce_mode = create_ce_mode(ci->stages[stage].mode);
+			ce->ce_flags = create_ce_flags(stage);
+			ce->ce_namelen = len;
+			oidcpy(&ce->oid, &ci->stages[stage].oid);
+			memcpy(ce->name, GITATTRIBUTES_FILE, len);
+			add_index_entry(attr_index, ce,
+					ADD_CACHE_OK_TO_ADD | ADD_CACHE_OK_TO_REPLACE);
+			get_stream_filter(attr_index, GITATTRIBUTES_FILE,
+					  &ce->oid);
+		}
+	}
+}
+
 static int merge_3way(struct merge_options *opt,
 		      const char *path,
 		      const struct object_id *o,

@@ -1215,6 +1272,9 @@ static int merge_3way(struct merge_options *opt,
 	char *base, *name1, *name2;
 	int merge_status;
 
+	if (!opt->priv->attr_index.initialized)
+		initialize_attr_index(opt);
+
 	ll_opts.renormalize = opt->renormalize;
 	ll_opts.extra_marker_size = extra_marker_size;
 	ll_opts.xdl_opts = opt->xdl_opts;

@@ -1253,7 +1313,7 @@ static int merge_3way(struct merge_options *opt,
 
 	merge_status = ll_merge(result_buf, path, &orig, base,
 				&src1, name1, &src2, name2,
-				opt->repo->index, &ll_opts);
+				&opt->priv->attr_index, &ll_opts);
 
 	free(base);
 	free(name1);

index cdc1e2fe7a24..c7083e3769aa 100644
@@ -2549,6 +2549,61 @@ static int string_list_df_name_compare(const char *one, const char *two)
 	return onelen - twolen;
 }
 
+static int read_oid_strbuf(struct merge_options *opt,
+			   const struct object_id *oid,
+			   struct strbuf *dst)
+{
+	void *buf;
+	enum object_type type;
+	unsigned long size;
+	buf = read_object_file(oid, &type, &size);
+	if (!buf)
+		return err(opt, _("cannot read object %s"), oid_to_hex(oid));
+	if (type != OBJ_BLOB) {
+		free(buf);
+		return err(opt, _("object %s is not a blob"), oid_to_hex(oid));
+	}
+	strbuf_attach(dst, buf, size, size + 1);
+	return 0;
+}
+
+static int blob_unchanged(struct merge_options *opt,
+			  const struct version_info *base,
+			  const struct version_info *side,
+			  const char *path)
+{
+	struct strbuf basebuf = STRBUF_INIT;
+	struct strbuf sidebuf = STRBUF_INIT;
+	int ret = 0; /* assume changed for safety */
+	const struct index_state *idx = &opt->priv->attr_index;
+
+	if (!idx->initialized)
+		initialize_attr_index(opt);
+
+	if (base->mode != side->mode)
+		return 0;
+	if (oideq(&base->oid, &side->oid))
+		return 1;
+
+	if (read_oid_strbuf(opt, &base->oid, &basebuf) ||
+	    read_oid_strbuf(opt, &side->oid, &sidebuf))
+		goto error_return;
+	/*
+	 * Note: binary | is used so that both renormalizations are
+	 * performed.  Comparison can be skipped if both files are
+	 * unchanged since their sha1s have already been compared.
+	 */
+	if (renormalize_buffer(idx, path, basebuf.buf, basebuf.len, &basebuf) |
+	    renormalize_buffer(idx, path, sidebuf.buf, sidebuf.len, &sidebuf))
+		ret = (basebuf.len == sidebuf.len &&
+		       !memcmp(basebuf.buf, sidebuf.buf, basebuf.len));
+
+error_return:
+	strbuf_release(&basebuf);
+	strbuf_release(&sidebuf);
+	return ret;
+}
+
 struct directory_versions {
 	/*
 	 * versions: list of (basename -> version_info)

@@ -3136,8 +3191,13 @@ static void process_entry(struct merge_options *opt,
 		modify_branch = (side == 1) ? opt->branch1 : opt->branch2;
 		delete_branch = (side == 1) ? opt->branch2 : opt->branch1;
 
-		if (ci->path_conflict &&
-		    oideq(&ci->stages[0].oid, &ci->stages[side].oid)) {
+		if (opt->renormalize &&
+		    blob_unchanged(opt, &ci->stages[0], &ci->stages[side],
+				   path)) {
+			ci->merged.is_null = 1;
+			ci->merged.clean = 1;
+		} else if (ci->path_conflict &&
+			   oideq(&ci->stages[0].oid, &ci->stages[side].oid)) {
 			/*
 			 * This came from a rename/delete; no action to take,
 			 * but avoid printing "modify/delete" conflict notice

index c7083e3769aa..c4fe234d8972 100644
@@ -3551,6 +3551,23 @@ void merge_finalize(struct merge_options *opt,
 
 /*** Function Grouping: helper functions for merge_incore_*() ***/
 
+static struct tree *shift_tree_object(struct repository *repo,
+				      struct tree *one, struct tree *two,
+				      const char *subtree_shift)
+{
+	struct object_id shifted;
+
+	if (!*subtree_shift) {
+		shift_tree(repo, &one->object.oid, &two->object.oid, &shifted, 0);
+	} else {
+		shift_tree_by(repo, &one->object.oid, &two->object.oid, &shifted,
+			      subtree_shift);
+	}
+	if (oideq(&two->object.oid, &shifted))
+		return two;
+	return lookup_tree(repo, &shifted);
+}
+
 static inline void set_commit_tree(struct commit *c, struct tree *t)
 {
 	c->maybe_tree = t;

@@ -3680,6 +3697,13 @@ static void merge_ort_nonrecursive_internal(struct merge_options *opt,
 {
 	struct object_id working_tree_oid;
 
+	if (opt->subtree_shift) {
+		side2 = shift_tree_object(opt->repo, side1, side2,
+					  opt->subtree_shift);
+		merge_base = shift_tree_object(opt->repo, side1, merge_base,
+					       opt->subtree_shift);
+	}
+
 	trace2_region_enter("merge", "collect_merge_info", opt->repo);
 	if (collect_merge_info(opt, merge_base, side1, side2) != 0) {
 		/*

index c4fe234d8972..303e89414274 100644
@@ -3369,23 +3369,27 @@ static int checkout(struct merge_options *opt,
 	return ret;
 }
 
-static int record_conflicted_index_entries(struct merge_options *opt,
-					   struct index_state *index,
-					   struct strmap *paths,
-					   struct strmap *conflicted)
+static int record_conflicted_index_entries(struct merge_options *opt)
 {
 	struct hashmap_iter iter;
 	struct strmap_entry *e;
+	struct index_state *index = opt->repo->index;
+	struct checkout state = CHECKOUT_INIT;
 	int errs = 0;
 	int original_cache_nr;
 
-	if (strmap_empty(conflicted))
+	if (strmap_empty(&opt->priv->conflicted))
 		return 0;
 
+	/* If any entries have skip_worktree set, we'll have to check 'em out */
+	state.force = 1;
+	state.quiet = 1;
+	state.refresh_cache = 1;
+	state.istate = index;
 	original_cache_nr = index->cache_nr;
 
 	/* Put every entry from paths into plist, then sort */
-	strmap_for_each_entry(conflicted, &iter, e) {
+	strmap_for_each_entry(&opt->priv->conflicted, &iter, e) {
 		const char *path = e->key;
 		struct conflict_info *ci = e->value;
 		int pos;

@@ -3426,9 +3430,23 @@ static int record_conflicted_index_entries(struct merge_options *opt,
 			 * the higher order stages.  Thus, we need override
 			 * the CE_SKIP_WORKTREE bit and manually write those
 			 * files to the working disk here.
-			 *
-			 * TODO: Implement this CE_SKIP_WORKTREE fixup.
 			 */
+			if (ce_skip_worktree(ce)) {
+				struct stat st;
+
+				if (!lstat(path, &st)) {
+					char *new_name = unique_path(&opt->priv->paths,
+								     path,
+								     "cruft");
+
+					path_msg(opt, path, 1,
+						 _("Note: %s not up to date and in way of checking out conflicted version; old copy renamed to %s"),
+						 path, new_name);
+					errs |= rename(path, new_name);
+					free(new_name);
+				}
+				errs |= checkout_entry(ce, &state, NULL, NULL);
+			}
 
 			/*
 			 * Mark this cache entry for removal and instead add

@@ -3478,8 +3496,6 @@ void merge_switch_to_result(struct merge_options *opt,
 {
 	assert(opt->priv == NULL);
 	if (result->clean >= 0 && update_worktree_and_index) {
-		struct merge_options_internal *opti = result->priv;
-
 		trace2_region_enter("merge", "checkout", opt->repo);
 		if (checkout(opt, head, result->tree)) {
 			/* failure to function */

@@ -3489,13 +3505,14 @@ void merge_switch_to_result(struct merge_options *opt,
 		trace2_region_leave("merge", "checkout", opt->repo);
 
 		trace2_region_enter("merge", "record_conflicted", opt->repo);
-		if (record_conflicted_index_entries(opt, opt->repo->index,
-						    &opti->paths,
-						    &opti->conflicted)) {
+		opt->priv = result->priv;
+		if (record_conflicted_index_entries(opt)) {
 			/* failure to function */
+			opt->priv = NULL;
 			result->clean = -1;
 			return;
 		}
+		opt->priv = NULL;
 		trace2_region_leave("merge", "record_conflicted", opt->repo);
 	}
 

index 9c9dae1eae32..b71a2de29dbe 100644
@@ -344,6 +344,7 @@ void remove_merge_branch_state(struct repository *r)
 	unlink(git_path_merge_rr(r));
 	unlink(git_path_merge_msg(r));
 	unlink(git_path_merge_mode(r));
+	unlink(git_path_auto_merge(r));
 	save_autostash(git_path_merge_autostash(r));
 }
 

index 840dbd7eb777..6c252d62758c 100644
@@ -737,6 +737,7 @@ static int finish_rebase(struct rebase_options *opts)
 	int ret = 0;
 
 	delete_ref(NULL, "REBASE_HEAD", NULL, REF_NO_DEREF);
+	unlink(git_path_auto_merge(the_repository));
 	apply_autostash(state_dir_path("autostash", opts));
 	close_object_store(the_repository->objects);
 	/*

index 303e89414274..e8f1a435f99a 100644
@@ -3496,6 +3496,9 @@ void merge_switch_to_result(struct merge_options *opt,
 {
 	assert(opt->priv == NULL);
 	if (result->clean >= 0 && update_worktree_and_index) {
+		const char *filename;
+		FILE *fp;
+
 		trace2_region_enter("merge", "checkout", opt->repo);
 		if (checkout(opt, head, result->tree)) {
 			/* failure to function */

@@ -3514,6 +3517,13 @@ void merge_switch_to_result(struct merge_options *opt,
 		}
 		opt->priv = NULL;
 		trace2_region_leave("merge", "record_conflicted", opt->repo);
+
+		trace2_region_enter("merge", "write_auto_merge", opt->repo);
+		filename = git_path_auto_merge(opt->repo);
+		fp = xfopen(filename, "w");
+		fprintf(fp, "%s\n", oid_to_hex(&result->tree->object.oid));
+		fclose(fp);
+		trace2_region_leave("merge", "write_auto_merge", opt->repo);
 	}
 
 	if (display_update_msgs) {

index 7b385e5eb282..9e883eb52446 100644
@@ -1534,5 +1534,6 @@ REPO_GIT_PATH_FUNC(merge_rr, "MERGE_RR")
 REPO_GIT_PATH_FUNC(merge_mode, "MERGE_MODE")
 REPO_GIT_PATH_FUNC(merge_head, "MERGE_HEAD")
 REPO_GIT_PATH_FUNC(merge_autostash, "MERGE_AUTOSTASH")
+REPO_GIT_PATH_FUNC(auto_merge, "AUTO_MERGE")
 REPO_GIT_PATH_FUNC(fetch_head, "FETCH_HEAD")
 REPO_GIT_PATH_FUNC(shallow, "shallow")

index e7e77da6aaa5..251c78d98000 100644
@@ -176,6 +176,7 @@ struct path_cache {
 	const char *merge_mode;
 	const char *merge_head;
 	const char *merge_autostash;
+	const char *auto_merge;
 	const char *fetch_head;
 	const char *shallow;
 };

@@ -191,6 +192,7 @@ const char *git_path_merge_rr(struct repository *r);
 const char *git_path_merge_mode(struct repository *r);
 const char *git_path_merge_head(struct repository *r);
 const char *git_path_merge_autostash(struct repository *r);
+const char *git_path_auto_merge(struct repository *r);
 const char *git_path_fetch_head(struct repository *r);
 const char *git_path_shallow(struct repository *r);
 

index d2332d3e1787..472cdd8c620d 100644
@@ -2096,6 +2096,7 @@ static int do_pick_commit(struct repository *r,
 		refs_delete_ref(get_main_ref_store(r), "", "CHERRY_PICK_HEAD",
 				NULL, 0);
 		unlink(git_path_merge_msg(r));
+		unlink(git_path_auto_merge(r));
 		fprintf(stderr,
 			_("dropping %s %s -- patch contents already upstream\n"),
 			oid_to_hex(&commit->object.oid), msg.subject);

@@ -2451,6 +2452,8 @@ void sequencer_post_commit_cleanup(struct repository *r, int verbose)
 		need_cleanup = 1;
 	}
 
+	unlink(git_path_auto_merge(r));
+
 	if (!need_cleanup)
 		return;
 

@@ -4111,6 +4114,7 @@ static int pick_commits(struct repository *r,
 			unlink(rebase_path_stopped_sha());
 			unlink(rebase_path_amend());
 			unlink(git_path_merge_head(r));
+			unlink(git_path_auto_merge(r));
 			delete_ref(NULL, "REBASE_HEAD", NULL, REF_NO_DEREF);
 
 			if (item->command == TODO_BREAK) {

@@ -4505,6 +4509,7 @@ static int commit_staged_changes(struct repository *r,
 		return error(_("could not commit staged changes."));
 	unlink(rebase_path_amend());
 	unlink(git_path_merge_head(r));
+	unlink(git_path_auto_merge(r));
 	if (final_fixup) {
 		unlink(rebase_path_fixup_msg());
 		unlink(rebase_path_squash_msg());

index b052974f191c..99a197597db5 100644
@@ -1075,6 +1075,11 @@ static int merge_3way(struct merge_options *opt,
 	read_mmblob(&src1, &a->oid);
 	read_mmblob(&src2, &b->oid);
 
+	/*
+	 * FIXME: Using a->path for normalization rules in ll_merge could be
+	 * wrong if we renamed from a->path to b->path.  We should use the
+	 * target path for where the file will be written.
+	 */
 	merge_status = ll_merge(result_buf, a->path, &orig, base,
 				&src1, name1, &src2, name2,
 				opt->repo->index, &ll_opts);

@@ -1154,6 +1159,8 @@ static void print_commit(struct commit *commit)
 	struct strbuf sb = STRBUF_INIT;
 	struct pretty_print_context ctx = {0};
 	ctx.date_mode.type = DATE_NORMAL;
+	/* FIXME: Merge this with output_commit_title() */
+	assert(!merge_remote_util(commit));
 	format_commit_message(commit, " %h: %m %s", &sb, &ctx);
 	fprintf(stderr, "%s\n", sb.buf);
 	strbuf_release(&sb);

@@ -1177,6 +1184,11 @@ static int merge_submodule(struct merge_options *opt,
 	int search = !opt->priv->call_depth;
 
 	/* store a in result in case we fail */
+	/* FIXME: This is the WRONG resolution for the recursive case when
+	 * we need to be careful to avoid accidentally matching either side.
+	 * Should probably use o instead there, much like we do for merging
+	 * binaries.
+	 */
 	oidcpy(result, a);
 
 	/* we can not handle deletion conflicts */

@@ -1301,6 +1313,13 @@ static int merge_mode_and_contents(struct merge_options *opt,
 
 	if ((S_IFMT & a->mode) != (S_IFMT & b->mode)) {
 		result->clean = 0;
+		/*
+		 * FIXME: This is a bad resolution for recursive case; for
+		 * the recursive case we want something that is unlikely to
+		 * accidentally match either side.  Also, while it makes
+		 * sense to prefer regular files over symlinks, it doesn't
+		 * make sense to prefer regular files over submodules.
+		 */
 		if (S_ISREG(a->mode)) {
 			result->blob.mode = a->mode;
 			oidcpy(&result->blob.oid, &a->oid);

@@ -1349,6 +1368,7 @@ static int merge_mode_and_contents(struct merge_options *opt,
 			free(result_buf.ptr);
 			if (ret)
 				return ret;
+			/* FIXME: bug, what if modes didn't match? */
 			result->clean = (merge_status == 0);
 		} else if (S_ISGITLINK(a->mode)) {
 			result->clean = merge_submodule(opt, &result->blob.oid,

@@ -2664,6 +2684,14 @@ static int process_renames(struct merge_options *opt,
 	struct string_list b_by_dst = STRING_LIST_INIT_NODUP;
 	const struct rename *sre;
 
+	/*
+	 * FIXME: As string-list.h notes, it's O(n^2) to build a sorted
+	 * string_list one-by-one, but O(n log n) to build it unsorted and
+	 * then sort it.  Note that as we build the list, we do not need to
+	 * check if the existing destination path is already in the list,
+	 * because the structure of diffcore_rename guarantees we won't
+	 * have duplicates.
+	 */
 	for (i = 0; i < a_renames->nr; i++) {
 		sre = a_renames->items[i].util;
 		string_list_insert(&a_by_dst, sre->pair->two->path)->util

@@ -3602,6 +3630,15 @@ static int merge_recursive_internal(struct merge_options *opt,
 			return err(opt, _("merge returned no commit"));
 	}
 
+	/*
+	 * FIXME: Since merge_recursive_internal() is only ever called by
+	 * places that ensure the index is loaded first
+	 * (e.g. builtin/merge.c, rebase/sequencer, etc.), in the common
+	 * case where the merge base was unique that means when we get here
+	 * we immediately discard the index and re-read it, which is a
+	 * complete waste of time.  We should only be discarding and
+	 * re-reading if we were forced to recurse.
+	 */
 	discard_index(opt->repo->index);
 	if (!opt->priv->call_depth)
 		repo_read_index(opt->repo);

index e8f1a435f99a..8258d3fd621e 100644
@@ -1636,18 +1636,7 @@ static void get_provisional_directory_renames(struct merge_options *opt,
 				 "no destination getting a majority of the "
 				 "files."),
 			       source_dir);
-			/*
-			 * We should mark this as unclean IF something attempts
-			 * to use this rename.  We do not yet have the logic
-			 * in place to detect if this directory rename is being
-			 * used, and optimizations that reduce the number of
-			 * renames cause this to falsely trigger.  For now,
-			 * just disable it, causing t6423 testcase 2a to break.
-			 * We'll later fix the detection, and when we do we
-			 * will re-enable setting *clean to 0 (and thereby fix
-			 * t6423 testcase 2a).
-			 */
-			/*   *clean = 0;   */
+			*clean = 0;
 		} else {
 			strmap_put(&renames->dir_renames[side],
 				   source_dir, (void*)best);

index 7f5750ce6ab0..34a91c435737 100644
@@ -2405,7 +2405,7 @@ static int detect_and_process_renames(struct merge_options *opt,
 	clean &= collect_renames(opt, &combined, MERGE_SIDE2,
 				 &renames->dir_renames[1],
 				 &renames->dir_renames[2]);
-	QSORT(combined.queue, combined.nr, compare_pairs);
+	STABLE_QSORT(combined.queue, combined.nr, compare_pairs);
 	trace2_region_leave("merge", "directory renames", opt->repo);
 
 	trace2_region_enter("merge", "process renames", opt->repo);

@@ -2550,6 +2550,7 @@ static void write_tree(struct object_id *result_oid,
 	 */
 	relevant_entries.items = versions->items + offset;
 	relevant_entries.nr = versions->nr - offset;
+	/* No need for STABLE_QSORT -- filenames must be unique */
 	QSORT(relevant_entries.items, relevant_entries.nr, tree_entry_order);
 
 	/* Pre-allocate some space in buf */

@@ -3325,6 +3326,11 @@ static int record_conflicted_index_entries(struct merge_options *opt,
 	 * entries we added to the end into their right locations.
 	 */
 	remove_marked_cache_entries(index, 1);
+	/*
+	 * No need for STABLE_QSORT -- cmp_cache_name_compare sorts primarily
+	 * on filename and secondarily on stage, and (name, stage #) are a
+	 * unique tuple.
+	 */
 	QSORT(index->cache, index->cache_nr, cmp_cache_name_compare);
 
 	return errs;

index 34a91c435737..3c606fa7e4b3 100644
@@ -18,6 +18,7 @@
 #include "merge-ort.h"
 
 #include "alloc.h"
+#include "attr.h"
 #include "blob.h"
 #include "cache-tree.h"
 #include "commit.h"

@@ -220,6 +221,16 @@ struct merge_options_internal {
 	 */
 	struct rename_info renames;
 
+	/*
+	 * attr_index: hacky minimal index used for renormalization
+	 *
+	 * renormalization code _requires_ an index, though it only needs to
+	 * find a .gitattributes file within the index.  So, when
+	 * renormalization is important, we create a special index with just
+	 * that one file.
+	 */
+	struct index_state attr_index;
+
 	/*
 	 * current_dir_name, toplevel_dir: temporary vars
 	 *

@@ -399,6 +410,9 @@ static void clear_or_reinit_internal_opts(struct merge_options_internal *opti,
 	string_list_clear(&opti->paths_to_free, 0);
 	opti->paths_to_free.strdup_strings = 0;
 
+	if (opti->attr_index.cache_nr)
+		discard_index(&opti->attr_index);
+
 	/* Free memory used by various renames maps */
 	for (i = MERGE_SIDE1; i <= MERGE_SIDE2; ++i) {
 		strintmap_func(&renames->dirs_removed[i]);

@@ -3407,6 +3421,8 @@ void merge_finalize(struct merge_options *opt,
 {
 	struct merge_options_internal *opti = result->priv;
 
+	if (opt->renormalize)
+		git_attr_set_direction(GIT_ATTR_CHECKIN);
 	assert(opt->priv == NULL);
 
 	clear_or_reinit_internal_opts(opti, 0);

@@ -3482,6 +3498,10 @@ static void merge_start(struct merge_options *opt, struct merge_result *result)
 	/* Default to histogram diff.  Actually, just hardcode it...for now. */
 	opt->xdl_opts = DIFF_WITH_ALG(opt, HISTOGRAM_DIFF);
 
+	/* Handle attr direction stuff for renormalization */
+	if (opt->renormalize)
+		git_attr_set_direction(GIT_ATTR_CHECKOUT);
+
 	/* Initialization of opt->priv, our internal merge data */
 	trace2_region_enter("merge", "allocate/init", opt->repo);
 	if (opt->priv) {

index 3c606fa7e4b3..cdc1e2fe7a24 100644
@@ -410,7 +410,7 @@ static void clear_or_reinit_internal_opts(struct merge_options_internal *opti,
 	string_list_clear(&opti->paths_to_free, 0);
 	opti->paths_to_free.strdup_strings = 0;
 
-	if (opti->attr_index.cache_nr)
+	if (opti->attr_index.cache_nr) /* true iff opt->renormalize */
 		discard_index(&opti->attr_index);
 
 	/* Free memory used by various renames maps */

@@ -1201,6 +1201,63 @@ static int merge_submodule(struct merge_options *opt,
 	return 0;
 }
 
+static void initialize_attr_index(struct merge_options *opt)
+{
+	/*
+	 * The renormalize_buffer() functions require attributes, and
+	 * annoyingly those can only be read from the working tree or from
+	 * an index_state.  merge-ort doesn't have an index_state, so we
+	 * generate a fake one containing only attribute information.
+	 */
+	struct merged_info *mi;
+	struct index_state *attr_index = &opt->priv->attr_index;
+	struct cache_entry *ce;
+
+	attr_index->initialized = 1;
+
+	if (!opt->renormalize)
+		return;
+
+	mi = strmap_get(&opt->priv->paths, GITATTRIBUTES_FILE);
+	if (!mi)
+		return;
+
+	if (mi->clean) {
+		int len = strlen(GITATTRIBUTES_FILE);
+		ce = make_empty_cache_entry(attr_index, len);
+		ce->ce_mode = create_ce_mode(mi->result.mode);
+		ce->ce_flags = create_ce_flags(0);
+		ce->ce_namelen = len;
+		oidcpy(&ce->oid, &mi->result.oid);
+		memcpy(ce->name, GITATTRIBUTES_FILE, len);
+		add_index_entry(attr_index, ce,
+				ADD_CACHE_OK_TO_ADD | ADD_CACHE_OK_TO_REPLACE);
+		get_stream_filter(attr_index, GITATTRIBUTES_FILE, &ce->oid);
+	} else {
+		int stage, len;
+		struct conflict_info *ci;
+
+		ASSIGN_AND_VERIFY_CI(ci, mi);
+		for (stage = 0; stage < 3; stage++) {
+			unsigned stage_mask = (1 << stage);
+
+			if (!(ci->filemask & stage_mask))
+				continue;
+			len = strlen(GITATTRIBUTES_FILE);
+			ce = make_empty_cache_entry(attr_index, len);
+			ce->ce_mode = create_ce_mode(ci->stages[stage].mode);
+			ce->ce_flags = create_ce_flags(stage);
+			ce->ce_namelen = len;
+			oidcpy(&ce->oid, &ci->stages[stage].oid);
+			memcpy(ce->name, GITATTRIBUTES_FILE, len);
+			add_index_entry(attr_index, ce,
+					ADD_CACHE_OK_TO_ADD | ADD_CACHE_OK_TO_REPLACE);
+			get_stream_filter(attr_index, GITATTRIBUTES_FILE,
+					  &ce->oid);
+		}
+	}
+}
+
 static int merge_3way(struct merge_options *opt,
 		      const char *path,
 		      const struct object_id *o,

@@ -1215,6 +1272,9 @@ static int merge_3way(struct merge_options *opt,
 	char *base, *name1, *name2;
 	int merge_status;
 
+	if (!opt->priv->attr_index.initialized)
+		initialize_attr_index(opt);
+
 	ll_opts.renormalize = opt->renormalize;
 	ll_opts.extra_marker_size = extra_marker_size;
 	ll_opts.xdl_opts = opt->xdl_opts;

@@ -1253,7 +1313,7 @@ static int merge_3way(struct merge_options *opt,
 
 	merge_status = ll_merge(result_buf, path, &orig, base,
 				&src1, name1, &src2, name2,
-				opt->repo->index, &ll_opts);
+				&opt->priv->attr_index, &ll_opts);
 
 	free(base);
 	free(name1);

index cdc1e2fe7a24..c7083e3769aa 100644
@@ -2549,6 +2549,61 @@ static int string_list_df_name_compare(const char *one, const char *two)
 	return onelen - twolen;
 }
 
+static int read_oid_strbuf(struct merge_options *opt,
+			   const struct object_id *oid,
+			   struct strbuf *dst)
+{
+	void *buf;
+	enum object_type type;
+	unsigned long size;
+	buf = read_object_file(oid, &type, &size);
+	if (!buf)
+		return err(opt, _("cannot read object %s"), oid_to_hex(oid));
+	if (type != OBJ_BLOB) {
+		free(buf);
+		return err(opt, _("object %s is not a blob"), oid_to_hex(oid));
+	}
+	strbuf_attach(dst, buf, size, size + 1);
+	return 0;
+}
+
+static int blob_unchanged(struct merge_options *opt,
+			  const struct version_info *base,
+			  const struct version_info *side,
+			  const char *path)
+{
+	struct strbuf basebuf = STRBUF_INIT;
+	struct strbuf sidebuf = STRBUF_INIT;
+	int ret = 0; /* assume changed for safety */
+	const struct index_state *idx = &opt->priv->attr_index;
+
+	if (!idx->initialized)
+		initialize_attr_index(opt);
+
+	if (base->mode != side->mode)
+		return 0;
+	if (oideq(&base->oid, &side->oid))
+		return 1;
+
+	if (read_oid_strbuf(opt, &base->oid, &basebuf) ||
+	    read_oid_strbuf(opt, &side->oid, &sidebuf))
+		goto error_return;
+	/*
+	 * Note: binary | is used so that both renormalizations are
+	 * performed.  Comparison can be skipped if both files are
+	 * unchanged since their sha1s have already been compared.
+	 */
+	if (renormalize_buffer(idx, path, basebuf.buf, basebuf.len, &basebuf) |
+	    renormalize_buffer(idx, path, sidebuf.buf, sidebuf.len, &sidebuf))
+		ret = (basebuf.len == sidebuf.len &&
+		       !memcmp(basebuf.buf, sidebuf.buf, basebuf.len));
+
+error_return:
+	strbuf_release(&basebuf);
+	strbuf_release(&sidebuf);
+	return ret;
+}
+
 struct directory_versions {
 	/*
 	 * versions: list of (basename -> version_info)

@@ -3136,8 +3191,13 @@ static void process_entry(struct merge_options *opt,
 		modify_branch = (side == 1) ? opt->branch1 : opt->branch2;
 		delete_branch = (side == 1) ? opt->branch2 : opt->branch1;
 
-		if (ci->path_conflict &&
-		    oideq(&ci->stages[0].oid, &ci->stages[side].oid)) {
+		if (opt->renormalize &&
+		    blob_unchanged(opt, &ci->stages[0], &ci->stages[side],
+				   path)) {
+			ci->merged.is_null = 1;
+			ci->merged.clean = 1;
+		} else if (ci->path_conflict &&
+			   oideq(&ci->stages[0].oid, &ci->stages[side].oid)) {
 			/*
 			 * This came from a rename/delete; no action to take,
 			 * but avoid printing "modify/delete" conflict notice

index c7083e3769aa..c4fe234d8972 100644
@@ -3551,6 +3551,23 @@ void merge_finalize(struct merge_options *opt,
 
 /*** Function Grouping: helper functions for merge_incore_*() ***/
 
+static struct tree *shift_tree_object(struct repository *repo,
+				      struct tree *one, struct tree *two,
+				      const char *subtree_shift)
+{
+	struct object_id shifted;
+
+	if (!*subtree_shift) {
+		shift_tree(repo, &one->object.oid, &two->object.oid, &shifted, 0);
+	} else {
+		shift_tree_by(repo, &one->object.oid, &two->object.oid, &shifted,
+			      subtree_shift);
+	}
+	if (oideq(&two->object.oid, &shifted))
+		return two;
+	return lookup_tree(repo, &shifted);
+}
+
 static inline void set_commit_tree(struct commit *c, struct tree *t)
 {
 	c->maybe_tree = t;

@@ -3680,6 +3697,13 @@ static void merge_ort_nonrecursive_internal(struct merge_options *opt,
 {
 	struct object_id working_tree_oid;
 
+	if (opt->subtree_shift) {
+		side2 = shift_tree_object(opt->repo, side1, side2,
+					  opt->subtree_shift);
+		merge_base = shift_tree_object(opt->repo, side1, merge_base,
+					       opt->subtree_shift);
+	}
+
 	trace2_region_enter("merge", "collect_merge_info", opt->repo);
 	if (collect_merge_info(opt, merge_base, side1, side2) != 0) {
 		/*

index c4fe234d8972..303e89414274 100644
@@ -3369,23 +3369,27 @@ static int checkout(struct merge_options *opt,
 	return ret;
 }
 
-static int record_conflicted_index_entries(struct merge_options *opt,
-					   struct index_state *index,
-					   struct strmap *paths,
-					   struct strmap *conflicted)
+static int record_conflicted_index_entries(struct merge_options *opt)
 {
 	struct hashmap_iter iter;
 	struct strmap_entry *e;
+	struct index_state *index = opt->repo->index;
+	struct checkout state = CHECKOUT_INIT;
 	int errs = 0;
 	int original_cache_nr;
 
-	if (strmap_empty(conflicted))
+	if (strmap_empty(&opt->priv->conflicted))
 		return 0;
 
+	/* If any entries have skip_worktree set, we'll have to check 'em out */
+	state.force = 1;
+	state.quiet = 1;
+	state.refresh_cache = 1;
+	state.istate = index;
 	original_cache_nr = index->cache_nr;
 
 	/* Put every entry from paths into plist, then sort */
-	strmap_for_each_entry(conflicted, &iter, e) {
+	strmap_for_each_entry(&opt->priv->conflicted, &iter, e) {
 		const char *path = e->key;
 		struct conflict_info *ci = e->value;
 		int pos;

@@ -3426,9 +3430,23 @@ static int record_conflicted_index_entries(struct merge_options *opt,
 			 * the higher order stages.  Thus, we need override
 			 * the CE_SKIP_WORKTREE bit and manually write those
 			 * files to the working disk here.
-			 *
-			 * TODO: Implement this CE_SKIP_WORKTREE fixup.
 			 */
+			if (ce_skip_worktree(ce)) {
+				struct stat st;
+
+				if (!lstat(path, &st)) {
+					char *new_name = unique_path(&opt->priv->paths,
+								     path,
+								     "cruft");
+
+					path_msg(opt, path, 1,
+						 _("Note: %s not up to date and in way of checking out conflicted version; old copy renamed to %s"),
+						 path, new_name);
+					errs |= rename(path, new_name);
+					free(new_name);
+				}
+				errs |= checkout_entry(ce, &state, NULL, NULL);
+			}
 
 			/*
 			 * Mark this cache entry for removal and instead add

@@ -3478,8 +3496,6 @@ void merge_switch_to_result(struct merge_options *opt,
 {
 	assert(opt->priv == NULL);
 	if (result->clean >= 0 && update_worktree_and_index) {
-		struct merge_options_internal *opti = result->priv;
-
 		trace2_region_enter("merge", "checkout", opt->repo);
 		if (checkout(opt, head, result->tree)) {
 			/* failure to function */

@@ -3489,13 +3505,14 @@ void merge_switch_to_result(struct merge_options *opt,
 		trace2_region_leave("merge", "checkout", opt->repo);
 
 		trace2_region_enter("merge", "record_conflicted", opt->repo);
-		if (record_conflicted_index_entries(opt, opt->repo->index,
-						    &opti->paths,
-						    &opti->conflicted)) {
+		opt->priv = result->priv;
+		if (record_conflicted_index_entries(opt)) {
 			/* failure to function */
+			opt->priv = NULL;
 			result->clean = -1;
 			return;
 		}
+		opt->priv = NULL;
 		trace2_region_leave("merge", "record_conflicted", opt->repo);
 	}
 

index 9c9dae1eae32..b71a2de29dbe 100644
@@ -344,6 +344,7 @@ void remove_merge_branch_state(struct repository *r)
 	unlink(git_path_merge_rr(r));
 	unlink(git_path_merge_msg(r));
 	unlink(git_path_merge_mode(r));
+	unlink(git_path_auto_merge(r));
 	save_autostash(git_path_merge_autostash(r));
 }
 

index 840dbd7eb777..6c252d62758c 100644
@@ -737,6 +737,7 @@ static int finish_rebase(struct rebase_options *opts)
 	int ret = 0;
 
 	delete_ref(NULL, "REBASE_HEAD", NULL, REF_NO_DEREF);
+	unlink(git_path_auto_merge(the_repository));
 	apply_autostash(state_dir_path("autostash", opts));
 	close_object_store(the_repository->objects);
 	/*

index 303e89414274..e8f1a435f99a 100644
@@ -3496,6 +3496,9 @@ void merge_switch_to_result(struct merge_options *opt,
 {
 	assert(opt->priv == NULL);
 	if (result->clean >= 0 && update_worktree_and_index) {
+		const char *filename;
+		FILE *fp;
+
 		trace2_region_enter("merge", "checkout", opt->repo);
 		if (checkout(opt, head, result->tree)) {
 			/* failure to function */

@@ -3514,6 +3517,13 @@ void merge_switch_to_result(struct merge_options *opt,
 		}
 		opt->priv = NULL;
 		trace2_region_leave("merge", "record_conflicted", opt->repo);
+
+		trace2_region_enter("merge", "write_auto_merge", opt->repo);
+		filename = git_path_auto_merge(opt->repo);
+		fp = xfopen(filename, "w");
+		fprintf(fp, "%s\n", oid_to_hex(&result->tree->object.oid));
+		fclose(fp);
+		trace2_region_leave("merge", "write_auto_merge", opt->repo);
 	}
 
 	if (display_update_msgs) {

index 7b385e5eb282..9e883eb52446 100644
@@ -1534,5 +1534,6 @@ REPO_GIT_PATH_FUNC(merge_rr, "MERGE_RR")
 REPO_GIT_PATH_FUNC(merge_mode, "MERGE_MODE")
 REPO_GIT_PATH_FUNC(merge_head, "MERGE_HEAD")
 REPO_GIT_PATH_FUNC(merge_autostash, "MERGE_AUTOSTASH")
+REPO_GIT_PATH_FUNC(auto_merge, "AUTO_MERGE")
 REPO_GIT_PATH_FUNC(fetch_head, "FETCH_HEAD")
 REPO_GIT_PATH_FUNC(shallow, "shallow")

index e7e77da6aaa5..251c78d98000 100644
@@ -176,6 +176,7 @@ struct path_cache {
 	const char *merge_mode;
 	const char *merge_head;
 	const char *merge_autostash;
+	const char *auto_merge;
 	const char *fetch_head;
 	const char *shallow;
 };

@@ -191,6 +192,7 @@ const char *git_path_merge_rr(struct repository *r);
 const char *git_path_merge_mode(struct repository *r);
 const char *git_path_merge_head(struct repository *r);
 const char *git_path_merge_autostash(struct repository *r);
+const char *git_path_auto_merge(struct repository *r);
 const char *git_path_fetch_head(struct repository *r);
 const char *git_path_shallow(struct repository *r);
 

index d2332d3e1787..472cdd8c620d 100644
@@ -2096,6 +2096,7 @@ static int do_pick_commit(struct repository *r,
 		refs_delete_ref(get_main_ref_store(r), "", "CHERRY_PICK_HEAD",
 				NULL, 0);
 		unlink(git_path_merge_msg(r));
+		unlink(git_path_auto_merge(r));
 		fprintf(stderr,
 			_("dropping %s %s -- patch contents already upstream\n"),
 			oid_to_hex(&commit->object.oid), msg.subject);

@@ -2451,6 +2452,8 @@ void sequencer_post_commit_cleanup(struct repository *r, int verbose)
 		need_cleanup = 1;
 	}
 
+	unlink(git_path_auto_merge(r));
+
 	if (!need_cleanup)
 		return;
 

@@ -4111,6 +4114,7 @@ static int pick_commits(struct repository *r,
 			unlink(rebase_path_stopped_sha());
 			unlink(rebase_path_amend());
 			unlink(git_path_merge_head(r));
+			unlink(git_path_auto_merge(r));
 			delete_ref(NULL, "REBASE_HEAD", NULL, REF_NO_DEREF);
 
 			if (item->command == TODO_BREAK) {

@@ -4505,6 +4509,7 @@ static int commit_staged_changes(struct repository *r,
 		return error(_("could not commit staged changes."));
 	unlink(rebase_path_amend());
 	unlink(git_path_merge_head(r));
+	unlink(git_path_auto_merge(r));
 	if (final_fixup) {
 		unlink(rebase_path_fixup_msg());
 		unlink(rebase_path_squash_msg());

index b052974f191c..99a197597db5 100644
@@ -1075,6 +1075,11 @@ static int merge_3way(struct merge_options *opt,
 	read_mmblob(&src1, &a->oid);
 	read_mmblob(&src2, &b->oid);
 
+	/*
+	 * FIXME: Using a->path for normalization rules in ll_merge could be
+	 * wrong if we renamed from a->path to b->path.  We should use the
+	 * target path for where the file will be written.
+	 */
 	merge_status = ll_merge(result_buf, a->path, &orig, base,
 				&src1, name1, &src2, name2,
 				opt->repo->index, &ll_opts);

@@ -1154,6 +1159,8 @@ static void print_commit(struct commit *commit)
 	struct strbuf sb = STRBUF_INIT;
 	struct pretty_print_context ctx = {0};
 	ctx.date_mode.type = DATE_NORMAL;
+	/* FIXME: Merge this with output_commit_title() */
+	assert(!merge_remote_util(commit));
 	format_commit_message(commit, " %h: %m %s", &sb, &ctx);
 	fprintf(stderr, "%s\n", sb.buf);
 	strbuf_release(&sb);

@@ -1177,6 +1184,11 @@ static int merge_submodule(struct merge_options *opt,
 	int search = !opt->priv->call_depth;
 
 	/* store a in result in case we fail */
+	/* FIXME: This is the WRONG resolution for the recursive case when
+	 * we need to be careful to avoid accidentally matching either side.
+	 * Should probably use o instead there, much like we do for merging
+	 * binaries.
+	 */
 	oidcpy(result, a);
 
 	/* we can not handle deletion conflicts */

@@ -1301,6 +1313,13 @@ static int merge_mode_and_contents(struct merge_options *opt,
 
 	if ((S_IFMT & a->mode) != (S_IFMT & b->mode)) {
 		result->clean = 0;
+		/*
+		 * FIXME: This is a bad resolution for recursive case; for
+		 * the recursive case we want something that is unlikely to
+		 * accidentally match either side.  Also, while it makes
+		 * sense to prefer regular files over symlinks, it doesn't
+		 * make sense to prefer regular files over submodules.
+		 */
 		if (S_ISREG(a->mode)) {
 			result->blob.mode = a->mode;
 			oidcpy(&result->blob.oid, &a->oid);

@@ -1349,6 +1368,7 @@ static int merge_mode_and_contents(struct merge_options *opt,
 			free(result_buf.ptr);
 			if (ret)
 				return ret;
+			/* FIXME: bug, what if modes didn't match? */
 			result->clean = (merge_status == 0);
 		} else if (S_ISGITLINK(a->mode)) {
 			result->clean = merge_submodule(opt, &result->blob.oid,

@@ -2664,6 +2684,14 @@ static int process_renames(struct merge_options *opt,
 	struct string_list b_by_dst = STRING_LIST_INIT_NODUP;
 	const struct rename *sre;
 
+	/*
+	 * FIXME: As string-list.h notes, it's O(n^2) to build a sorted
+	 * string_list one-by-one, but O(n log n) to build it unsorted and
+	 * then sort it.  Note that as we build the list, we do not need to
+	 * check if the existing destination path is already in the list,
+	 * because the structure of diffcore_rename guarantees we won't
+	 * have duplicates.
+	 */
 	for (i = 0; i < a_renames->nr; i++) {
 		sre = a_renames->items[i].util;
 		string_list_insert(&a_by_dst, sre->pair->two->path)->util

@@ -3602,6 +3630,15 @@ static int merge_recursive_internal(struct merge_options *opt,
 			return err(opt, _("merge returned no commit"));
 	}
 
+	/*
+	 * FIXME: Since merge_recursive_internal() is only ever called by
+	 * places that ensure the index is loaded first
+	 * (e.g. builtin/merge.c, rebase/sequencer, etc.), in the common
+	 * case where the merge base was unique that means when we get here
+	 * we immediately discard the index and re-read it, which is a
+	 * complete waste of time.  We should only be discarding and
+	 * re-reading if we were forced to recurse.
+	 */
 	discard_index(opt->repo->index);
 	if (!opt->priv->call_depth)
 		repo_read_index(opt->repo);

index e8f1a435f99a..8258d3fd621e 100644
@@ -1636,18 +1636,7 @@ static void get_provisional_directory_renames(struct merge_options *opt,
 				 "no destination getting a majority of the "
 				 "files."),
 			       source_dir);
-			/*
-			 * We should mark this as unclean IF something attempts
-			 * to use this rename.  We do not yet have the logic
-			 * in place to detect if this directory rename is being
-			 * used, and optimizations that reduce the number of
-			 * renames cause this to falsely trigger.  For now,
-			 * just disable it, causing t6423 testcase 2a to break.
-			 * We'll later fix the detection, and when we do we
-			 * will re-enable setting *clean to 0 (and thereby fix
-			 * t6423 testcase 2a).
-			 */
-			/*   *clean = 0;   */
+			*clean = 0;
 		} else {
 			strmap_put(&renames->dir_renames[side],
 				   source_dir, (void*)best);