1 files changed, 416 insertions, 297 deletions

diff --git a/merge-recursive.c b/merge-recursive.c
index acc2f64a4e..4851825aeb 100644
--- a/merge-recursive.c
+++ b/merge-recursive.c
@@ -146,7 +146,8 @@ static int err(struct merge_options *o, const char *err, ...)
 	return -1;
 }
 
-static struct tree *shift_tree_object(struct tree *one, struct tree *two,
+static struct tree *shift_tree_object(struct repository *repo,
+				      struct tree *one, struct tree *two,
 				      const char *subtree_shift)
 {
 	struct object_id shifted;
@@ -159,12 +160,14 @@ static struct tree *shift_tree_object(struct tree *one, struct tree *two,
 	}
 	if (oideq(&two->object.oid, &shifted))
 		return two;
-	return lookup_tree(the_repository, &shifted);
+	return lookup_tree(repo, &shifted);
 }
 
-static struct commit *make_virtual_commit(struct tree *tree, const char *comment)
+static struct commit *make_virtual_commit(struct repository *repo,
+					  struct tree *tree,
+					  const char *comment)
 {
-	struct commit *commit = alloc_commit_node(the_repository);
+	struct commit *commit = alloc_commit_node(repo);
 
 	set_merge_remote_desc(commit, comment, (struct object *)commit);
 	commit->maybe_tree = tree;
@@ -186,6 +189,7 @@ static int oid_eq(const struct object_id *a, const struct object_id *b)
 enum rename_type {
 	RENAME_NORMAL = 0,
 	RENAME_VIA_DIR,
+	RENAME_ADD,
 	RENAME_DELETE,
 	RENAME_ONE_FILE_TO_ONE,
 	RENAME_ONE_FILE_TO_TWO,
@@ -228,6 +232,7 @@ static inline void setup_rename_conflict_info(enum rename_type rename_type,
 					      struct stage_data *src_entry1,
 					      struct stage_data *src_entry2)
 {
+	int ostage1 = 0, ostage2;
 	struct rename_conflict_info *ci;
 
 	/*
@@ -264,18 +269,22 @@ static inline void setup_rename_conflict_info(enum rename_type rename_type,
 		dst_entry2->rename_conflict_info = ci;
 	}
 
-	if (rename_type == RENAME_TWO_FILES_TO_ONE) {
-		/*
-		 * For each rename, there could have been
-		 * modifications on the side of history where that
-		 * file was not renamed.
-		 */
-		int ostage1 = o->branch1 == branch1 ? 3 : 2;
-		int ostage2 = ostage1 ^ 1;
+	/*
+	 * For each rename, there could have been
+	 * modifications on the side of history where that
+	 * file was not renamed.
+	 */
+	if (rename_type == RENAME_ADD ||
+	    rename_type == RENAME_TWO_FILES_TO_ONE) {
+		ostage1 = o->branch1 == branch1 ? 3 : 2;
 
 		ci->ren1_other.path = pair1->one->path;
 		oidcpy(&ci->ren1_other.oid, &src_entry1->stages[ostage1].oid);
 		ci->ren1_other.mode = src_entry1->stages[ostage1].mode;
+	}
+
+	if (rename_type == RENAME_TWO_FILES_TO_ONE) {
+		ostage2 = ostage1 ^ 1;
 
 		ci->ren2_other.path = pair2->one->path;
 		oidcpy(&ci->ren2_other.oid, &src_entry2->stages[ostage2].oid);
@@ -337,22 +346,24 @@ static int add_cacheinfo(struct merge_options *o,
 			 unsigned int mode, const struct object_id *oid,
 			 const char *path, int stage, int refresh, int options)
 {
+	struct index_state *istate = o->repo->index;
 	struct cache_entry *ce;
 	int ret;
 
-	ce = make_cache_entry(&the_index, mode, oid ? oid : &null_oid, path, stage, 0);
+	ce = make_cache_entry(istate, mode, oid ? oid : &null_oid, path, stage, 0);
 	if (!ce)
 		return err(o, _("add_cacheinfo failed for path '%s'; merge aborting."), path);
 
-	ret = add_cache_entry(ce, options);
+	ret = add_index_entry(istate, ce, options);
 	if (refresh) {
 		struct cache_entry *nce;
 
-		nce = refresh_cache_entry(&the_index, ce, CE_MATCH_REFRESH | CE_MATCH_IGNORE_MISSING);
+		nce = refresh_cache_entry(istate, ce,
+					  CE_MATCH_REFRESH | CE_MATCH_IGNORE_MISSING);
 		if (!nce)
 			return err(o, _("add_cacheinfo failed to refresh for path '%s'; merge aborting."), path);
 		if (nce != ce)
-			ret = add_cache_entry(nce, options);
+			ret = add_index_entry(istate, nce, options);
 	}
 	return ret;
 }
@@ -380,7 +391,7 @@ static int unpack_trees_start(struct merge_options *o,
 	o->unpack_opts.merge = 1;
 	o->unpack_opts.head_idx = 2;
 	o->unpack_opts.fn = threeway_merge;
-	o->unpack_opts.src_index = &the_index;
+	o->unpack_opts.src_index = o->repo->index;
 	o->unpack_opts.dst_index = &tmp_index;
 	o->unpack_opts.aggressive = !merge_detect_rename(o);
 	setup_unpack_trees_porcelain(&o->unpack_opts, "merge");
@@ -390,16 +401,16 @@ static int unpack_trees_start(struct merge_options *o,
 	init_tree_desc_from_tree(t+2, merge);
 
 	rc = unpack_trees(3, t, &o->unpack_opts);
-	cache_tree_free(&active_cache_tree);
+	cache_tree_free(&o->repo->index->cache_tree);
 
 	/*
-	 * Update the_index to match the new results, AFTER saving a copy
+	 * Update o->repo->index to match the new results, AFTER saving a copy
 	 * in o->orig_index.  Update src_index to point to the saved copy.
 	 * (verify_uptodate() checks src_index, and the original index is
 	 * the one that had the necessary modification timestamps.)
 	 */
-	o->orig_index = the_index;
-	the_index = tmp_index;
+	o->orig_index = *o->repo->index;
+	*o->repo->index = tmp_index;
 	o->unpack_opts.src_index = &o->orig_index;
 
 	return rc;
@@ -414,12 +425,13 @@ static void unpack_trees_finish(struct merge_options *o)
 struct tree *write_tree_from_memory(struct merge_options *o)
 {
 	struct tree *result = NULL;
+	struct index_state *istate = o->repo->index;
 
-	if (unmerged_cache()) {
+	if (unmerged_index(istate)) {
 		int i;
 		fprintf(stderr, "BUG: There are unmerged index entries:\n");
-		for (i = 0; i < active_nr; i++) {
-			const struct cache_entry *ce = active_cache[i];
+		for (i = 0; i < istate->cache_nr; i++) {
+			const struct cache_entry *ce = istate->cache[i];
 			if (ce_stage(ce))
 				fprintf(stderr, "BUG: %d %.*s\n", ce_stage(ce),
 					(int)ce_namelen(ce), ce->name);
@@ -427,16 +439,16 @@ struct tree *write_tree_from_memory(struct merge_options *o)
 		BUG("unmerged index entries in merge-recursive.c");
 	}
 
-	if (!active_cache_tree)
-		active_cache_tree = cache_tree();
+	if (!istate->cache_tree)
+		istate->cache_tree = cache_tree();
 
-	if (!cache_tree_fully_valid(active_cache_tree) &&
-	    cache_tree_update(&the_index, 0) < 0) {
+	if (!cache_tree_fully_valid(istate->cache_tree) &&
+	    cache_tree_update(istate, 0) < 0) {
 		err(o, _("error building trees"));
 		return NULL;
 	}
 
-	result = lookup_tree(the_repository, &active_cache_tree->oid);
+	result = lookup_tree(o->repo, &istate->cache_tree->oid);
 
 	return result;
 }
@@ -463,7 +475,8 @@ static void get_files_dirs(struct merge_options *o, struct tree *tree)
 {
 	struct pathspec match_all;
 	memset(&match_all, 0, sizeof(match_all));
-	read_tree_recursive(tree, "", 0, 0, &match_all, save_files_dirs, o);
+	read_tree_recursive(the_repository, tree, "", 0, 0,
+			    &match_all, save_files_dirs, o);
 }
 
 static int get_tree_entry_if_blob(const struct object_id *tree,
@@ -506,17 +519,17 @@ static struct stage_data *insert_stage_data(const char *path,
  * Create a dictionary mapping file names to stage_data objects. The
  * dictionary contains one entry for every path with a non-zero stage entry.
  */
-static struct string_list *get_unmerged(void)
+static struct string_list *get_unmerged(struct index_state *istate)
 {
 	struct string_list *unmerged = xcalloc(1, sizeof(struct string_list));
 	int i;
 
 	unmerged->strdup_strings = 1;
 
-	for (i = 0; i < active_nr; i++) {
+	for (i = 0; i < istate->cache_nr; i++) {
 		struct string_list_item *item;
 		struct stage_data *e;
-		const struct cache_entry *ce = active_cache[i];
+		const struct cache_entry *ce = istate->cache[i];
 		if (!ce_stage(ce))
 			continue;
 
@@ -676,7 +689,7 @@ static int update_stages(struct merge_options *opt, const char *path,
 	int clear = 1;
 	int options = ADD_CACHE_OK_TO_ADD | ADD_CACHE_SKIP_DFCHECK;
 	if (clear)
-		if (remove_file_from_cache(path))
+		if (remove_file_from_index(opt->repo->index, path))
 			return -1;
 	if (o)
 		if (add_cacheinfo(opt, o->mode, &o->oid, path, 1, 0, options))
@@ -690,27 +703,6 @@ static int update_stages(struct merge_options *opt, const char *path,
 	return 0;
 }
 
-static int update_stages_for_stage_data(struct merge_options *opt,
-					const char *path,
-					const struct stage_data *stage_data)
-{
-	struct diff_filespec o, a, b;
-
-	o.mode = stage_data->stages[1].mode;
-	oidcpy(&o.oid, &stage_data->stages[1].oid);
-
-	a.mode = stage_data->stages[2].mode;
-	oidcpy(&a.oid, &stage_data->stages[2].oid);
-
-	b.mode = stage_data->stages[3].mode;
-	oidcpy(&b.oid, &stage_data->stages[3].oid);
-
-	return update_stages(opt, path,
-			     is_null_oid(&o.oid) ? NULL : &o,
-			     is_null_oid(&a.oid) ? NULL : &a,
-			     is_null_oid(&b.oid) ? NULL : &b);
-}
-
 static void update_entry(struct stage_data *entry,
 			 struct diff_filespec *o,
 			 struct diff_filespec *a,
@@ -732,13 +724,14 @@ static int remove_file(struct merge_options *o, int clean,
 	int update_working_directory = !o->call_depth && !no_wd;
 
 	if (update_cache) {
-		if (remove_file_from_cache(path))
+		if (remove_file_from_index(o->repo->index, path))
 			return -1;
 	}
 	if (update_working_directory) {
 		if (ignore_case) {
 			struct cache_entry *ce;
-			ce = cache_file_exists(path, strlen(path), ignore_case);
+			ce = index_file_exists(o->repo->index, path, strlen(path),
+					       ignore_case);
 			if (ce && ce_stage(ce) == 0 && strcmp(path, ce->name))
 				return 0;
 		}
@@ -788,7 +781,8 @@ static char *unique_path(struct merge_options *o, const char *path, const char *
  * check the working directory.  If empty_ok is non-zero, also return
  * 0 in the case where the working-tree dir exists but is empty.
  */
-static int dir_in_way(const char *path, int check_working_copy, int empty_ok)
+static int dir_in_way(struct index_state *istate, const char *path,
+		      int check_working_copy, int empty_ok)
 {
 	int pos;
 	struct strbuf dirpath = STRBUF_INIT;
@@ -797,12 +791,12 @@ static int dir_in_way(const char *path, int check_working_copy, int empty_ok)
 	strbuf_addstr(&dirpath, path);
 	strbuf_addch(&dirpath, '/');
 
-	pos = cache_name_pos(dirpath.buf, dirpath.len);
+	pos = index_name_pos(istate, dirpath.buf, dirpath.len);
 
 	if (pos < 0)
 		pos = -1 - pos;
-	if (pos < active_nr &&
-	    !strncmp(dirpath.buf, active_cache[pos]->name, dirpath.len)) {
+	if (pos < istate->cache_nr &&
+	    !strncmp(dirpath.buf, istate->cache[pos]->name, dirpath.len)) {
 		strbuf_release(&dirpath);
 		return 1;
 	}
@@ -845,8 +839,10 @@ static int was_tracked(struct merge_options *o, const char *path)
 	return 0;
 }
 
-static int would_lose_untracked(const char *path)
+static int would_lose_untracked(struct merge_options *o, const char *path)
 {
+	struct index_state *istate = o->repo->index;
+
 	/*
 	 * This may look like it can be simplified to:
 	 *   return !was_tracked(o, path) && file_exists(path)
@@ -864,19 +860,19 @@ static int would_lose_untracked(const char *path)
 	 * update_file()/would_lose_untracked(); see every comment in this
 	 * file which mentions "update_stages".
 	 */
-	int pos = cache_name_pos(path, strlen(path));
+	int pos = index_name_pos(istate, path, strlen(path));
 
 	if (pos < 0)
 		pos = -1 - pos;
-	while (pos < active_nr &&
-	       !strcmp(path, active_cache[pos]->name)) {
+	while (pos < istate->cache_nr &&
+	       !strcmp(path, istate->cache[pos]->name)) {
 		/*
 		 * If stage #0, it is definitely tracked.
 		 * If it has stage #2 then it was tracked
 		 * before this merge started.  All other
 		 * cases the path was not tracked.
 		 */
-		switch (ce_stage(active_cache[pos])) {
+		switch (ce_stage(istate->cache[pos])) {
 		case 0:
 		case 2:
 			return 0;
@@ -936,7 +932,7 @@ static int make_room_for_path(struct merge_options *o, const char *path)
 	 * Do not unlink a file in the work tree if we are not
 	 * tracking it.
 	 */
-	if (would_lose_untracked(path))
+	if (would_lose_untracked(o, path))
 		return err(o, _("refusing to lose untracked file at '%s'"),
 			   path);
 
@@ -986,7 +982,7 @@ static int update_file_flags(struct merge_options *o,
 		}
 		if (S_ISREG(mode)) {
 			struct strbuf strbuf = STRBUF_INIT;
-			if (convert_to_working_tree(&the_index, path, buf, size, &strbuf)) {
+			if (convert_to_working_tree(o->repo->index, path, buf, size, &strbuf)) {
 				free(buf);
 				size = strbuf.len;
 				buf = strbuf_detach(&strbuf, NULL);
@@ -1058,7 +1054,8 @@ static int merge_3way(struct merge_options *o,
 		      const struct diff_filespec *a,
 		      const struct diff_filespec *b,
 		      const char *branch1,
-		      const char *branch2)
+		      const char *branch2,
+		      const int extra_marker_size)
 {
 	mmfile_t orig, src1, src2;
 	struct ll_merge_options ll_opts = {0};
@@ -1066,6 +1063,7 @@ static int merge_3way(struct merge_options *o,
 	int merge_status;
 
 	ll_opts.renormalize = o->renormalize;
+	ll_opts.extra_marker_size = extra_marker_size;
 	ll_opts.xdl_opts = o->xdl_opts;
 
 	if (o->call_depth) {
@@ -1104,7 +1102,7 @@ static int merge_3way(struct merge_options *o,
 
 	merge_status = ll_merge(result_buf, a->path, &orig, base_name,
 				&src1, name1, &src2, name2,
-				&the_index, &ll_opts);
+				o->repo->index, &ll_opts);
 
 	free(base_name);
 	free(name1);
@@ -1115,7 +1113,8 @@ static int merge_3way(struct merge_options *o,
 	return merge_status;
 }
 
-static int find_first_merges(struct object_array *result, const char *path,
+static int find_first_merges(struct repository *repo,
+			     struct object_array *result, const char *path,
 			     struct commit *a, struct commit *b)
 {
 	int i, j;
@@ -1135,7 +1134,7 @@ static int find_first_merges(struct object_array *result, const char *path,
 	/* get all revisions that merge commit a */
 	xsnprintf(merged_revision, sizeof(merged_revision), "^%s",
 		  oid_to_hex(&a->object.oid));
-	repo_init_revisions(the_repository, &revs, NULL);
+	repo_init_revisions(repo, &revs, NULL);
 	rev_opts.submodule = path;
 	/* FIXME: can't handle linked worktrees in submodules yet */
 	revs.single_worktree = path != NULL;
@@ -1213,9 +1212,9 @@ static int merge_submodule(struct merge_options *o,
 		return 0;
 	}
 
-	if (!(commit_base = lookup_commit_reference(the_repository, base)) ||
-	    !(commit_a = lookup_commit_reference(the_repository, a)) ||
-	    !(commit_b = lookup_commit_reference(the_repository, b))) {
+	if (!(commit_base = lookup_commit_reference(o->repo, base)) ||
+	    !(commit_a = lookup_commit_reference(o->repo, a)) ||
+	    !(commit_b = lookup_commit_reference(o->repo, b))) {
 		output(o, 1, _("Failed to merge submodule %s (commits not present)"), path);
 		return 0;
 	}
@@ -1265,7 +1264,8 @@ static int merge_submodule(struct merge_options *o,
 		return 0;
 
 	/* find commit which merges them */
-	parent_count = find_first_merges(&merges, path, commit_a, commit_b);
+	parent_count = find_first_merges(o->repo, &merges, path,
+					 commit_a, commit_b);
 	switch (parent_count) {
 	case 0:
 		output(o, 1, _("Failed to merge submodule %s (merge following commits not found)"), path);
@@ -1301,6 +1301,7 @@ static int merge_mode_and_contents(struct merge_options *o,
 				   const char *filename,
 				   const char *branch1,
 				   const char *branch2,
+				   const int extra_marker_size,
 				   struct merge_file_info *result)
 {
 	if (o->branch1 != branch1) {
@@ -1311,7 +1312,8 @@ static int merge_mode_and_contents(struct merge_options *o,
 		 */
 		return merge_mode_and_contents(o, one, b, a,
 					       filename,
-					       branch2, branch1, result);
+					       branch2, branch1,
+					       extra_marker_size, result);
 	}
 
 	result->merge = 0;
@@ -1352,7 +1354,8 @@ static int merge_mode_and_contents(struct merge_options *o,
 			int ret = 0, merge_status;
 
 			merge_status = merge_3way(o, &result_buf, one, a, b,
-						  branch1, branch2);
+						  branch1, branch2,
+						  extra_marker_size);
 
 			if ((merge_status < 0) || !result_buf.ptr)
 				ret = err(o, _("Failed to execute internal merge"));
@@ -1410,7 +1413,7 @@ static int handle_rename_via_dir(struct merge_options *o,
 	 */
 	const struct diff_filespec *dest = pair->two;
 
-	if (!o->call_depth && would_lose_untracked(dest->path)) {
+	if (!o->call_depth && would_lose_untracked(o, dest->path)) {
 		char *alt_path = unique_path(o, dest->path, rename_branch);
 
 		output(o, 1, _("Error: Refusing to lose untracked file at %s; "
@@ -1448,8 +1451,8 @@ static int handle_change_delete(struct merge_options *o,
 	const char *update_path = path;
 	int ret = 0;
 
-	if (dir_in_way(path, !o->call_depth, 0) ||
-	    (!o->call_depth && would_lose_untracked(path))) {
+	if (dir_in_way(o->repo->index, path, !o->call_depth, 0) ||
+	    (!o->call_depth && would_lose_untracked(o, path))) {
 		update_path = alt_path = unique_path(o, path, change_branch);
 	}
 
@@ -1459,7 +1462,7 @@ static int handle_change_delete(struct merge_options *o,
 		 * correct; since there is no true "middle point" between
 		 * them, simply reuse the base version for virtual merge base.
 		 */
-		ret = remove_file_from_cache(path);
+		ret = remove_file_from_index(o->repo->index, path);
 		if (!ret)
 			ret = update_file(o, 0, o_oid, o_mode, update_path);
 	} else {
@@ -1535,7 +1538,7 @@ static int handle_rename_delete(struct merge_options *o,
 		return -1;
 
 	if (o->call_depth)
-		return remove_file_from_cache(dest->path);
+		return remove_file_from_index(o->repo->index, dest->path);
 	else
 		return update_stages(o, dest->path, NULL,
 				     rename_branch == o->branch1 ? dest : NULL,
@@ -1555,80 +1558,203 @@ static struct diff_filespec *filespec_from_entry(struct diff_filespec *target,
 	return target;
 }
 
-static int handle_file(struct merge_options *o,
-			struct diff_filespec *rename,
-			int stage,
-			struct rename_conflict_info *ci)
+static int handle_file_collision(struct merge_options *o,
+				 const char *collide_path,
+				 const char *prev_path1,
+				 const char *prev_path2,
+				 const char *branch1, const char *branch2,
+				 const struct object_id *a_oid,
+				 unsigned int a_mode,
+				 const struct object_id *b_oid,
+				 unsigned int b_mode)
 {
-	char *dst_name = rename->path;
-	struct stage_data *dst_entry;
-	const char *cur_branch, *other_branch;
-	struct diff_filespec other;
-	struct diff_filespec *add;
-	int ret;
+	struct merge_file_info mfi;
+	struct diff_filespec null, a, b;
+	char *alt_path = NULL;
+	const char *update_path = collide_path;
 
-	if (stage == 2) {
-		dst_entry = ci->dst_entry1;
-		cur_branch = ci->branch1;
-		other_branch = ci->branch2;
-	} else {
-		dst_entry = ci->dst_entry2;
-		cur_branch = ci->branch2;
-		other_branch = ci->branch1;
+	/*
+	 * It's easiest to get the correct things into stage 2 and 3, and
+	 * to make sure that the content merge puts HEAD before the other
+	 * branch if we just ensure that branch1 == o->branch1.  So, simply
+	 * flip arguments around if we don't have that.
+	 */
+	if (branch1 != o->branch1) {
+		return handle_file_collision(o, collide_path,
+					     prev_path2, prev_path1,
+					     branch2, branch1,
+					     b_oid, b_mode,
+					     a_oid, a_mode);
 	}
 
-	add = filespec_from_entry(&other, dst_entry, stage ^ 1);
-	if (add) {
-		int ren_src_was_dirty = was_dirty(o, rename->path);
-		char *add_name = unique_path(o, rename->path, other_branch);
-		if (update_file(o, 0, &add->oid, add->mode, add_name))
-			return -1;
+	/*
+	 * In the recursive case, we just opt to undo renames
+	 */
+	if (o->call_depth && (prev_path1 || prev_path2)) {
+		/* Put first file (a_oid, a_mode) in its original spot */
+		if (prev_path1) {
+			if (update_file(o, 1, a_oid, a_mode, prev_path1))
+				return -1;
+		} else {
+			if (update_file(o, 1, a_oid, a_mode, collide_path))
+				return -1;
+		}
 
-		if (ren_src_was_dirty) {
-			output(o, 1, _("Refusing to lose dirty file at %s"),
-			       rename->path);
+		/* Put second file (b_oid, b_mode) in its original spot */
+		if (prev_path2) {
+			if (update_file(o, 1, b_oid, b_mode, prev_path2))
+				return -1;
+		} else {
+			if (update_file(o, 1, b_oid, b_mode, collide_path))
+				return -1;
 		}
+
+		/* Don't leave something at collision path if unrenaming both */
+		if (prev_path1 && prev_path2)
+			remove_file(o, 1, collide_path, 0);
+
+		return 0;
+	}
+
+	/* Remove rename sources if rename/add or rename/rename(2to1) */
+	if (prev_path1)
+		remove_file(o, 1, prev_path1,
+			    o->call_depth || would_lose_untracked(o, prev_path1));
+	if (prev_path2)
+		remove_file(o, 1, prev_path2,
+			    o->call_depth || would_lose_untracked(o, prev_path2));
+
+	/*
+	 * Remove the collision path, if it wouldn't cause dirty contents
+	 * or an untracked file to get lost.  We'll either overwrite with
+	 * merged contents, or just write out to differently named files.
+	 */
+	if (was_dirty(o, collide_path)) {
+		output(o, 1, _("Refusing to lose dirty file at %s"),
+		       collide_path);
+		update_path = alt_path = unique_path(o, collide_path, "merged");
+	} else if (would_lose_untracked(o, collide_path)) {
 		/*
-		 * Because the double negatives somehow keep confusing me...
-		 *    1) update_wd iff !ren_src_was_dirty.
-		 *    2) no_wd iff !update_wd
-		 *    3) so, no_wd == !!ren_src_was_dirty == ren_src_was_dirty
+		 * Only way we get here is if both renames were from
+		 * a directory rename AND user had an untracked file
+		 * at the location where both files end up after the
+		 * two directory renames.  See testcase 10d of t6043.
 		 */
-		remove_file(o, 0, rename->path, ren_src_was_dirty);
-		dst_name = unique_path(o, rename->path, cur_branch);
+		output(o, 1, _("Refusing to lose untracked file at "
+			       "%s, even though it's in the way."),
+		       collide_path);
+		update_path = alt_path = unique_path(o, collide_path, "merged");
 	} else {
-		if (dir_in_way(rename->path, !o->call_depth, 0)) {
-			dst_name = unique_path(o, rename->path, cur_branch);
-			output(o, 1, _("%s is a directory in %s adding as %s instead"),
-			       rename->path, other_branch, dst_name);
-		} else if (!o->call_depth &&
-			   would_lose_untracked(rename->path)) {
-			dst_name = unique_path(o, rename->path, cur_branch);
-			output(o, 1, _("Refusing to lose untracked file at %s; "
-				       "adding as %s instead"),
-			       rename->path, dst_name);
-		}
+		/*
+		 * FIXME: It's possible that the two files are identical
+		 * and that the current working copy happens to match, in
+		 * which case we are unnecessarily touching the working
+		 * tree file.  It's not a likely enough scenario that I
+		 * want to code up the checks for it and a better fix is
+		 * available if we restructure how unpack_trees() and
+		 * merge-recursive interoperate anyway, so punting for
+		 * now...
+		 */
+		remove_file(o, 0, collide_path, 0);
 	}
-	if ((ret = update_file(o, 0, &rename->oid, rename->mode, dst_name)))
-		; /* fall through, do allow dst_name to be released */
-	else if (stage == 2)
-		ret = update_stages(o, rename->path, NULL, rename, add);
-	else
-		ret = update_stages(o, rename->path, NULL, add, rename);
 
-	if (dst_name != rename->path)
-		free(dst_name);
+	/* Store things in diff_filespecs for functions that need it */
+	memset(&a, 0, sizeof(struct diff_filespec));
+	memset(&b, 0, sizeof(struct diff_filespec));
+	null.path = a.path = b.path = (char *)collide_path;
+	oidcpy(&null.oid, &null_oid);
+	null.mode = 0;
+	oidcpy(&a.oid, a_oid);
+	a.mode = a_mode;
+	a.oid_valid = 1;
+	oidcpy(&b.oid, b_oid);
+	b.mode = b_mode;
+	b.oid_valid = 1;
 
-	return ret;
+	if (merge_mode_and_contents(o, &null, &a, &b, collide_path,
+				    branch1, branch2, o->call_depth * 2, &mfi))
+		return -1;
+	mfi.clean &= !alt_path;
+	if (update_file(o, mfi.clean, &mfi.oid, mfi.mode, update_path))
+		return -1;
+	if (!mfi.clean && !o->call_depth &&
+	    update_stages(o, collide_path, NULL, &a, &b))
+		return -1;
+	free(alt_path);
+	/*
+	 * FIXME: If both a & b both started with conflicts (only possible
+	 * if they came from a rename/rename(2to1)), but had IDENTICAL
+	 * contents including those conflicts, then in the next line we claim
+	 * it was clean.  If someone cares about this case, we should have the
+	 * caller notify us if we started with conflicts.
+	 */
+	return mfi.clean;
+}
+
+static int handle_rename_add(struct merge_options *o,
+			     struct rename_conflict_info *ci)
+{
+	/* a was renamed to c, and a separate c was added. */
+	struct diff_filespec *a = ci->pair1->one;
+	struct diff_filespec *c = ci->pair1->two;
+	char *path = c->path;
+	char *prev_path_desc;
+	struct merge_file_info mfi;
+
+	int other_stage = (ci->branch1 == o->branch1 ? 3 : 2);
+
+	output(o, 1, _("CONFLICT (rename/add): "
+	       "Rename %s->%s in %s.  Added %s in %s"),
+	       a->path, c->path, ci->branch1,
+	       c->path, ci->branch2);
+
+	prev_path_desc = xstrfmt("version of %s from %s", path, a->path);
+	if (merge_mode_and_contents(o, a, c, &ci->ren1_other, prev_path_desc,
+				    o->branch1, o->branch2,
+				    1 + o->call_depth * 2, &mfi))
+		return -1;
+	free(prev_path_desc);
+
+	return handle_file_collision(o,
+				     c->path, a->path, NULL,
+				     ci->branch1, ci->branch2,
+				     &mfi.oid, mfi.mode,
+				     &ci->dst_entry1->stages[other_stage].oid,
+				     ci->dst_entry1->stages[other_stage].mode);
+}
+
+static char *find_path_for_conflict(struct merge_options *o,
+				    const char *path,
+				    const char *branch1,
+				    const char *branch2)
+{
+	char *new_path = NULL;
+	if (dir_in_way(o->repo->index, path, !o->call_depth, 0)) {
+		new_path = unique_path(o, path, branch1);
+		output(o, 1, _("%s is a directory in %s adding "
+			       "as %s instead"),
+		       path, branch2, new_path);
+	} else if (would_lose_untracked(o, path)) {
+		new_path = unique_path(o, path, branch1);
+		output(o, 1, _("Refusing to lose untracked file"
+			       " at %s; adding as %s instead"),
+		       path, new_path);
+	}
+
+	return new_path;
 }
 
 static int handle_rename_rename_1to2(struct merge_options *o,
 				     struct rename_conflict_info *ci)
 {
 	/* One file was renamed in both branches, but to different names. */
+	struct merge_file_info mfi;
+	struct diff_filespec other;
+	struct diff_filespec *add;
 	struct diff_filespec *one = ci->pair1->one;
 	struct diff_filespec *a = ci->pair1->two;
 	struct diff_filespec *b = ci->pair2->two;
+	char *path_desc;
 
 	output(o, 1, _("CONFLICT (rename/rename): "
 	       "Rename \"%s\"->\"%s\" in branch \"%s\" "
@@ -1636,14 +1762,16 @@ static int handle_rename_rename_1to2(struct merge_options *o,
 	       one->path, a->path, ci->branch1,
 	       one->path, b->path, ci->branch2,
 	       o->call_depth ? _(" (left unresolved)") : "");
-	if (o->call_depth) {
-		struct merge_file_info mfi;
-		struct diff_filespec other;
-		struct diff_filespec *add;
-		if (merge_mode_and_contents(o, one, a, b, one->path,
-					    ci->branch1, ci->branch2, &mfi))
-			return -1;
 
+	path_desc = xstrfmt("%s and %s, both renamed from %s",
+			    a->path, b->path, one->path);
+	if (merge_mode_and_contents(o, one, a, b, path_desc,
+				    ci->branch1, ci->branch2,
+				    o->call_depth * 2, &mfi))
+		return -1;
+	free(path_desc);
+
+	if (o->call_depth) {
 		/*
 		 * FIXME: For rename/add-source conflicts (if we could detect
 		 * such), this is wrong.  We should instead find a unique
@@ -1667,16 +1795,58 @@ static int handle_rename_rename_1to2(struct merge_options *o,
 				return -1;
 		}
 		else
-			remove_file_from_cache(a->path);
+			remove_file_from_index(o->repo->index, a->path);
 		add = filespec_from_entry(&other, ci->dst_entry2, 3 ^ 1);
 		if (add) {
 			if (update_file(o, 0, &add->oid, add->mode, b->path))
 				return -1;
 		}
 		else
-			remove_file_from_cache(b->path);
-	} else if (handle_file(o, a, 2, ci) || handle_file(o, b, 3, ci))
-		return -1;
+			remove_file_from_index(o->repo->index, b->path);
+	} else {
+		/*
+		 * For each destination path, we need to see if there is a
+		 * rename/add collision.  If not, we can write the file out
+		 * to the specified location.
+		 */
+		add = filespec_from_entry(&other, ci->dst_entry1, 2 ^ 1);
+		if (add) {
+			if (handle_file_collision(o, a->path,
+						  NULL, NULL,
+						  ci->branch1, ci->branch2,
+						  &mfi.oid, mfi.mode,
+						  &add->oid, add->mode) < 0)
+				return -1;
+		} else {
+			char *new_path = find_path_for_conflict(o, a->path,
+								ci->branch1,
+								ci->branch2);
+			if (update_file(o, 0, &mfi.oid, mfi.mode, new_path ? new_path : a->path))
+				return -1;
+			free(new_path);
+			if (update_stages(o, a->path, NULL, a, NULL))
+				return -1;
+		}
+
+		add = filespec_from_entry(&other, ci->dst_entry2, 3 ^ 1);
+		if (add) {
+			if (handle_file_collision(o, b->path,
+						  NULL, NULL,
+						  ci->branch1, ci->branch2,
+						  &add->oid, add->mode,
+						  &mfi.oid, mfi.mode) < 0)
+				return -1;
+		} else {
+			char *new_path = find_path_for_conflict(o, b->path,
+								ci->branch2,
+								ci->branch1);
+			if (update_file(o, 0, &mfi.oid, mfi.mode, new_path ? new_path : b->path))
+				return -1;
+			free(new_path);
+			if (update_stages(o, b->path, NULL, NULL, b))
+				return -1;
+		}
+	}
 
 	return 0;
 }
@@ -1694,7 +1864,6 @@ static int handle_rename_rename_2to1(struct merge_options *o,
 	char *path_side_2_desc;
 	struct merge_file_info mfi_c1;
 	struct merge_file_info mfi_c2;
-	int ret;
 
 	output(o, 1, _("CONFLICT (rename/rename): "
 	       "Rename %s->%s in %s. "
@@ -1702,79 +1871,22 @@ static int handle_rename_rename_2to1(struct merge_options *o,
 	       a->path, c1->path, ci->branch1,
 	       b->path, c2->path, ci->branch2);
 
-	remove_file(o, 1, a->path, o->call_depth || would_lose_untracked(a->path));
-	remove_file(o, 1, b->path, o->call_depth || would_lose_untracked(b->path));
-
 	path_side_1_desc = xstrfmt("version of %s from %s", path, a->path);
 	path_side_2_desc = xstrfmt("version of %s from %s", path, b->path);
 	if (merge_mode_and_contents(o, a, c1, &ci->ren1_other, path_side_1_desc,
-				    o->branch1, o->branch2, &mfi_c1) ||
+				    o->branch1, o->branch2,
+				    1 + o->call_depth * 2, &mfi_c1) ||
 	    merge_mode_and_contents(o, b, &ci->ren2_other, c2, path_side_2_desc,
-				    o->branch1, o->branch2, &mfi_c2))
+				    o->branch1, o->branch2,
+				    1 + o->call_depth * 2, &mfi_c2))
 		return -1;
 	free(path_side_1_desc);
 	free(path_side_2_desc);
 
-	if (o->call_depth) {
-		/*
-		 * If mfi_c1.clean && mfi_c2.clean, then it might make
-		 * sense to do a two-way merge of those results.  But, I
-		 * think in all cases, it makes sense to have the virtual
-		 * merge base just undo the renames; they can be detected
-		 * again later for the non-recursive merge.
-		 */
-		remove_file(o, 0, path, 0);
-		ret = update_file(o, 0, &mfi_c1.oid, mfi_c1.mode, a->path);
-		if (!ret)
-			ret = update_file(o, 0, &mfi_c2.oid, mfi_c2.mode,
-					  b->path);
-	} else {
-		char *new_path1 = unique_path(o, path, ci->branch1);
-		char *new_path2 = unique_path(o, path, ci->branch2);
-		output(o, 1, _("Renaming %s to %s and %s to %s instead"),
-		       a->path, new_path1, b->path, new_path2);
-		if (was_dirty(o, path))
-			output(o, 1, _("Refusing to lose dirty file at %s"),
-			       path);
-		else if (would_lose_untracked(path))
-			/*
-			 * Only way we get here is if both renames were from
-			 * a directory rename AND user had an untracked file
-			 * at the location where both files end up after the
-			 * two directory renames.  See testcase 10d of t6043.
-			 */
-			output(o, 1, _("Refusing to lose untracked file at "
-				       "%s, even though it's in the way."),
-			       path);
-		else
-			remove_file(o, 0, path, 0);
-		ret = update_file(o, 0, &mfi_c1.oid, mfi_c1.mode, new_path1);
-		if (!ret)
-			ret = update_file(o, 0, &mfi_c2.oid, mfi_c2.mode,
-					  new_path2);
-		/*
-		 * unpack_trees() actually populates the index for us for
-		 * "normal" rename/rename(2to1) situtations so that the
-		 * correct entries are at the higher stages, which would
-		 * make the call below to update_stages_for_stage_data
-		 * unnecessary.  However, if either of the renames came
-		 * from a directory rename, then unpack_trees() will not
-		 * have gotten the right data loaded into the index, so we
-		 * need to do so now.  (While it'd be tempting to move this
-		 * call to update_stages_for_stage_data() to
-		 * apply_directory_rename_modifications(), that would break
-		 * our intermediate calls to would_lose_untracked() since
-		 * those rely on the current in-memory index.  See also the
-		 * big "NOTE" in update_stages()).
-		 */
-		if (update_stages_for_stage_data(o, path, ci->dst_entry1))
-			ret = -1;
-
-		free(new_path2);
-		free(new_path1);
-	}
-
-	return ret;
+	return handle_file_collision(o, path, a->path, b->path,
+				     ci->branch1, ci->branch2,
+				     &mfi_c1.oid, mfi_c1.mode,
+				     &mfi_c2.oid, mfi_c2.mode);
 }
 
 /*
@@ -1787,7 +1899,7 @@ static struct diff_queue_struct *get_diffpairs(struct merge_options *o,
 	struct diff_queue_struct *ret;
 	struct diff_options opts;
 
-	repo_diff_setup(the_repository, &opts);
+	repo_diff_setup(o->repo, &opts);
 	opts.flags.recursive = 1;
 	opts.flags.rename_empty = 0;
 	opts.detect_rename = merge_detect_rename(o);
@@ -2732,47 +2844,23 @@ static int process_renames(struct merge_options *o,
 						      0  /* update_wd    */))
 					clean_merge = -1;
 			} else if (!oid_eq(&dst_other.oid, &null_oid)) {
-				clean_merge = 0;
-				try_merge = 1;
-				output(o, 1, _("CONFLICT (rename/add): Rename %s->%s in %s. "
-				       "%s added in %s"),
-				       ren1_src, ren1_dst, branch1,
-				       ren1_dst, branch2);
-				if (o->call_depth) {
-					struct merge_file_info mfi;
-					struct diff_filespec one, a, b;
-
-					oidcpy(&one.oid, &null_oid);
-					one.mode = 0;
-					one.path = ren1->pair->two->path;
-
-					oidcpy(&a.oid, &ren1->pair->two->oid);
-					a.mode = ren1->pair->two->mode;
-					a.path = one.path;
-
-					oidcpy(&b.oid, &dst_other.oid);
-					b.mode = dst_other.mode;
-					b.path = one.path;
-
-					if (merge_mode_and_contents(o, &one, &a, &b, ren1_dst,
-								    branch1, branch2,
-								    &mfi)) {
-						clean_merge = -1;
-						goto cleanup_and_return;
-					}
-					output(o, 1, _("Adding merged %s"), ren1_dst);
-					if (update_file(o, 0, &mfi.oid,
-							mfi.mode, ren1_dst))
-						clean_merge = -1;
-					try_merge = 0;
-				} else {
-					char *new_path = unique_path(o, ren1_dst, branch2);
-					output(o, 1, _("Adding as %s instead"), new_path);
-					if (update_file(o, 0, &dst_other.oid,
-							dst_other.mode, new_path))
-						clean_merge = -1;
-					free(new_path);
-				}
+				/*
+				 * Probably not a clean merge, but it's
+				 * premature to set clean_merge to 0 here,
+				 * because if the rename merges cleanly and
+				 * the merge exactly matches the newly added
+				 * file, then the merge will be clean.
+				 */
+				setup_rename_conflict_info(RENAME_ADD,
+							   ren1->pair,
+							   NULL,
+							   branch1,
+							   branch2,
+							   ren1->dst_entry,
+							   NULL,
+							   o,
+							   ren1->src_entry,
+							   NULL);
 			} else
 				try_merge = 1;
 
@@ -2966,8 +3054,8 @@ static int blob_unchanged(struct merge_options *opt,
 	 * performed.  Comparison can be skipped if both files are
 	 * unchanged since their sha1s have already been compared.
 	 */
-	if (renormalize_buffer(&the_index, path, o.buf, o.len, &o) |
-	    renormalize_buffer(&the_index, path, a.buf, a.len, &a))
+	if (renormalize_buffer(opt->repo->index, path, o.buf, o.len, &o) |
+	    renormalize_buffer(opt->repo->index, path, a.buf, a.len, &a))
 		ret = (o.len == a.len && !memcmp(o.buf, a.buf, o.len));
 
 error_return:
@@ -3048,12 +3136,13 @@ static int handle_content_merge(struct merge_options *o,
 		a.path = (char *)path1;
 		b.path = (char *)path2;
 
-		if (dir_in_way(path, !o->call_depth,
+		if (dir_in_way(o->repo->index, path, !o->call_depth,
 			       S_ISGITLINK(pair1->two->mode)))
 			df_conflict_remains = 1;
 	}
 	if (merge_mode_and_contents(o, &one, &a, &b, path,
-				    o->branch1, o->branch2, &mfi))
+				    o->branch1, o->branch2,
+				    o->call_depth * 2, &mfi))
 		return -1;
 
 	/*
@@ -3081,8 +3170,8 @@ static int handle_content_merge(struct merge_options *o,
 		pos = index_name_pos(&o->orig_index, path, strlen(path));
 		ce = o->orig_index.cache[pos];
 		if (ce_skip_worktree(ce)) {
-			pos = index_name_pos(&the_index, path, strlen(path));
-			ce = the_index.cache[pos];
+			pos = index_name_pos(o->repo->index, path, strlen(path));
+			ce = o->repo->index->cache[pos];
 			ce->ce_flags |= CE_SKIP_WORKTREE;
 		}
 		return mfi.clean;
@@ -3101,7 +3190,7 @@ static int handle_content_merge(struct merge_options *o,
 	if (df_conflict_remains || is_dirty) {
 		char *new_path;
 		if (o->call_depth) {
-			remove_file_from_cache(path);
+			remove_file_from_index(o->repo->index, path);
 		} else {
 			if (!mfi.clean) {
 				if (update_stages(o, path, &one, &a, &b))
@@ -3183,6 +3272,15 @@ static int process_entry(struct merge_options *o,
 						  conflict_info->branch2))
 				clean_merge = -1;
 			break;
+		case RENAME_ADD:
+			/*
+			 * Probably unclean merge, but if the renamed file
+			 * merges cleanly and the result can then be
+			 * two-way merged cleanly with the added file, I
+			 * guess it's a clean merge?
+			 */
+			clean_merge = handle_rename_add(o, conflict_info);
+			break;
 		case RENAME_DELETE:
 			clean_merge = 0;
 			if (handle_rename_delete(o,
@@ -3197,9 +3295,14 @@ static int process_entry(struct merge_options *o,
 				clean_merge = -1;
 			break;
 		case RENAME_TWO_FILES_TO_ONE:
-			clean_merge = 0;
-			if (handle_rename_rename_2to1(o, conflict_info))
-				clean_merge = -1;
+			/*
+			 * Probably unclean merge, but if the two renamed
+			 * files merge cleanly and the two resulting files
+			 * can then be two-way merged cleanly, I guess it's
+			 * a clean merge?
+			 */
+			clean_merge = handle_rename_rename_2to1(o,
+								conflict_info);
 			break;
 		default:
 			entry->processed = 0;
@@ -3247,7 +3350,7 @@ static int process_entry(struct merge_options *o,
 			oid = b_oid;
 			conf = _("directory/file");
 		}
-		if (dir_in_way(path,
+		if (dir_in_way(o->repo->index, path,
 			       !o->call_depth && !S_ISGITLINK(a_mode),
 			       0)) {
 			char *new_path = unique_path(o, path, add_branch);
@@ -3258,7 +3361,7 @@ static int process_entry(struct merge_options *o,
 			if (update_file(o, 0, oid, mode, new_path))
 				clean_merge = -1;
 			else if (o->call_depth)
-				remove_file_from_cache(path);
+				remove_file_from_index(o->repo->index, path);
 			free(new_path);
 		} else {
 			output(o, 2, _("Adding %s"), path);
@@ -3267,14 +3370,27 @@ static int process_entry(struct merge_options *o,
 				clean_merge = -1;
 		}
 	} else if (a_oid && b_oid) {
-		/* Case C: Added in both (check for same permissions) and */
-		/* case D: Modified in both, but differently. */
-		int is_dirty = 0; /* unpack_trees would have bailed if dirty */
-		clean_merge = handle_content_merge(o, path, is_dirty,
-						   o_oid, o_mode,
-						   a_oid, a_mode,
-						   b_oid, b_mode,
-						   NULL);
+		if (!o_oid) {
+			/* Case C: Added in both (check for same permissions) */
+			output(o, 1,
+			       _("CONFLICT (add/add): Merge conflict in %s"),
+			       path);
+			clean_merge = handle_file_collision(o,
+							    path, NULL, NULL,
+							    o->branch1,
+							    o->branch2,
+							    a_oid, a_mode,
+							    b_oid, b_mode);
+		} else {
+			/* case D: Modified in both, but differently. */
+			int is_dirty = 0; /* unpack_trees would have bailed if dirty */
+			clean_merge = handle_content_merge(o, path,
+							   is_dirty,
+							   o_oid, o_mode,
+							   a_oid, a_mode,
+							   b_oid, b_mode,
+							   NULL);
+		}
 	} else if (!o_oid && !a_oid && !b_oid) {
 		/*
 		 * this entry was deleted altogether. a_mode == 0 means
@@ -3293,18 +3409,19 @@ int merge_trees(struct merge_options *o,
 		struct tree *common,
 		struct tree **result)
 {
+	struct index_state *istate = o->repo->index;
 	int code, clean;
 	struct strbuf sb = STRBUF_INIT;
 
-	if (!o->call_depth && index_has_changes(&the_index, head, &sb)) {
+	if (!o->call_depth && repo_index_has_changes(o->repo, head, &sb)) {
 		err(o, _("Your local changes to the following files would be overwritten by merge:\n  %s"),
 		    sb.buf);
 		return -1;
 	}
 
 	if (o->subtree_shift) {
-		merge = shift_tree_object(head, merge, o->subtree_shift);
-		common = shift_tree_object(head, common, o->subtree_shift);
+		merge = shift_tree_object(o->repo, head, merge, o->subtree_shift);
+		common = shift_tree_object(o->repo, head, common, o->subtree_shift);
 	}
 
 	if (oid_eq(&common->object.oid, &merge->object.oid)) {
@@ -3324,7 +3441,7 @@ int merge_trees(struct merge_options *o,
 		return -1;
 	}
 
-	if (unmerged_cache()) {
+	if (unmerged_index(istate)) {
 		struct string_list *entries;
 		struct rename_info re_info;
 		int i;
@@ -3339,7 +3456,7 @@ int merge_trees(struct merge_options *o,
 		get_files_dirs(o, head);
 		get_files_dirs(o, merge);
 
-		entries = get_unmerged();
+		entries = get_unmerged(o->repo->index);
 		clean = detect_and_process_renames(o, common, head, merge,
 						   entries, &re_info);
 		record_df_conflict_files(o, entries);
@@ -3440,8 +3557,8 @@ int merge_recursive(struct merge_options *o,
 		/* if there is no common ancestor, use an empty tree */
 		struct tree *tree;
 
-		tree = lookup_tree(the_repository, the_repository->hash_algo->empty_tree);
-		merged_common_ancestors = make_virtual_commit(tree, "ancestor");
+		tree = lookup_tree(o->repo, o->repo->hash_algo->empty_tree);
+		merged_common_ancestors = make_virtual_commit(o->repo, tree, "ancestor");
 	}
 
 	for (iter = ca; iter; iter = iter->next) {
@@ -3455,7 +3572,7 @@ int merge_recursive(struct merge_options *o,
 		 * overwritten it: the committed "conflicts" were
 		 * already resolved.
 		 */
-		discard_cache();
+		discard_index(o->repo->index);
 		saved_b1 = o->branch1;
 		saved_b2 = o->branch2;
 		o->branch1 = "Temporary merge branch 1";
@@ -3471,9 +3588,9 @@ int merge_recursive(struct merge_options *o,
 			return err(o, _("merge returned no commit"));
 	}
 
-	discard_cache();
+	discard_index(o->repo->index);
 	if (!o->call_depth)
-		read_cache();
+		repo_read_index(o->repo);
 
 	o->ancestor = "merged common ancestors";
 	clean = merge_trees(o, get_commit_tree(h1), get_commit_tree(h2),
@@ -3485,7 +3602,7 @@ int merge_recursive(struct merge_options *o,
 	}
 
 	if (o->call_depth) {
-		*result = make_virtual_commit(mrtree, "merged tree");
+		*result = make_virtual_commit(o->repo, mrtree, "merged tree");
 		commit_list_insert(h1, &(*result)->parents);
 		commit_list_insert(h2, &(*result)->parents->next);
 	}
@@ -3498,17 +3615,17 @@ int merge_recursive(struct merge_options *o,
 	return clean;
 }
 
-static struct commit *get_ref(const struct object_id *oid, const char *name)
+static struct commit *get_ref(struct repository *repo, const struct object_id *oid,
+			      const char *name)
 {
 	struct object *object;
 
-	object = deref_tag(the_repository, parse_object(the_repository, oid),
-			   name,
-			   strlen(name));
+	object = deref_tag(repo, parse_object(repo, oid),
+			   name, strlen(name));
 	if (!object)
 		return NULL;
 	if (object->type == OBJ_TREE)
-		return make_virtual_commit((struct tree*)object, name);
+		return make_virtual_commit(repo, (struct tree*)object, name);
 	if (object->type != OBJ_COMMIT)
 		return NULL;
 	if (parse_commit((struct commit *)object))
@@ -3525,22 +3642,22 @@ int merge_recursive_generic(struct merge_options *o,
 {
 	int clean;
 	struct lock_file lock = LOCK_INIT;
-	struct commit *head_commit = get_ref(head, o->branch1);
-	struct commit *next_commit = get_ref(merge, o->branch2);
+	struct commit *head_commit = get_ref(o->repo, head, o->branch1);
+	struct commit *next_commit = get_ref(o->repo, merge, o->branch2);
 	struct commit_list *ca = NULL;
 
 	if (base_list) {
 		int i;
 		for (i = 0; i < num_base_list; ++i) {
 			struct commit *base;
-			if (!(base = get_ref(base_list[i], oid_to_hex(base_list[i]))))
+			if (!(base = get_ref(o->repo, base_list[i], oid_to_hex(base_list[i]))))
 				return err(o, _("Could not parse object '%s'"),
 					   oid_to_hex(base_list[i]));
 			commit_list_insert(base, &ca);
 		}
 	}
 
-	hold_locked_index(&lock, LOCK_DIE_ON_ERROR);
+	repo_hold_locked_index(o->repo, &lock, LOCK_DIE_ON_ERROR);
 	clean = merge_recursive(o, head_commit, next_commit, ca,
 				result);
 	if (clean < 0) {
@@ -3548,7 +3665,7 @@ int merge_recursive_generic(struct merge_options *o,
 		return clean;
 	}
 
-	if (write_locked_index(&the_index, &lock,
+	if (write_locked_index(o->repo->index, &lock,
 			       COMMIT_LOCK | SKIP_IF_UNCHANGED))
 		return err(o, _("Unable to write index."));
 
@@ -3572,10 +3689,12 @@ static void merge_recursive_config(struct merge_options *o)
 	git_config(git_xmerge_config, NULL);
 }
 
-void init_merge_options(struct merge_options *o)
+void init_merge_options(struct merge_options *o,
+			struct repository *repo)
 {
 	const char *merge_verbosity;
 	memset(o, 0, sizeof(struct merge_options));
+	o->repo = repo;
 	o->verbosity = 2;
 	o->buffer_output = 1;
 	o->diff_rename_limit = -1;