diff --git a/builtin/checkout.c b/builtin/checkout.c
index 27f173eb46..2a24503264 100644
--- a/builtin/checkout.c
+++ b/builtin/checkout.c
@@ -921,7 +921,7 @@ static int merge_working_tree(const struct checkout_opts *opts,
 		}
 	}
 
-	if (!cache_tree_fully_valid(the_repository->index->cache_tree))
+	if (!cache_tree_fully_valid(the_repository, the_repository->index->cache_tree))
 		cache_tree_update(the_repository->index, WRITE_TREE_SILENT | WRITE_TREE_REPAIR);
 
 	if (write_locked_index(the_repository->index, &lock_file, COMMIT_LOCK))
diff --git a/builtin/commit.c b/builtin/commit.c
index e96c663bd5..7f3e962667 100644
--- a/builtin/commit.c
+++ b/builtin/commit.c
@@ -484,7 +484,7 @@ static const char *prepare_index(const char **argv, const char *prefix,
 				       LOCK_DIE_ON_ERROR);
 		refresh_cache_or_die(refresh_flags);
 		if (the_repository->index->cache_changed
-		    || !cache_tree_fully_valid(the_repository->index->cache_tree))
+		    || !cache_tree_fully_valid(the_repository, the_repository->index->cache_tree))
 			cache_tree_update(the_repository->index, WRITE_TREE_SILENT);
 		if (write_locked_index(the_repository->index, &index_lock,
 				       COMMIT_LOCK | SKIP_IF_UNCHANGED))
diff --git a/builtin/fetch.c b/builtin/fetch.c
index ab7db2be06..533fdfe7d8 100644
--- a/builtin/fetch.c
+++ b/builtin/fetch.c
@@ -2681,7 +2681,7 @@ int cmd_fetch(int argc,
 		int *rs = config.recurse_submodules == RECURSE_SUBMODULES_DEFAULT
 			  ? &config.recurse_submodules : NULL;
 
-		fetch_config_from_gitmodules(sfjc, rs);
+		fetch_config_from_gitmodules(the_repository, sfjc, rs);
 	}
 
 
diff --git a/builtin/grep.c b/builtin/grep.c
index d3d86abe01..b045f8a488 100644
--- a/builtin/grep.c
+++ b/builtin/grep.c
@@ -463,16 +463,6 @@ static int grep_submodule(struct grep_opt *opt,
 	ALLOC_GROW(repos_to_free, repos_to_free_nr + 1, repos_to_free_alloc);
 	repos_to_free[repos_to_free_nr++] = subrepo;
 
-	/*
-	 * NEEDSWORK: repo_read_gitmodules() might call
-	 * odb_add_to_alternates_memory() via config_from_gitmodules(). This
-	 * operation causes a race condition with concurrent object readings
-	 * performed by the worker threads. That's why we need obj_read_lock()
-	 * here. It should be removed once it's no longer necessary to add the
-	 * subrepo's odbs to the in-memory alternates list.
-	 */
-	obj_read_lock();
-
 	/*
 	 * NEEDSWORK: when reading a submodule, the sparsity settings in the
 	 * superproject are incorrectly forgotten or misused. For example:
@@ -498,18 +488,14 @@ static int grep_submodule(struct grep_opt *opt,
 	 *	ditto.
 	 *
 	 * Note that this list is not exhaustive.
+	 *
+	 * NEEDSWORK: initializing the subrepository is not thread-safe,
+	 * either, as it may cause us to race around `get_main_ref_store()`. We
+	 * thus need to hold the object-read lock to serialize all readers with
+	 * one another.
 	 */
+	obj_read_lock();
 	repo_read_gitmodules(subrepo, 0);
-
-	/*
-	 * All code paths tested by test code no longer need submodule ODBs to
-	 * be added as alternates, but add it to the list just in case.
-	 * Submodule ODBs added through add_submodule_odb_by_path() will be
-	 * lazily registered as alternates when needed (and except in an
-	 * unexpected code interaction, it won't be needed).
-	 */
-	odb_add_submodule_source_by_path(the_repository->objects,
-					 subrepo->objects->sources->path);
 	obj_read_unlock();
 
 	memcpy(&subopt, opt, sizeof(subopt));
@@ -897,7 +883,7 @@ static int grep_objects(struct grep_opt *opt, const struct pathspec *pathspec,
 		if (recurse_submodules) {
 			submodule_free(opt->repo);
 			obj_read_lock();
-			gitmodules_config_oid(&real_obj->oid);
+			gitmodules_config_oid(the_repository, &real_obj->oid);
 			obj_read_unlock();
 		}
 		if (grep_object(opt, pathspec, real_obj, list->objects[i].name,
diff --git a/builtin/multi-pack-index.c b/builtin/multi-pack-index.c
index 6e73c85cde..753bd53a70 100644
--- a/builtin/multi-pack-index.c
+++ b/builtin/multi-pack-index.c
@@ -90,7 +90,8 @@ static struct odb_source_files *handle_object_dir_option(struct repository *repo
 {
 	struct odb_source *source = odb_find_source(repo->objects, opts.object_dir);
 	if (!source)
-		source = odb_add_to_alternates_memory(repo->objects, opts.object_dir);
+		die(_("object directory is not an alternate of the current repository: '%s'"),
+		    opts.object_dir);
 	return odb_source_files_downcast(source);
 }
 
diff --git a/builtin/submodule--helper.c b/builtin/submodule--helper.c
index 1eb73de674..bf392521dd 100644
--- a/builtin/submodule--helper.c
+++ b/builtin/submodule--helper.c
@@ -3041,7 +3041,7 @@ static int module_update(int argc, const char **argv, const char *prefix,
 		NULL
 	};
 
-	update_clone_config_from_gitmodules(&opt.max_jobs);
+	update_clone_config_from_gitmodules(the_repository, &opt.max_jobs);
 	repo_config(the_repository, git_update_clone_config, &opt.max_jobs);
 
 	argc = parse_options(argc, argv, prefix, module_update_options,
@@ -3255,7 +3255,7 @@ static int module_set_url(int argc, const char **argv, const char *prefix,
 		    path);
 
 	config_name = xstrfmt("submodule.%s.url", sub->name);
-	ret = config_set_in_gitmodules_file_gently(config_name, newurl);
+	ret = config_set_in_gitmodules_file_gently(the_repository, config_name, newurl);
 
 	if (!ret) {
 		repo_read_gitmodules(the_repository, 0);
@@ -3311,7 +3311,7 @@ static int module_set_branch(int argc, const char **argv, const char *prefix,
 		    path);
 
 	config_name = xstrfmt("submodule.%s.branch", sub->name);
-	ret = config_set_in_gitmodules_file_gently(config_name, opt_branch);
+	ret = config_set_in_gitmodules_file_gently(the_repository, config_name, opt_branch);
 
 	free(config_name);
 	return !!ret;
@@ -3511,7 +3511,7 @@ static int config_submodule_in_gitmodules(const char *name, const char *var, con
 		die(_("please make sure that the .gitmodules file is in the working tree"));
 
 	key = xstrfmt("submodule.%s.%s", name, var);
-	ret = config_set_in_gitmodules_file_gently(key, value);
+	ret = config_set_in_gitmodules_file_gently(the_repository, key, value);
 	free(key);
 
 	return ret;
diff --git a/cache-tree.c b/cache-tree.c
index a220372a42..6e4d82f3e8 100644
--- a/cache-tree.c
+++ b/cache-tree.c
@@ -1,4 +1,3 @@
-#define USE_THE_REPOSITORY_VARIABLE
 #define DISABLE_SIGN_COMPARE_WARNINGS
 
 #include "git-compat-util.h"
@@ -275,28 +274,30 @@ static void discard_unused_subtrees(struct cache_tree *it)
 	}
 }
 
-int cache_tree_fully_valid(struct cache_tree *it)
+int cache_tree_fully_valid(struct repository *repo, struct cache_tree *it)
 {
 	int i;
 	if (!it)
 		return 0;
 	if (it->entry_count < 0 ||
-	    !odb_has_object(the_repository->objects, &it->oid,
+	    !odb_has_object(repo->objects, &it->oid,
 			    ODB_HAS_OBJECT_RECHECK_PACKED | ODB_HAS_OBJECT_FETCH_PROMISOR))
 		return 0;
 	for (i = 0; i < it->subtree_nr; i++) {
-		if (!cache_tree_fully_valid(it->down[i]->cache_tree))
+		if (!cache_tree_fully_valid(repo, it->down[i]->cache_tree))
 			return 0;
 	}
 	return 1;
 }
 
-static int must_check_existence(const struct cache_entry *ce)
+static int must_check_existence(const struct cache_entry *ce, void *cb_data)
 {
-	return !(repo_has_promisor_remote(the_repository) && ce_skip_worktree(ce));
+	struct repository *repo = cb_data;
+	return !(repo_has_promisor_remote(repo) && ce_skip_worktree(ce));
 }
 
-static int update_one(struct cache_tree *it,
+static int update_one(struct repository *repo,
+		      struct cache_tree *it,
 		      struct cache_entry **cache,
 		      int entries,
 		      const char *base,
@@ -334,7 +335,7 @@ static int update_one(struct cache_tree *it,
 	}
 
 	if (0 <= it->entry_count &&
-	    odb_has_object(the_repository->objects, &it->oid,
+	    odb_has_object(repo->objects, &it->oid,
 			   ODB_HAS_OBJECT_RECHECK_PACKED | ODB_HAS_OBJECT_FETCH_PROMISOR))
 		return it->entry_count;
 
@@ -375,7 +376,8 @@ static int update_one(struct cache_tree *it,
 		sub = find_subtree(it, path + baselen, sublen, 1);
 		if (!sub->cache_tree)
 			sub->cache_tree = cache_tree();
-		subcnt = update_one(sub->cache_tree,
+		subcnt = update_one(repo,
+				    sub->cache_tree,
 				    cache + i, entries - i,
 				    path,
 				    baselen + sublen + 1,
@@ -439,10 +441,10 @@ static int update_one(struct cache_tree *it,
 		}
 
 		ce_missing_ok = mode == S_IFGITLINK || missing_ok ||
-			!must_check_existence(ce);
+			!must_check_existence(ce, repo);
 		if (is_null_oid(oid) ||
 		    (!ce_missing_ok &&
-		     !odb_has_object(the_repository->objects, oid,
+		     !odb_has_object(repo->objects, oid,
 				     ODB_HAS_OBJECT_RECHECK_PACKED | ODB_HAS_OBJECT_FETCH_PROMISOR))) {
 			strbuf_release(&buffer);
 			if (expected_missing)
@@ -474,12 +476,12 @@ static int update_one(struct cache_tree *it,
 		/*
 		 * "sub" can be an empty tree if all subentries are i-t-a.
 		 */
-		if (contains_ita && is_empty_tree_oid(oid, the_repository->hash_algo))
+		if (contains_ita && is_empty_tree_oid(oid, repo->hash_algo))
 			continue;
 
 		strbuf_grow(&buffer, entlen + 100);
 		strbuf_addf(&buffer, "%o %.*s%c", mode, entlen, path + baselen, '\0');
-		strbuf_add(&buffer, oid->hash, the_hash_algo->rawsz);
+		strbuf_add(&buffer, oid->hash, repo->hash_algo->rawsz);
 
 #if DEBUG_CACHE_TREE
 		fprintf(stderr, "cache-tree update-one %o %.*s\n",
@@ -489,16 +491,16 @@ static int update_one(struct cache_tree *it,
 
 	if (repair) {
 		struct object_id oid;
-		hash_object_file(the_hash_algo, buffer.buf, buffer.len,
+		hash_object_file(repo->hash_algo, buffer.buf, buffer.len,
 				 OBJ_TREE, &oid);
-		if (odb_has_object(the_repository->objects, &oid, ODB_HAS_OBJECT_RECHECK_PACKED))
+		if (odb_has_object(repo->objects, &oid, ODB_HAS_OBJECT_RECHECK_PACKED))
 			oidcpy(&it->oid, &oid);
 		else
 			to_invalidate = 1;
 	} else if (dryrun) {
-		hash_object_file(the_hash_algo, buffer.buf, buffer.len,
+		hash_object_file(repo->hash_algo, buffer.buf, buffer.len,
 				 OBJ_TREE, &it->oid);
-	} else if (odb_write_object_ext(the_repository->objects, buffer.buf, buffer.len, OBJ_TREE,
+	} else if (odb_write_object_ext(repo->objects, buffer.buf, buffer.len, OBJ_TREE,
 					&it->oid, NULL, flags & WRITE_TREE_SILENT ? ODB_WRITE_OBJECT_SILENT : 0)) {
 		strbuf_release(&buffer);
 		return -1;
@@ -516,7 +518,7 @@ static int update_one(struct cache_tree *it,
 
 int cache_tree_update(struct index_state *istate, int flags)
 {
-	int inflight = !!the_repository->objects->transaction;
+	int inflight = !!istate->repo->objects->transaction;
 	struct odb_transaction *transaction;
 	int skip, i;
 
@@ -528,14 +530,14 @@ int cache_tree_update(struct index_state *istate, int flags)
 	if (!istate->cache_tree)
 		istate->cache_tree = cache_tree();
 
-	if (!(flags & WRITE_TREE_MISSING_OK) && repo_has_promisor_remote(the_repository))
-		prefetch_cache_entries(istate, must_check_existence);
+	if (!(flags & WRITE_TREE_MISSING_OK) && repo_has_promisor_remote(istate->repo))
+		prefetch_cache_entries(istate, must_check_existence, istate->repo);
 
 	trace_performance_enter();
 	trace2_region_enter("cache_tree", "update", istate->repo);
 	if (!inflight)
-		odb_transaction_begin_or_die(the_repository->objects, &transaction, 0);
-	i = update_one(istate->cache_tree, istate->cache, istate->cache_nr,
+		odb_transaction_begin_or_die(istate->repo->objects, &transaction, 0);
+	i = update_one(istate->repo, istate->cache_tree, istate->cache, istate->cache_nr,
 		       "", 0, &skip, flags);
 	if (!inflight)
 		odb_transaction_commit_and_finalize_or_die(transaction);
@@ -547,7 +549,8 @@ int cache_tree_update(struct index_state *istate, int flags)
 	return 0;
 }
 
-static void write_one(struct strbuf *buffer, struct cache_tree *it,
+static void write_one(struct repository *repo,
+		      struct strbuf *buffer, struct cache_tree *it,
 		      const char *path, int pathlen)
 {
 	int i;
@@ -573,7 +576,7 @@ static void write_one(struct strbuf *buffer, struct cache_tree *it,
 #endif
 
 	if (0 <= it->entry_count) {
-		strbuf_add(buffer, it->oid.hash, the_hash_algo->rawsz);
+		strbuf_add(buffer, it->oid.hash, repo->hash_algo->rawsz);
 	}
 	for (i = 0; i < it->subtree_nr; i++) {
 		struct cache_tree_sub *down = it->down[i];
@@ -583,15 +586,16 @@ static void write_one(struct strbuf *buffer, struct cache_tree *it,
 					     prev->name, prev->namelen) <= 0)
 				die("fatal - unsorted cache subtree");
 		}
-		write_one(buffer, down->cache_tree, down->name, down->namelen);
+		write_one(repo, buffer, down->cache_tree, down->name, down->namelen);
 	}
 }
 
-void cache_tree_write(struct strbuf *sb, struct cache_tree *root)
+void cache_tree_write(struct repository *repo,
+		      struct strbuf *sb, struct cache_tree *root)
 {
-	trace2_region_enter("cache_tree", "write", the_repository);
-	write_one(sb, root, "", 0);
-	trace2_region_leave("cache_tree", "write", the_repository);
+	trace2_region_enter("cache_tree", "write", repo);
+	write_one(repo, sb, root, "", 0);
+	trace2_region_leave("cache_tree", "write", repo);
 }
 
 static int parse_int(const char **ptr, unsigned long *len_p, int *out)
@@ -625,13 +629,14 @@ static int parse_int(const char **ptr, unsigned long *len_p, int *out)
 	return 0;
 }
 
-static struct cache_tree *read_one(const char **buffer, unsigned long *size_p)
+static struct cache_tree *read_one(struct repository *repo,
+				   const char **buffer, unsigned long *size_p)
 {
 	const char *buf = *buffer;
 	unsigned long size = *size_p;
 	struct cache_tree *it;
 	int i, subtree_nr;
-	const unsigned rawsz = the_hash_algo->rawsz;
+	const unsigned rawsz = repo->hash_algo->rawsz;
 
 	it = NULL;
 	/* skip name, but make sure name exists */
@@ -658,7 +663,7 @@ static struct cache_tree *read_one(const char **buffer, unsigned long *size_p)
 		if (size < rawsz)
 			goto free_return;
 		oidread(&it->oid, (const unsigned char *)buf,
-			the_repository->hash_algo);
+			repo->hash_algo);
 		buf += rawsz;
 		size -= rawsz;
 	}
@@ -686,7 +691,7 @@ static struct cache_tree *read_one(const char **buffer, unsigned long *size_p)
 		struct cache_tree_sub *subtree;
 		const char *name = buf;
 
-		sub = read_one(&buf, &size);
+		sub = read_one(repo, &buf, &size);
 		if (!sub)
 			goto free_return;
 		subtree = cache_tree_sub(it, name);
@@ -703,16 +708,17 @@ static struct cache_tree *read_one(const char **buffer, unsigned long *size_p)
 	return NULL;
 }
 
-struct cache_tree *cache_tree_read(const char *buffer, unsigned long size)
+struct cache_tree *cache_tree_read(struct repository *repo,
+				   const char *buffer, unsigned long size)
 {
 	struct cache_tree *result;
 
 	if (buffer[0])
 		return NULL; /* not the whole tree */
 
-	trace2_region_enter("cache_tree", "read", the_repository);
-	result = read_one(&buffer, &size);
-	trace2_region_leave("cache_tree", "read", the_repository);
+	trace2_region_enter("cache_tree", "read", repo);
+	result = read_one(repo, &buffer, &size);
+	trace2_region_leave("cache_tree", "read", repo);
 
 	return result;
 }
@@ -775,7 +781,7 @@ struct tree *write_in_core_index_as_tree(struct repository *repo,
 	int was_valid, ret;
 
 	was_valid = index_state->cache_tree &&
-		    cache_tree_fully_valid(index_state->cache_tree);
+		    cache_tree_fully_valid(repo, index_state->cache_tree);
 
 	ret = write_index_as_tree_internal(&o, index_state, was_valid, 0, NULL);
 	if (ret == WRITE_TREE_UNMERGED_INDEX) {
@@ -803,7 +809,7 @@ int write_index_as_tree(struct object_id *oid, struct index_state *index_state,
 	hold_lock_file_for_update(&lock_file, index_path, LOCK_DIE_ON_ERROR);
 
 	entries = read_index_from(index_state, index_path,
-				  repo_get_git_dir(the_repository));
+				  repo_get_git_dir(index_state->repo));
 	if (entries < 0) {
 		ret = WRITE_TREE_UNREADABLE_INDEX;
 		goto out;
@@ -811,7 +817,7 @@ int write_index_as_tree(struct object_id *oid, struct index_state *index_state,
 
 	was_valid = !(flags & WRITE_TREE_IGNORE_CACHE_TREE) &&
 		    index_state->cache_tree &&
-		    cache_tree_fully_valid(index_state->cache_tree);
+		    cache_tree_fully_valid(index_state->repo, index_state->cache_tree);
 
 	ret = write_index_as_tree_internal(oid, index_state, was_valid, flags,
 					   prefix);
@@ -859,7 +865,7 @@ static void prime_cache_tree_rec(struct repository *r,
 			struct cache_tree_sub *sub;
 			struct tree *subtree = lookup_tree(r, &entry.oid);
 
-			if (repo_parse_tree(the_repository, subtree) < 0)
+			if (repo_parse_tree(r, subtree) < 0)
 				exit(128);
 			sub = cache_tree_sub(it, entry.path);
 			sub->cache_tree = cache_tree();
diff --git a/cache-tree.h b/cache-tree.h
index f8bddae523..5d49308de9 100644
--- a/cache-tree.h
+++ b/cache-tree.h
@@ -28,10 +28,11 @@ struct cache_tree_sub *cache_tree_sub(struct cache_tree *, const char *);
 
 int cache_tree_subtree_pos(struct cache_tree *it, const char *path, int pathlen);
 
-void cache_tree_write(struct strbuf *, struct cache_tree *root);
-struct cache_tree *cache_tree_read(const char *buffer, unsigned long size);
+void cache_tree_write(struct repository *repo, struct strbuf *, struct cache_tree *root);
+struct cache_tree *cache_tree_read(struct repository *repo,
+				   const char *buffer, unsigned long size);
 
-int cache_tree_fully_valid(struct cache_tree *);
+int cache_tree_fully_valid(struct repository *, struct cache_tree *);
 int cache_tree_update(struct index_state *, int);
 int cache_tree_verify(struct repository *, struct index_state *);
 
diff --git a/odb.c b/odb.c
index 5d6db482e2..3e39fece4a 100644
--- a/odb.c
+++ b/odb.c
@@ -238,12 +238,6 @@ static struct odb_source *odb_add_alternate_recursively(struct object_database *
 	return alternate;
 }
 
-struct odb_source *odb_add_to_alternates_memory(struct object_database *odb,
-						const char *dir)
-{
-	return odb_add_alternate_recursively(odb, dir, 0);
-}
-
 struct odb_source *odb_set_temporary_primary_source(struct object_database *odb,
 						    const char *dir, int will_destroy,
 						    struct odb_source **prev_source)
@@ -379,12 +373,6 @@ struct odb_source *odb_find_source_or_die(struct object_database *odb, const cha
 	return source;
 }
 
-void odb_add_submodule_source_by_path(struct object_database *odb,
-				      const char *path)
-{
-	string_list_insert(&odb->submodule_source_paths, path);
-}
-
 static void fill_alternate_refs_command(struct repository *repo,
 					struct child_process *cmd,
 					const char *repo_path)
@@ -540,23 +528,6 @@ void disable_obj_read_lock(void)
 	pthread_mutex_destroy(&obj_read_mutex);
 }
 
-static int register_all_submodule_sources(struct object_database *odb)
-{
-	int ret = odb->submodule_source_paths.nr;
-
-	for (size_t i = 0; i < odb->submodule_source_paths.nr; i++)
-		odb_add_to_alternates_memory(odb,
-					     odb->submodule_source_paths.items[i].string);
-	if (ret) {
-		string_list_clear(&odb->submodule_source_paths, 0);
-		trace2_data_intmax("submodule", odb->repo,
-				   "register_all_submodule_sources/registered", ret);
-		if (git_env_bool("GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB", 0))
-			BUG("register_all_submodule_sources() called");
-	}
-	return ret;
-}
-
 static enum odb_read_status do_oid_object_info_extended(struct object_database *odb,
 							const struct object_id *oid,
 							struct object_info *oi, unsigned flags)
@@ -605,16 +576,6 @@ static enum odb_read_status do_oid_object_info_extended(struct object_database *
 			}
 		}
 
-		/*
-		 * This might be an attempt at accessing a submodule object as
-		 * if it were in main object store (having called
-		 * `odb_add_submodule_source_by_path()` on that submodule's
-		 * ODB). If any such ODBs exist, register them and try again.
-		 */
-		if (register_all_submodule_sources(odb))
-			/* We added some alternates; retry */
-			continue;
-
 		/* Check if it is a missing object */
 		if (odb->repo->fetch_if_missing && repo_has_promisor_remote(odb->repo) &&
 		    !already_retried &&
@@ -1100,7 +1061,6 @@ struct object_database *odb_new(struct repository *repo,
 	CALLOC_ARRAY(o, 1);
 	o->repo = repo;
 	pthread_mutex_init(&o->replace_mutex, NULL);
-	string_list_init_dup(&o->submodule_source_paths);
 	hashmap_init(&o->source_by_path, odb_source_by_path_cmp, o, 0);
 	o->source_paths_icase = -1;
 
@@ -1157,8 +1117,6 @@ void odb_free(struct object_database *o)
 	odb_close(o);
 	odb_free_sources(o);
 
-	string_list_clear(&o->submodule_source_paths, 0);
-
 	free(o);
 }
 
diff --git a/odb.h b/odb.h
index 9ccc0e281d..797eecbb94 100644
--- a/odb.h
+++ b/odb.h
@@ -89,12 +89,6 @@ struct object_database {
 	unsigned long object_count;
 	unsigned object_count_flags;
 	unsigned object_count_valid : 1;
-
-	/*
-	 * Submodule source paths that will be added as additional sources to
-	 * allow lookup of submodule objects via the main object database.
-	 */
-	struct string_list submodule_source_paths;
 };
 
 enum odb_new_flags {
@@ -257,14 +251,6 @@ void odb_restore_primary_source(struct object_database *odb,
 				struct odb_source *restore_source,
 				const char *old_path);
 
-/*
- * Call odb_add_submodule_source_by_path() to add the submodule at the given
- * path to a list. The object stores of all submodules in that list will be
- * added as additional sources in the object store when looking up objects.
- */
-void odb_add_submodule_source_by_path(struct object_database *odb,
-				      const char *path);
-
 /*
  * Iterate through all alternates of the database and execute the provided
  * callback function for each of them. Stop iterating once the callback
@@ -298,14 +284,6 @@ int odb_mkstemp(struct object_database *odb,
  */
 int odb_has_alternates(struct object_database *odb);
 
-/*
- * Add the directory to the in-memory list of alternate sources (along with any
- * recursive alternates it points to), but do not modify the on-disk alternates
- * file.
- */
-struct odb_source *odb_add_to_alternates_memory(struct object_database *odb,
-						const char *dir);
-
 /*
  * Read an object from the database. Returns the object data and assigns object
  * type and size to the `type` and `size` pointers, if these pointers are
diff --git a/odb/source-packed.c b/odb/source-packed.c
index b4d05914e6..27c6d843bc 100644
--- a/odb/source-packed.c
+++ b/odb/source-packed.c
@@ -845,6 +845,7 @@ static void odb_source_packed_free(struct odb_source *source)
 
 	chdir_notify_unregister(odb_source_packed_reparent, packed);
 
+	odb_source_close(source);
 	for (struct packfile_list_entry *e = packed->packs.head; e; e = e->next)
 		free(e->pack);
 	packfile_list_clear(&packed->packs);
diff --git a/read-cache-ll.h b/read-cache-ll.h
index 8eb266cfd1..066dd8bc3b 100644
--- a/read-cache-ll.h
+++ b/read-cache-ll.h
@@ -269,9 +269,10 @@ void validate_cache_entries(const struct index_state *istate);
  * the given predicate. This function should only be called if
  * repo_has_promisor_remote() returns true.
  */
-typedef int (*must_prefetch_predicate)(const struct cache_entry *);
+typedef int (*must_prefetch_predicate)(const struct cache_entry *, void *cb_data);
 void prefetch_cache_entries(const struct index_state *istate,
-			    must_prefetch_predicate must_prefetch);
+			    must_prefetch_predicate must_prefetch,
+			    void *cb_data);
 
 /* Initialize and use the cache information */
 struct lock_file;
diff --git a/read-cache.c b/read-cache.c
index 8044ff820b..e40f290bb3 100644
--- a/read-cache.c
+++ b/read-cache.c
@@ -1748,7 +1748,7 @@ static int read_index_extension(struct index_state *istate,
 {
 	switch (CACHE_EXT(ext)) {
 	case CACHE_EXT_TREE:
-		istate->cache_tree = cache_tree_read(data, sz);
+		istate->cache_tree = cache_tree_read(istate->repo, data, sz);
 		break;
 	case CACHE_EXT_RESOLVE_UNDO:
 		istate->resolve_undo = resolve_undo_read(data, sz, the_hash_algo);
@@ -3012,7 +3012,7 @@ static int do_write_index(struct index_state *istate, struct tempfile *tempfile,
 	    !drop_cache_tree && istate->cache_tree) {
 		strbuf_reset(&sb);
 
-		cache_tree_write(&sb, istate->cache_tree);
+		cache_tree_write(istate->repo, &sb, istate->cache_tree);
 		err = write_index_ext_header(f, eoie_c, CACHE_EXT_TREE, sb.len) < 0;
 		hashwrite(f, sb.buf, sb.len);
 		if (err) {
@@ -3733,7 +3733,8 @@ static void write_ieot_extension(struct strbuf *sb, struct index_entry_offset_ta
 }
 
 void prefetch_cache_entries(const struct index_state *istate,
-			    must_prefetch_predicate must_prefetch)
+			    must_prefetch_predicate must_prefetch,
+			    void *cb_data)
 {
 	int i;
 	struct oid_array to_fetch = OID_ARRAY_INIT;
@@ -3741,7 +3742,7 @@ void prefetch_cache_entries(const struct index_state *istate,
 	for (i = 0; i < istate->cache_nr; i++) {
 		struct cache_entry *ce = istate->cache[i];
 
-		if (S_ISGITLINK(ce->ce_mode) || !must_prefetch(ce))
+		if (S_ISGITLINK(ce->ce_mode) || !must_prefetch(ce, cb_data))
 			continue;
 		if (!odb_read_object_info_extended(the_repository->objects,
 						   &ce->oid, NULL,
diff --git a/sequencer.c b/sequencer.c
index 892a7b8930..754d460b49 100644
--- a/sequencer.c
+++ b/sequencer.c
@@ -821,7 +821,7 @@ static int do_recursive_merge(struct repository *r,
 
 static struct object_id *get_cache_tree_oid(struct index_state *istate)
 {
-	if (!cache_tree_fully_valid(istate->cache_tree))
+	if (!cache_tree_fully_valid(istate->repo, istate->cache_tree))
 		if (cache_tree_update(istate, 0)) {
 			error(_("unable to update cache tree"));
 			return NULL;
diff --git a/sparse-index.c b/sparse-index.c
index c1fa231a89..102a9dadeb 100644
--- a/sparse-index.c
+++ b/sparse-index.c
@@ -228,7 +228,7 @@ int convert_to_sparse(struct index_state *istate, int flags)
 	if (index_has_unmerged_entries(istate))
 		return 0;
 
-	if (!cache_tree_fully_valid(istate->cache_tree)) {
+	if (!cache_tree_fully_valid(istate->repo, istate->cache_tree)) {
 		/* Clear and recompute the cache-tree */
 		cache_tree_free(&istate->cache_tree);
 
diff --git a/submodule-config.c b/submodule-config.c
index f75997402a..37c3be377b 100644
--- a/submodule-config.c
+++ b/submodule-config.c
@@ -1,4 +1,3 @@
-#define USE_THE_REPOSITORY_VARIABLE
 #define DISABLE_SIGN_COMPARE_WARNINGS
 
 #include "git-compat-util.h"
@@ -133,7 +132,9 @@ void submodule_cache_free(struct submodule_cache *cache)
 static unsigned int hash_oid_string(const struct object_id *oid,
 				    const char *string)
 {
-	return memhash(oid->hash, the_hash_algo->rawsz) + strhash(string);
+	if (oid->algo == GIT_HASH_UNKNOWN)
+		BUG("hashing an object ID with unknown algorithm");
+	return memhash(oid->hash, hash_algos[oid->algo].rawsz) + strhash(string);
 }
 
 static void cache_put_path(struct submodule_cache *cache,
@@ -667,19 +668,20 @@ static int parse_config(const char *var, const char *value,
 	return ret;
 }
 
-static int gitmodule_oid_from_commit(const struct object_id *treeish_name,
+static int gitmodule_oid_from_commit(struct repository *repo,
+				     const struct object_id *treeish_name,
 				     struct object_id *gitmodules_oid,
 				     struct strbuf *rev)
 {
 	int ret = 0;
 
 	if (is_null_oid(treeish_name)) {
-		oidclr(gitmodules_oid, the_repository->hash_algo);
+		oidclr(gitmodules_oid, repo->hash_algo);
 		return 1;
 	}
 
 	strbuf_addf(rev, "%s:.gitmodules", oid_to_hex(treeish_name));
-	if (repo_get_oid(the_repository, rev->buf, gitmodules_oid) >= 0)
+	if (repo_get_oid(repo, rev->buf, gitmodules_oid) >= 0)
 		ret = 1;
 
 	return ret;
@@ -689,9 +691,11 @@ static int gitmodule_oid_from_commit(const struct object_id *treeish_name,
  * (key) with on-demand reading of the appropriate .gitmodules from
  * revisions.
  */
-static const struct submodule *config_from(struct submodule_cache *cache,
-		const struct object_id *treeish_name, const char *key,
-		enum lookup_type lookup_type)
+static const struct submodule *config_from(struct repository *repo,
+					   struct submodule_cache *cache,
+					   const struct object_id *treeish_name,
+					   const char *key,
+					   enum lookup_type lookup_type)
 {
 	struct strbuf rev = STRBUF_INIT;
 	size_t config_size;
@@ -718,7 +722,7 @@ static const struct submodule *config_from(struct submodule_cache *cache,
 		return entry->config;
 	}
 
-	if (!gitmodule_oid_from_commit(treeish_name, &oid, &rev))
+	if (!gitmodule_oid_from_commit(repo, treeish_name, &oid, &rev))
 		goto out;
 
 	switch (lookup_type) {
@@ -732,7 +736,7 @@ static const struct submodule *config_from(struct submodule_cache *cache,
 	if (submodule)
 		goto out;
 
-	config = odb_read_object(the_repository->objects, &oid,
+	config = odb_read_object(repo->objects, &oid,
 				 &type, &config_size);
 	if (!config || type != OBJ_BLOB)
 		goto out;
@@ -798,9 +802,6 @@ static void config_from_gitmodules(config_fn_t fn, struct repository *repo, void
 		} else if (repo_get_oid(repo, GITMODULES_INDEX, &oid) >= 0 ||
 			   repo_get_oid(repo, GITMODULES_HEAD, &oid) >= 0) {
 			config_source.blob = oidstr = xstrdup(oid_to_hex(&oid));
-			if (repo != the_repository)
-				odb_add_submodule_source_by_path(the_repository->objects,
-								 repo->objects->sources->path);
 		} else {
 			goto out;
 		}
@@ -821,7 +822,7 @@ static int gitmodules_cb(const char *var, const char *value,
 
 	parameter.cache = repo->submodule_cache;
 	parameter.treeish_name = NULL;
-	parameter.gitmodules_oid = null_oid(the_hash_algo);
+	parameter.gitmodules_oid = null_oid(repo->hash_algo);
 	parameter.overwrite = 1;
 
 	return parse_config(var, value, ctx, &parameter);
@@ -843,21 +844,22 @@ void repo_read_gitmodules(struct repository *repo, int skip_if_read)
 	repo->submodule_cache->gitmodules_read = 1;
 }
 
-void gitmodules_config_oid(const struct object_id *commit_oid)
+void gitmodules_config_oid(struct repository *repo,
+			   const struct object_id *commit_oid)
 {
 	struct strbuf rev = STRBUF_INIT;
 	struct object_id oid;
 
-	submodule_cache_check_init(the_repository);
+	submodule_cache_check_init(repo);
 
-	if (gitmodule_oid_from_commit(commit_oid, &oid, &rev)) {
+	if (gitmodule_oid_from_commit(repo, commit_oid, &oid, &rev)) {
 		git_config_from_blob_oid(gitmodules_cb, rev.buf,
-					 the_repository, &oid, the_repository,
+					 repo, &oid, repo,
 					 CONFIG_SCOPE_UNKNOWN);
 	}
 	strbuf_release(&rev);
 
-	the_repository->submodule_cache->gitmodules_read = 1;
+	repo->submodule_cache->gitmodules_read = 1;
 }
 
 const struct submodule *submodule_from_name(struct repository *r,
@@ -865,7 +867,7 @@ const struct submodule *submodule_from_name(struct repository *r,
 		const char *name)
 {
 	repo_read_gitmodules(r, 1);
-	return config_from(r->submodule_cache, treeish_name, name, lookup_name);
+	return config_from(r, r->submodule_cache, treeish_name, name, lookup_name);
 }
 
 const struct submodule *submodule_from_path(struct repository *r,
@@ -873,7 +875,7 @@ const struct submodule *submodule_from_path(struct repository *r,
 		const char *path)
 {
 	repo_read_gitmodules(r, 1);
-	return config_from(r->submodule_cache, treeish_name, path, lookup_path);
+	return config_from(r, r->submodule_cache, treeish_name, path, lookup_path);
 }
 
 /**
@@ -980,11 +982,12 @@ int print_config_from_gitmodules(struct repository *repo, const char *key)
 	return 0;
 }
 
-int config_set_in_gitmodules_file_gently(const char *key, const char *value)
+int config_set_in_gitmodules_file_gently(struct repository *repo,
+					 const char *key, const char *value)
 {
 	int ret;
 
-	ret = repo_config_set_in_file_gently(the_repository, GITMODULES_FILE, key, NULL, value);
+	ret = repo_config_set_in_file_gently(repo, GITMODULES_FILE, key, NULL, value);
 	if (ret < 0)
 		/* Maybe the user already did that, don't error out here */
 		warning(_("Could not update .gitmodules entry %s"), key);
@@ -1017,13 +1020,15 @@ static int gitmodules_fetch_config(const char *var, const char *value,
 	return 0;
 }
 
-void fetch_config_from_gitmodules(int *max_children, int *recurse_submodules)
+void fetch_config_from_gitmodules(struct repository *repo,
+				  int *max_children,
+				  int *recurse_submodules)
 {
 	struct fetch_config config = {
 		.max_children = max_children,
 		.recurse_submodules = recurse_submodules
 	};
-	config_from_gitmodules(gitmodules_fetch_config, the_repository, &config);
+	config_from_gitmodules(gitmodules_fetch_config, repo, &config);
 }
 
 static int gitmodules_update_clone_config(const char *var, const char *value,
@@ -1036,7 +1041,7 @@ static int gitmodules_update_clone_config(const char *var, const char *value,
 	return 0;
 }
 
-void update_clone_config_from_gitmodules(int *max_jobs)
+void update_clone_config_from_gitmodules(struct repository *repo, int *max_jobs)
 {
-	config_from_gitmodules(gitmodules_update_clone_config, the_repository, max_jobs);
+	config_from_gitmodules(gitmodules_update_clone_config, repo, max_jobs);
 }
diff --git a/submodule-config.h b/submodule-config.h
index f55d4e3b61..755570d5d1 100644
--- a/submodule-config.h
+++ b/submodule-config.h
@@ -57,7 +57,8 @@ int option_fetch_parse_recurse_submodules(const struct option *opt,
 int parse_update_recurse_submodules_arg(const char *opt, const char *arg);
 int parse_push_recurse_submodules_arg(const char *opt, const char *arg);
 void repo_read_gitmodules(struct repository *repo, int skip_if_read);
-void gitmodules_config_oid(const struct object_id *commit_oid);
+void gitmodules_config_oid(struct repository *repo,
+			   const struct object_id *commit_oid);
 
 /**
  * Same as submodule_from_path but lookup by name.
@@ -80,7 +81,8 @@ const struct submodule *submodule_from_path(struct repository *r,
 void submodule_free(struct repository *r);
 
 int print_config_from_gitmodules(struct repository *repo, const char *key);
-int config_set_in_gitmodules_file_gently(const char *key, const char *value);
+int config_set_in_gitmodules_file_gently(struct repository *repo,
+					 const char *key, const char *value);
 
 /*
  * Returns 0 if the name is syntactically acceptable as a submodule "name"
@@ -100,8 +102,10 @@ int check_submodule_url(const char *url);
  * New helpers to retrieve arbitrary configuration from the '.gitmodules' file
  * should NOT be added.
  */
-void fetch_config_from_gitmodules(int *max_children, int *recurse_submodules);
-void update_clone_config_from_gitmodules(int *max_jobs);
+void fetch_config_from_gitmodules(struct repository *repo,
+				  int *max_children,
+				  int *recurse_submodules);
+void update_clone_config_from_gitmodules(struct repository *repo, int *max_jobs);
 
 /*
  * Submodule entry that contains relevant information about a
diff --git a/submodule.c b/submodule.c
index 5c92575888..6fcb606f7e 100644
--- a/submodule.c
+++ b/submodule.c
@@ -133,7 +133,7 @@ int update_path_in_gitmodules(const char *oldpath, const char *newpath)
 	strbuf_addstr(&entry, "submodule.");
 	strbuf_addstr(&entry, submodule->name);
 	strbuf_addstr(&entry, ".path");
-	ret = config_set_in_gitmodules_file_gently(entry.buf, newpath);
+	ret = config_set_in_gitmodules_file_gently(the_repository, entry.buf, newpath);
 	strbuf_release(&entry);
 	return ret;
 }
diff --git a/t/README b/t/README
index 9a9daaf2af..f831c5355b 100644
--- a/t/README
+++ b/t/README
@@ -462,13 +462,6 @@ GIT_TEST_CHECKOUT_WORKERS=<n> overrides the 'checkout.workers' setting
 to <n> and 'checkout.thresholdForParallelism' to 0, forcing the
 execution of the parallel-checkout code.
 
-GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB=<boolean>, when true, makes
-registering submodule ODBs as alternates a fatal action. Support for
-this environment variable can be removed once the migration to
-explicitly providing repositories when accessing submodule objects is
-complete or needs to be abandoned for whatever reason (in which case the
-migrated codepaths still retain their performance benefits).
-
 GIT_TEST_REQUIRE_PREREQ=<list> allows specifying a space separated list of
 prereqs that are required to succeed. If a prereq in this list is triggered by
 a test and then fails then the whole test run will abort. This can help to make
diff --git a/t/helper/test-read-midx.c b/t/helper/test-read-midx.c
index 27a05da957..1f7a1927e4 100644
--- a/t/helper/test-read-midx.c
+++ b/t/helper/test-read-midx.c
@@ -5,34 +5,42 @@
 #include "midx.h"
 #include "repository.h"
 #include "odb.h"
+#include "odb/source-packed.h"
 #include "pack-bitmap.h"
 #include "packfile.h"
 #include "setup.h"
 #include "gettext.h"
 #include "pack-revindex.h"
 
-static struct multi_pack_index *setup_midx(const char *object_dir)
+static struct multi_pack_index *setup_midx(const char *object_dir,
+					   struct odb_source_packed **out)
 {
-	struct odb_source_files *files;
+	struct odb_source_packed *packed;
 	struct odb_source *source;
-	setup_git_directory(the_repository);
-	source = odb_find_source(the_repository->objects, object_dir);
-	if (!source)
-		source = odb_add_to_alternates_memory(the_repository->objects,
-						      object_dir);
-	files = odb_source_files_downcast(source);
 
-	return load_multi_pack_index(files->packed);
+	setup_git_directory(the_repository);
+
+	source = odb_find_source(the_repository->objects, object_dir);
+	if (source) {
+		packed = odb_source_files_downcast(source)->packed;
+	} else {
+		packed = odb_source_packed_new(the_repository->objects,
+					       object_dir, false);
+		*out = packed;
+	}
+
+	return load_multi_pack_index(packed);
 }
 
 static int read_midx_file(const char *object_dir, const char *checksum,
 			  int show_objects)
 {
+	struct odb_source_packed *packed = NULL;
 	uint32_t i;
 	struct multi_pack_index *m, *tip;
 	int ret = 0;
 
-	m = tip = setup_midx(object_dir);
+	m = tip = setup_midx(object_dir, &packed);
 
 	if (!m)
 		return 1;
@@ -91,29 +99,35 @@ static int read_midx_file(const char *object_dir, const char *checksum,
 
 out:
 	close_midx(tip);
+	if (packed)
+		odb_source_free(&packed->base);
 
 	return ret;
 }
 
 static int read_midx_checksum(const char *object_dir)
 {
+	struct odb_source_packed *packed = NULL;
 	struct multi_pack_index *m;
 
-	m = setup_midx(object_dir);
+	m = setup_midx(object_dir, &packed);
 	if (!m)
 		return 1;
 	printf("%s\n", midx_get_checksum_hex(m));
 
 	close_midx(m);
+	if (packed)
+		odb_source_free(&packed->base);
 	return 0;
 }
 
 static int read_midx_preferred_pack(const char *object_dir)
 {
+	struct odb_source_packed *packed = NULL;
 	struct multi_pack_index *midx = NULL;
 	uint32_t preferred_pack;
 
-	midx = setup_midx(object_dir);
+	midx = setup_midx(object_dir, &packed);
 	if (!midx)
 		return 1;
 
@@ -124,17 +138,21 @@ static int read_midx_preferred_pack(const char *object_dir)
 	}
 
 	printf("%s\n", midx->pack_names[preferred_pack]);
+
 	close_midx(midx);
+	if (packed)
+		odb_source_free(&packed->base);
 	return 0;
 }
 
 static int read_midx_bitmapped_packs(const char *object_dir)
 {
+	struct odb_source_packed *packed = NULL;
 	struct multi_pack_index *midx = NULL;
 	struct bitmapped_pack pack;
 	uint32_t i;
 
-	midx = setup_midx(object_dir);
+	midx = setup_midx(object_dir, &packed);
 	if (!midx)
 		return 1;
 
@@ -150,7 +168,8 @@ static int read_midx_bitmapped_packs(const char *object_dir)
 	}
 
 	close_midx(midx);
-
+	if (packed)
+		odb_source_free(&packed->base);
 	return 0;
 }
 
diff --git a/t/helper/test-ref-store.c b/t/helper/test-ref-store.c
index 5a9a3053d9..db58f00589 100644
--- a/t/helper/test-ref-store.c
+++ b/t/helper/test-ref-store.c
@@ -74,14 +74,6 @@ static const char **get_store(const char **argv, struct ref_store **refs)
 	} else if (!strcmp(argv[0], "main")) {
 		*refs = get_main_ref_store(the_repository);
 	} else if (skip_prefix(argv[0], "submodule:", &gitdir)) {
-		struct strbuf sb = STRBUF_INIT;
-
-		if (!repo_submodule_path_append(the_repository,
-						&sb, gitdir, "objects/"))
-			die("computing submodule path failed");
-		odb_add_to_alternates_memory(the_repository->objects, sb.buf);
-		strbuf_release(&sb);
-
 		*refs = repo_get_submodule_ref_store(the_repository, gitdir);
 	} else if (skip_prefix(argv[0], "worktree:", &gitdir)) {
 		struct worktree **p, **worktrees = get_worktrees(the_repository);
diff --git a/t/helper/test-submodule.c b/t/helper/test-submodule.c
index 3c5c4c4a09..ea9bef0904 100644
--- a/t/helper/test-submodule.c
+++ b/t/helper/test-submodule.c
@@ -168,7 +168,7 @@ static int cmd__submodule_config_set(int argc, const char **argv)
 		if (!is_writing_gitmodules_ok())
 			die("please make sure that the .gitmodules file is in the working tree");
 
-		return config_set_in_gitmodules_file_gently(argv[1], argv[2]);
+		return config_set_in_gitmodules_file_gently(the_repository, argv[1], argv[2]);
 	}
 	usage_with_options(usage, options);
 }
@@ -188,7 +188,7 @@ static int cmd__submodule_config_unset(int argc, const char **argv)
 	if (argc == 2) {
 		if (!is_writing_gitmodules_ok())
 			die("please make sure that the .gitmodules file is in the working tree");
-		return config_set_in_gitmodules_file_gently(argv[1], NULL);
+		return config_set_in_gitmodules_file_gently(the_repository, argv[1], NULL);
 	}
 	usage_with_options(usage, options);
 }
diff --git a/t/t5319-multi-pack-index.sh b/t/t5319-multi-pack-index.sh
index 20b010c33b..d32897a7f5 100755
--- a/t/t5319-multi-pack-index.sh
+++ b/t/t5319-multi-pack-index.sh
@@ -711,10 +711,9 @@ test_expect_success 'force some 64-bit offsets with pack-objects' '
 	corrupt_data $idx64 $(test_oid idxoff) "\02" &&
 	# objects64 is not a real repository, but can serve as an alternate
 	# anyway so we can write a MIDX into it
-	git init repo &&
-	test_when_finished "rm -fr repo" &&
+	git init repo64 &&
 	(
-		cd repo &&
+		cd repo64 &&
 		( cd ../objects64 && pwd ) >.git/objects/info/alternates &&
 		midx64=$(git multi-pack-index --object-dir=../objects64 write)
 	) &&
@@ -722,7 +721,7 @@ test_expect_success 'force some 64-bit offsets with pack-objects' '
 '
 
 test_expect_success 'verify multi-pack-index with 64-bit offsets' '
-	git multi-pack-index verify --object-dir=objects64
+	git -C repo64 multi-pack-index verify --object-dir=../objects64
 '
 
 NUM_OBJECTS=63
@@ -734,7 +733,7 @@ MIDX_BYTE_LARGE_OFFSET=$(($MIDX_OFFSET_LARGE_OFFSETS + 3))
 
 test_expect_success 'verify incorrect 64-bit offset' '
 	corrupt_midx_and_verify $MIDX_BYTE_LARGE_OFFSET "\07" objects64 \
-		"incorrect object offset"
+		"incorrect object offset" "git -C repo64 multi-pack-index verify --object-dir=../objects64"
 '
 
 test_expect_success 'setup expire tests' '
diff --git a/t/t5526-fetch-submodules.sh b/t/t5526-fetch-submodules.sh
index 7b3b7359da..37d7373b36 100755
--- a/t/t5526-fetch-submodules.sh
+++ b/t/t5526-fetch-submodules.sh
@@ -3,9 +3,6 @@
 
 test_description='Recursive "git fetch" for submodules'
 
-GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB=1
-export GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB
-
 . ./test-lib.sh
 
 pwd=$(pwd)
diff --git a/t/t5531-deep-submodule-push.sh b/t/t5531-deep-submodule-push.sh
index 7d239dd31f..73429ec6e3 100755
--- a/t/t5531-deep-submodule-push.sh
+++ b/t/t5531-deep-submodule-push.sh
@@ -5,9 +5,6 @@ test_description='test push with submodules'
 GIT_TEST_DEFAULT_INITIAL_BRANCH_NAME=main
 export GIT_TEST_DEFAULT_INITIAL_BRANCH_NAME
 
-GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB=1
-export GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB
-
 . ./test-lib.sh
 
 test_expect_success setup '
diff --git a/t/t5545-push-options.sh b/t/t5545-push-options.sh
index fb13549da7..239edd7d62 100755
--- a/t/t5545-push-options.sh
+++ b/t/t5545-push-options.sh
@@ -5,9 +5,6 @@ test_description='pushing to a repository using push options'
 GIT_TEST_DEFAULT_INITIAL_BRANCH_NAME=main
 export GIT_TEST_DEFAULT_INITIAL_BRANCH_NAME
 
-GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB=1
-export GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB
-
 . ./test-lib.sh
 
 mk_repo_pair () {
diff --git a/t/t5572-pull-submodule.sh b/t/t5572-pull-submodule.sh
index 42d14328b6..9969a3294e 100755
--- a/t/t5572-pull-submodule.sh
+++ b/t/t5572-pull-submodule.sh
@@ -2,9 +2,6 @@
 
 test_description='pull can handle submodules'
 
-GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB=1
-export GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB
-
 . ./test-lib.sh
 . "$TEST_DIRECTORY"/lib-submodule-update.sh
 
diff --git a/t/t6437-submodule-merge.sh b/t/t6437-submodule-merge.sh
index 107e13afbc..1546d5f773 100755
--- a/t/t6437-submodule-merge.sh
+++ b/t/t6437-submodule-merge.sh
@@ -5,9 +5,6 @@ test_description='merging with submodules'
 GIT_TEST_DEFAULT_INITIAL_BRANCH_NAME=main
 export GIT_TEST_DEFAULT_INITIAL_BRANCH_NAME
 
-GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB=1
-export GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB
-
 . ./test-lib.sh
 
 #
diff --git a/t/t7418-submodule-sparse-gitmodules.sh b/t/t7418-submodule-sparse-gitmodules.sh
index dde11ecce8..cf94e30e78 100755
--- a/t/t7418-submodule-sparse-gitmodules.sh
+++ b/t/t7418-submodule-sparse-gitmodules.sh
@@ -12,9 +12,6 @@ The test setup uses a sparse checkout, however the same scenario can be set up
 also by committing .gitmodules and then just removing it from the filesystem.
 '
 
-GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB=1
-export GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB
-
 . ./test-lib.sh
 
 test_expect_success 'setup' '
diff --git a/t/t7814-grep-recurse-submodules.sh b/t/t7814-grep-recurse-submodules.sh
index e1cf53dc9e..3d149d34c1 100755
--- a/t/t7814-grep-recurse-submodules.sh
+++ b/t/t7814-grep-recurse-submodules.sh
@@ -9,9 +9,6 @@ submodules.
 TEST_CREATE_REPO_NO_TEMPLATE=1
 . ./test-lib.sh
 
-GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB=1
-export GIT_TEST_FATAL_REGISTER_SUBMODULE_ODB
-
 test_expect_success 'setup directory structure and submodule' '
 	echo "(1|2)d(3|4)" >a &&
 	mkdir b &&
diff --git a/tmp-objdir.c b/tmp-objdir.c
index 0eaa79ffd7..deaaf6ba2e 100644
--- a/tmp-objdir.c
+++ b/tmp-objdir.c
@@ -321,11 +321,6 @@ const char **tmp_objdir_env(const struct tmp_objdir *t)
 	return t->env.v;
 }
 
-void tmp_objdir_add_as_alternate(const struct tmp_objdir *t)
-{
-	odb_add_to_alternates_memory(t->repo->objects, t->path.buf);
-}
-
 struct odb_source *tmp_objdir_replace_primary_odb(struct tmp_objdir *t,
 						  int will_destroy)
 {
diff --git a/tmp-objdir.h b/tmp-objdir.h
index 81eb927413..05f0d08d10 100644
--- a/tmp-objdir.h
+++ b/tmp-objdir.h
@@ -55,12 +55,6 @@ int tmp_objdir_destroy(struct tmp_objdir *);
  */
 void tmp_objdir_discard_objects(struct tmp_objdir *);
 
-/*
- * Add the temporary object directory as an alternate object store in the
- * current process.
- */
-void tmp_objdir_add_as_alternate(const struct tmp_objdir *);
-
 /*
  * Replaces the writable object store in the current process with the temporary
  * object directory and makes the former main object store an alternate.
diff --git a/unpack-trees.c b/unpack-trees.c
index 154d6d40a1..20e6d6d824 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -416,7 +416,8 @@ static void report_collided_checkout(struct index_state *index)
 	string_list_clear(&list, 0);
 }
 
-static int must_checkout(const struct cache_entry *ce)
+static int must_checkout(const struct cache_entry *ce,
+			 void *cb_data UNUSED)
 {
 	return ce->ce_flags & CE_UPDATE;
 }
@@ -477,7 +478,7 @@ static int check_updates(struct unpack_trees_options *o,
 		 * Prefetch the objects that are to be checked out in the loop
 		 * below.
 		 */
-		prefetch_cache_entries(index, must_checkout);
+		prefetch_cache_entries(index, must_checkout, NULL);
 
 	get_parallel_checkout_configs(&pc_workers, &pc_threshold);
 
@@ -487,7 +488,7 @@ static int check_updates(struct unpack_trees_options *o,
 	for (i = 0; i < index->cache_nr; i++) {
 		struct cache_entry *ce = index->cache[i];
 
-		if (must_checkout(ce)) {
+		if (must_checkout(ce, NULL)) {
 			size_t last_pc_queue_size = pc_queue_size();
 
 			if (ce->ce_flags & CE_WT_REMOVE)
@@ -2086,7 +2087,7 @@ int unpack_trees(unsigned len, struct tree_desc *t, struct unpack_trees_options
 			}
 
 			if (!o->skip_cache_tree_update &&
-			    !cache_tree_fully_valid(o->internal.result.cache_tree))
+			    !cache_tree_fully_valid(the_repository, o->internal.result.cache_tree))
 				cache_tree_update(&o->internal.result,
 						  WRITE_TREE_SILENT |
 						  WRITE_TREE_REPAIR);