diff --git a/builtin/rebase.c b/builtin/rebase.c
index 2e41ad5..966b953 100644
--- a/builtin/rebase.c
+++ b/builtin/rebase.c
@@ -1568,8 +1568,7 @@
 				branch_name = options.head_name;
 
 		} else {
-			free(options.head_name);
-			options.head_name = NULL;
+			FREE_AND_NULL(options.head_name);
 			branch_name = "HEAD";
 		}
 		if (get_oid("HEAD", &options.orig_head))
@@ -1769,7 +1768,7 @@
 	 * we just fast-forwarded.
 	 */
 	strbuf_reset(&msg);
-	if (!oidcmp(&merge_base, &options.orig_head)) {
+	if (oideq(&merge_base, &options.orig_head)) {
 		printf(_("Fast-forwarded %s to %s.\n"),
 			branch_name, options.onto_name);
 		strbuf_addf(&msg, "rebase finished: %s onto %s",
diff --git a/builtin/show-branch.c b/builtin/show-branch.c
index 934e514..082daea 100644
--- a/builtin/show-branch.c
+++ b/builtin/show-branch.c
@@ -753,7 +753,8 @@
 				/* Ah, that is a date spec... */
 				timestamp_t at;
 				at = approxidate(reflog_base);
-				read_ref_at(ref, flags, at, -1, &oid, NULL,
+				read_ref_at(get_main_ref_store(the_repository),
+					    ref, flags, at, -1, &oid, NULL,
 					    NULL, NULL, &base);
 			}
 		}
@@ -765,7 +766,8 @@
 			timestamp_t timestamp;
 			int tz;
 
-			if (read_ref_at(ref, flags, 0, base + i, &oid, &logmsg,
+			if (read_ref_at(get_main_ref_store(the_repository),
+					ref, flags, 0, base + i, &oid, &logmsg,
 					&timestamp, &tz, NULL)) {
 				reflog = i;
 				break;
diff --git a/cache.h b/cache.h
index 9f2fb7b..67cc2e1 100644
--- a/cache.h
+++ b/cache.h
@@ -1047,8 +1047,10 @@
  * Note that while this version avoids the static buffer, it is not fully
  * reentrant, as it calls into other non-reentrant git code.
  */
-extern const char *find_unique_abbrev(const struct object_id *oid, int len);
-extern int find_unique_abbrev_r(char *hex, const struct object_id *oid, int len);
+const char *repo_find_unique_abbrev(struct repository *r, const struct object_id *oid, int len);
+#define find_unique_abbrev(oid, len) repo_find_unique_abbrev(the_repository, oid, len)
+int repo_find_unique_abbrev_r(struct repository *r, char *hex, const struct object_id *oid, int len);
+#define find_unique_abbrev_r(hex, oid, len) repo_find_unique_abbrev_r(the_repository, hex, oid, len)
 
 extern const unsigned char null_sha1[GIT_MAX_RAWSZ];
 extern const struct object_id null_oid;
@@ -1380,20 +1382,32 @@
 		       */
 };
 
-extern int get_oid(const char *str, struct object_id *oid);
-extern int get_oidf(struct object_id *oid, const char *fmt, ...);
-extern int get_oid_commit(const char *str, struct object_id *oid);
-extern int get_oid_committish(const char *str, struct object_id *oid);
-extern int get_oid_tree(const char *str, struct object_id *oid);
-extern int get_oid_treeish(const char *str, struct object_id *oid);
-extern int get_oid_blob(const char *str, struct object_id *oid);
-extern void maybe_die_on_misspelt_object_name(const char *name, const char *prefix);
+int repo_get_oid(struct repository *r, const char *str, struct object_id *oid);
+int get_oidf(struct object_id *oid, const char *fmt, ...);
+int repo_get_oid_commit(struct repository *r, const char *str, struct object_id *oid);
+int repo_get_oid_committish(struct repository *r, const char *str, struct object_id *oid);
+int repo_get_oid_tree(struct repository *r, const char *str, struct object_id *oid);
+int repo_get_oid_treeish(struct repository *r, const char *str, struct object_id *oid);
+int repo_get_oid_blob(struct repository *r, const char *str, struct object_id *oid);
+int repo_get_oid_mb(struct repository *r, const char *str, struct object_id *oid);
+void maybe_die_on_misspelt_object_name(struct repository *repo,
+				       const char *name,
+				       const char *prefix);
 extern enum get_oid_result get_oid_with_context(struct repository *repo, const char *str,
 				unsigned flags, struct object_id *oid,
 				struct object_context *oc);
 
+#define get_oid(str, oid)		repo_get_oid(the_repository, str, oid)
+#define get_oid_commit(str, oid)	repo_get_oid_commit(the_repository, str, oid)
+#define get_oid_committish(str, oid)	repo_get_oid_committish(the_repository, str, oid)
+#define get_oid_tree(str, oid)		repo_get_oid_tree(the_repository, str, oid)
+#define get_oid_treeish(str, oid)	repo_get_oid_treeish(the_repository, str, oid)
+#define get_oid_blob(str, oid)		repo_get_oid_blob(the_repository, str, oid)
+#define get_oid_mb(str, oid) 		repo_get_oid_mb(the_repository, str, oid)
+
 typedef int each_abbrev_fn(const struct object_id *oid, void *);
-extern int for_each_abbrev(const char *prefix, each_abbrev_fn, void *);
+int repo_for_each_abbrev(struct repository *r, const char *prefix, each_abbrev_fn, void *);
+#define for_each_abbrev(prefix, fn, data) repo_for_each_abbrev(the_repository, prefix, fn, data)
 
 extern int set_disambiguate_hint_config(const char *var, const char *value);
 
@@ -1471,9 +1485,12 @@
 #define INTERPRET_BRANCH_LOCAL (1<<0)
 #define INTERPRET_BRANCH_REMOTE (1<<1)
 #define INTERPRET_BRANCH_HEAD (1<<2)
-extern int interpret_branch_name(const char *str, int len, struct strbuf *,
-				 unsigned allowed);
-extern int get_oid_mb(const char *str, struct object_id *oid);
+int repo_interpret_branch_name(struct repository *r,
+			       const char *str, int len,
+			       struct strbuf *buf,
+			       unsigned allowed);
+#define interpret_branch_name(str, len, buf, allowed) \
+	repo_interpret_branch_name(the_repository, str, len, buf, allowed)
 
 extern int validate_headref(const char *ref);
 
@@ -1487,8 +1504,11 @@
 					unsigned long *size,
 					struct object_id *oid_ret);
 
-extern struct object *peel_to_type(const char *name, int namelen,
-				   struct object *o, enum object_type);
+struct object *repo_peel_to_type(struct repository *r,
+				 const char *name, int namelen,
+				 struct object *o, enum object_type);
+#define peel_to_type(name, namelen, obj, type) \
+	repo_peel_to_type(the_repository, name, namelen, obj, type)
 
 enum date_mode_type {
 	DATE_NORMAL = 0,
diff --git a/commit-graph.c b/commit-graph.c
index 66865ac..7bcc9bb 100644
--- a/commit-graph.c
+++ b/commit-graph.c
@@ -397,6 +397,11 @@
 	item->generation = get_be32(commit_data + g->hash_len + 8) >> 2;
 }
 
+static inline void set_commit_tree(struct commit *c, struct tree *t)
+{
+	c->maybe_tree = t;
+}
+
 static int fill_commit_in_graph(struct repository *r,
 				struct commit *item,
 				struct commit_graph *g, uint32_t pos)
@@ -410,7 +415,7 @@
 	item->object.parsed = 1;
 	item->graph_pos = pos;
 
-	item->maybe_tree = NULL;
+	set_commit_tree(item, NULL);
 
 	date_high = get_be32(commit_data + g->hash_len + 8) & 0x3;
 	date_low = get_be32(commit_data + g->hash_len + 12);
@@ -496,7 +501,7 @@
 					   GRAPH_DATA_WIDTH * (c->graph_pos);
 
 	hashcpy(oid.hash, commit_data);
-	c->maybe_tree = lookup_tree(r, &oid);
+	set_commit_tree(c, lookup_tree(r, &oid));
 
 	return c->maybe_tree;
 }
diff --git a/commit.c b/commit.c
index a5333c7..a9e7464 100644
--- a/commit.c
+++ b/commit.c
@@ -340,7 +340,13 @@
 	}
 }
 
-struct tree *get_commit_tree(const struct commit *commit)
+static inline void set_commit_tree(struct commit *c, struct tree *t)
+{
+	c->maybe_tree = t;
+}
+
+struct tree *repo_get_commit_tree(struct repository *r,
+				  const struct commit *commit)
 {
 	if (commit->maybe_tree || !commit->object.parsed)
 		return commit->maybe_tree;
@@ -348,7 +354,7 @@
 	if (commit->graph_pos == COMMIT_NOT_FROM_GRAPH)
 		BUG("commit has NULL tree, but was not loaded from commit-graph");
 
-	return get_commit_tree_in_graph(the_repository, commit);
+	return get_commit_tree_in_graph(r, commit);
 }
 
 struct object_id *get_commit_tree_oid(const struct commit *commit)
@@ -358,7 +364,7 @@
 
 void release_commit_memory(struct parsed_object_pool *pool, struct commit *c)
 {
-	c->maybe_tree = NULL;
+	set_commit_tree(c, NULL);
 	c->index = 0;
 	free_commit_buffer(pool, c);
 	free_commit_list(c->parents);
@@ -406,7 +412,7 @@
 	if (get_oid_hex(bufptr + 5, &parent) < 0)
 		return error("bad tree pointer in commit %s",
 			     oid_to_hex(&item->object.oid));
-	item->maybe_tree = lookup_tree(r, &parent);
+	set_commit_tree(item, lookup_tree(r, &parent));
 	bufptr += tree_entry_len + 1; /* "tree " + "hex sha1" + "\n" */
 	pptr = &item->parents;
 
diff --git a/commit.h b/commit.h
index 8f1f39f..cc19cb5 100644
--- a/commit.h
+++ b/commit.h
@@ -32,7 +32,7 @@
 
 	/*
 	 * If the commit is loaded from the commit-graph file, then this
-	 * member may be NULL. Only access it through get_commit_tree()
+	 * member may be NULL. Only access it through repo_get_commit_tree()
 	 * or get_commit_tree_oid().
 	 */
 	struct tree *maybe_tree;
@@ -149,7 +149,8 @@
  */
 void free_commit_buffer(struct parsed_object_pool *pool, struct commit *);
 
-struct tree *get_commit_tree(const struct commit *);
+struct tree *repo_get_commit_tree(struct repository *, const struct commit *);
+#define get_commit_tree(c) repo_get_commit_tree(the_repository, c)
 struct object_id *get_commit_tree_oid(const struct commit *);
 
 /*
diff --git a/contrib/coccinelle/commit.cocci b/contrib/coccinelle/commit.cocci
index c49aa55..d034533 100644
--- a/contrib/coccinelle/commit.cocci
+++ b/contrib/coccinelle/commit.cocci
@@ -10,19 +10,25 @@
 - c->maybe_tree->object.oid.hash
 + get_commit_tree_oid(c)->hash
 
-// These excluded functions must access c->maybe_tree direcly.
 @@
-identifier f !~ "^(get_commit_tree|get_commit_tree_in_graph_one|load_tree_for_commit)$";
+identifier f !~ "^set_commit_tree$";
+expression c;
+expression s;
+@@
+  f(...) {<...
+- c->maybe_tree = s
++ set_commit_tree(c, s)
+  ...>}
+
+// These excluded functions must access c->maybe_tree direcly.
+// Note that if c->maybe_tree is written somewhere outside of these
+// functions, then the recommended transformation will be bogus with
+// repo_get_commit_tree() on the LHS.
+@@
+identifier f !~ "^(repo_get_commit_tree|get_commit_tree_in_graph_one|load_tree_for_commit|set_commit_tree)$";
 expression c;
 @@
   f(...) {<...
 - c->maybe_tree
-+ get_commit_tree(c)
++ repo_get_commit_tree(specify_the_right_repo_here, c)
   ...>}
-
-@@
-expression c;
-expression s;
-@@
-- get_commit_tree(c) = s
-+ c->maybe_tree = s
diff --git a/dir.c b/dir.c
index 0a3ddcf..2ccd4db 100644
--- a/dir.c
+++ b/dir.c
@@ -2316,6 +2316,14 @@
 	return lstat(f, &sb) == 0;
 }
 
+int repo_file_exists(struct repository *repo, const char *path)
+{
+	if (repo != the_repository)
+		BUG("do not know how to check file existence in arbitrary repo");
+
+	return file_exists(path);
+}
+
 static int cmp_icase(char a, char b)
 {
 	if (a == b)
diff --git a/dir.h b/dir.h
index 823bae6..c23313b 100644
--- a/dir.h
+++ b/dir.h
@@ -269,7 +269,9 @@
 			int baselen, struct exclude_list *el, int srcpos);
 extern void clear_exclude_list(struct exclude_list *el);
 extern void clear_directory(struct dir_struct *dir);
-extern int file_exists(const char *);
+
+int repo_file_exists(struct repository *repo, const char *path);
+int file_exists(const char *);
 
 extern int is_inside_dir(const char *dir);
 extern int dir_inside_of(const char *subdir, const char *dir);
diff --git a/merge-recursive.c b/merge-recursive.c
index 69abd6e..a7bcfcb 100644
--- a/merge-recursive.c
+++ b/merge-recursive.c
@@ -163,6 +163,11 @@
 	return lookup_tree(repo, &shifted);
 }
 
+static inline void set_commit_tree(struct commit *c, struct tree *t)
+{
+	c->maybe_tree = t;
+}
+
 static struct commit *make_virtual_commit(struct repository *repo,
 					  struct tree *tree,
 					  const char *comment)
@@ -170,7 +175,7 @@
 	struct commit *commit = alloc_commit_node(repo);
 
 	set_merge_remote_desc(commit, comment, (struct object *)commit);
-	commit->maybe_tree = tree;
+	set_commit_tree(commit, tree);
 	commit->object.parsed = 1;
 	return commit;
 }
diff --git a/packfile.c b/packfile.c
index cdf6b6e..9f52af9 100644
--- a/packfile.c
+++ b/packfile.c
@@ -903,25 +903,25 @@
  * all unreachable objects about to be pruned, in which case they're not really
  * interesting as a measure of repo size in the first place.
  */
-unsigned long approximate_object_count(void)
+unsigned long repo_approximate_object_count(struct repository *r)
 {
-	if (!the_repository->objects->approximate_object_count_valid) {
+	if (!r->objects->approximate_object_count_valid) {
 		unsigned long count;
 		struct multi_pack_index *m;
 		struct packed_git *p;
 
-		prepare_packed_git(the_repository);
+		prepare_packed_git(r);
 		count = 0;
-		for (m = get_multi_pack_index(the_repository); m; m = m->next)
+		for (m = get_multi_pack_index(r); m; m = m->next)
 			count += m->num_objects;
-		for (p = the_repository->objects->packed_git; p; p = p->next) {
+		for (p = r->objects->packed_git; p; p = p->next) {
 			if (open_pack_index(p))
 				continue;
 			count += p->num_objects;
 		}
-		the_repository->objects->approximate_object_count = count;
+		r->objects->approximate_object_count = count;
 	}
-	return the_repository->objects->approximate_object_count;
+	return r->objects->approximate_object_count;
 }
 
 static void *get_next_packed_git(const void *p)
diff --git a/packfile.h b/packfile.h
index 12baa61..b678d35 100644
--- a/packfile.h
+++ b/packfile.h
@@ -63,7 +63,8 @@
  * Give a rough count of objects in the repository. This sacrifices accuracy
  * for speed.
  */
-unsigned long approximate_object_count(void);
+unsigned long repo_approximate_object_count(struct repository *r);
+#define approximate_object_count() repo_approximate_object_count(the_repository)
 
 struct packed_git *find_sha1_pack(const unsigned char *sha1,
 				  struct packed_git *packs);
diff --git a/refs.c b/refs.c
index 142888a..92d1f6d 100644
--- a/refs.c
+++ b/refs.c
@@ -241,9 +241,14 @@
 	return read_ref_full(refname, RESOLVE_REF_READING, oid, NULL);
 }
 
+static int refs_ref_exists(struct ref_store *refs, const char *refname)
+{
+	return !!refs_resolve_ref_unsafe(refs, refname, RESOLVE_REF_READING, NULL, NULL);
+}
+
 int ref_exists(const char *refname)
 {
-	return !!resolve_ref_unsafe(refname, RESOLVE_REF_READING, NULL, NULL);
+	return refs_ref_exists(get_main_ref_store(the_repository), refname);
 }
 
 static int match_ref_pattern(const char *refname,
@@ -534,10 +539,11 @@
  * later free()ing) if the string passed in is a magic short-hand form
  * to name a branch.
  */
-static char *substitute_branch_name(const char **string, int *len)
+static char *substitute_branch_name(struct repository *r,
+				    const char **string, int *len)
 {
 	struct strbuf buf = STRBUF_INIT;
-	int ret = interpret_branch_name(*string, *len, &buf, 0);
+	int ret = repo_interpret_branch_name(r, *string, *len, &buf, 0);
 
 	if (ret == *len) {
 		size_t size;
@@ -549,15 +555,22 @@
 	return NULL;
 }
 
-int dwim_ref(const char *str, int len, struct object_id *oid, char **ref)
+int repo_dwim_ref(struct repository *r, const char *str, int len,
+		  struct object_id *oid, char **ref)
 {
-	char *last_branch = substitute_branch_name(&str, &len);
-	int   refs_found  = expand_ref(str, len, oid, ref);
+	char *last_branch = substitute_branch_name(r, &str, &len);
+	int   refs_found  = expand_ref(r, str, len, oid, ref);
 	free(last_branch);
 	return refs_found;
 }
 
-int expand_ref(const char *str, int len, struct object_id *oid, char **ref)
+int dwim_ref(const char *str, int len, struct object_id *oid, char **ref)
+{
+	return repo_dwim_ref(the_repository, str, len, oid, ref);
+}
+
+int expand_ref(struct repository *repo, const char *str, int len,
+	       struct object_id *oid, char **ref)
 {
 	const char **p, *r;
 	int refs_found = 0;
@@ -572,8 +585,9 @@
 		this_result = refs_found ? &oid_from_ref : oid;
 		strbuf_reset(&fullref);
 		strbuf_addf(&fullref, *p, len, str);
-		r = resolve_ref_unsafe(fullref.buf, RESOLVE_REF_READING,
-				       this_result, &flag);
+		r = refs_resolve_ref_unsafe(get_main_ref_store(repo),
+					    fullref.buf, RESOLVE_REF_READING,
+					    this_result, &flag);
 		if (r) {
 			if (!refs_found++)
 				*ref = xstrdup(r);
@@ -589,9 +603,11 @@
 	return refs_found;
 }
 
-int dwim_log(const char *str, int len, struct object_id *oid, char **log)
+int repo_dwim_log(struct repository *r, const char *str, int len,
+		  struct object_id *oid, char **log)
 {
-	char *last_branch = substitute_branch_name(&str, &len);
+	struct ref_store *refs = get_main_ref_store(r);
+	char *last_branch = substitute_branch_name(r, &str, &len);
 	const char **p;
 	int logs_found = 0;
 	struct strbuf path = STRBUF_INIT;
@@ -603,13 +619,15 @@
 
 		strbuf_reset(&path);
 		strbuf_addf(&path, *p, len, str);
-		ref = resolve_ref_unsafe(path.buf, RESOLVE_REF_READING,
-					 &hash, NULL);
+		ref = refs_resolve_ref_unsafe(refs, path.buf,
+					      RESOLVE_REF_READING,
+					      &hash, NULL);
 		if (!ref)
 			continue;
-		if (reflog_exists(path.buf))
+		if (refs_reflog_exists(refs, path.buf))
 			it = path.buf;
-		else if (strcmp(ref, path.buf) && reflog_exists(ref))
+		else if (strcmp(ref, path.buf) &&
+			 refs_reflog_exists(refs, ref))
 			it = ref;
 		else
 			continue;
@@ -625,6 +643,11 @@
 	return logs_found;
 }
 
+int dwim_log(const char *str, int len, struct object_id *oid, char **log)
+{
+	return repo_dwim_log(the_repository, str, len, oid, log);
+}
+
 static int is_per_worktree_ref(const char *refname)
 {
 	return !strcmp(refname, "HEAD") ||
@@ -944,7 +967,8 @@
 	return 1;
 }
 
-int read_ref_at(const char *refname, unsigned int flags, timestamp_t at_time, int cnt,
+int read_ref_at(struct ref_store *refs, const char *refname,
+		unsigned int flags, timestamp_t at_time, int cnt,
 		struct object_id *oid, char **msg,
 		timestamp_t *cutoff_time, int *cutoff_tz, int *cutoff_cnt)
 {
@@ -960,7 +984,7 @@
 	cb.cutoff_cnt = cutoff_cnt;
 	cb.oid = oid;
 
-	for_each_reflog_ent_reverse(refname, read_ref_at_ent, &cb);
+	refs_for_each_reflog_ent_reverse(refs, refname, read_ref_at_ent, &cb);
 
 	if (!cb.reccnt) {
 		if (flags & GET_OID_QUIETLY)
@@ -971,7 +995,7 @@
 	if (cb.found_it)
 		return 0;
 
-	for_each_reflog_ent(refname, read_ref_at_ent_oldest, &cb);
+	refs_for_each_reflog_ent(refs, refname, read_ref_at_ent_oldest, &cb);
 
 	return 1;
 }
@@ -1164,7 +1188,8 @@
 			       old_oid, flags, onerr);
 }
 
-char *shorten_unambiguous_ref(const char *refname, int strict)
+char *refs_shorten_unambiguous_ref(struct ref_store *refs,
+				   const char *refname, int strict)
 {
 	int i;
 	static char **scanf_fmts;
@@ -1242,7 +1267,7 @@
 			strbuf_reset(&resolved_buf);
 			strbuf_addf(&resolved_buf, rule,
 				    short_name_len, short_name);
-			if (ref_exists(resolved_buf.buf))
+			if (refs_ref_exists(refs, resolved_buf.buf))
 				break;
 		}
 
@@ -1261,6 +1286,12 @@
 	return xstrdup(refname);
 }
 
+char *shorten_unambiguous_ref(const char *refname, int strict)
+{
+	return refs_shorten_unambiguous_ref(get_main_ref_store(the_repository),
+					    refname, strict);
+}
+
 static struct string_list *hide_refs;
 
 int parse_hide_refs_config(const char *var, const char *value, const char *section)
diff --git a/refs.h b/refs.h
index 308fa1f..8f9cbf8 100644
--- a/refs.h
+++ b/refs.h
@@ -148,7 +148,9 @@
 struct argv_array;
 void expand_ref_prefix(struct argv_array *prefixes, const char *prefix);
 
-int expand_ref(const char *str, int len, struct object_id *oid, char **ref);
+int expand_ref(struct repository *r, const char *str, int len, struct object_id *oid, char **ref);
+int repo_dwim_ref(struct repository *r, const char *str, int len, struct object_id *oid, char **ref);
+int repo_dwim_log(struct repository *r, const char *str, int len, struct object_id *oid, char **ref);
 int dwim_ref(const char *str, int len, struct object_id *oid, char **ref);
 int dwim_log(const char *str, int len, struct object_id *oid, char **ref);
 
@@ -386,7 +388,8 @@
 int safe_create_reflog(const char *refname, int force_create, struct strbuf *err);
 
 /** Reads log for the value of ref during at_time. **/
-int read_ref_at(const char *refname, unsigned int flags,
+int read_ref_at(struct ref_store *refs,
+		const char *refname, unsigned int flags,
 		timestamp_t at_time, int cnt,
 		struct object_id *oid, char **msg,
 		timestamp_t *cutoff_time, int *cutoff_tz, int *cutoff_cnt);
@@ -462,6 +465,8 @@
 
 const char *prettify_refname(const char *refname);
 
+char *refs_shorten_unambiguous_ref(struct ref_store *refs,
+				   const char *refname, int strict);
 char *shorten_unambiguous_ref(const char *refname, int strict);
 
 /** rename ref, return 0 on success **/
diff --git a/setup.c b/setup.c
index d0c958c..8dcb463 100644
--- a/setup.c
+++ b/setup.c
@@ -164,7 +164,8 @@
 	die_errno(_("failed to stat '%s'"), arg);
 }
 
-static void NORETURN die_verify_filename(const char *prefix,
+static void NORETURN die_verify_filename(struct repository *r,
+					 const char *prefix,
 					 const char *arg,
 					 int diagnose_misspelt_rev)
 {
@@ -179,7 +180,7 @@
 	 * let maybe_die_on_misspelt_object_name() even trigger.
 	 */
 	if (!(arg[0] == ':' && !isalnum(arg[1])))
-		maybe_die_on_misspelt_object_name(arg, prefix);
+		maybe_die_on_misspelt_object_name(r, arg, prefix);
 
 	/* ... or fall back the most general message. */
 	die(_("ambiguous argument '%s': unknown revision or path not in the working tree.\n"
@@ -234,7 +235,7 @@
 		die(_("option '%s' must come before non-option arguments"), arg);
 	if (looks_like_pathspec(arg) || check_filename(prefix, arg))
 		return;
-	die_verify_filename(prefix, arg, diagnose_misspelt_rev);
+	die_verify_filename(the_repository, prefix, arg, diagnose_misspelt_rev);
 }
 
 /*
diff --git a/sha1-name.c b/sha1-name.c
index 7754d3a..775a73d 100644
--- a/sha1-name.c
+++ b/sha1-name.c
@@ -12,18 +12,20 @@
 #include "packfile.h"
 #include "object-store.h"
 #include "repository.h"
+#include "submodule.h"
 #include "midx.h"
 #include "commit-reach.h"
 
-static int get_oid_oneline(const char *, struct object_id *, struct commit_list *);
+static int get_oid_oneline(struct repository *r, const char *, struct object_id *, struct commit_list *);
 
-typedef int (*disambiguate_hint_fn)(const struct object_id *, void *);
+typedef int (*disambiguate_hint_fn)(struct repository *, const struct object_id *, void *);
 
 struct disambiguate_state {
 	int len; /* length of prefix in hex chars */
 	char hex_pfx[GIT_MAX_HEXSZ + 1];
 	struct object_id bin_pfx;
 
+	struct repository *repo;
 	disambiguate_hint_fn fn;
 	void *cb_data;
 	struct object_id candidate;
@@ -38,7 +40,7 @@
 static void update_candidates(struct disambiguate_state *ds, const struct object_id *current)
 {
 	if (ds->always_call_fn) {
-		ds->ambiguous = ds->fn(current, ds->cb_data) ? 1 : 0;
+		ds->ambiguous = ds->fn(ds->repo, current, ds->cb_data) ? 1 : 0;
 		return;
 	}
 	if (!ds->candidate_exists) {
@@ -58,7 +60,7 @@
 	}
 
 	if (!ds->candidate_checked) {
-		ds->candidate_ok = ds->fn(&ds->candidate, ds->cb_data);
+		ds->candidate_ok = ds->fn(ds->repo, &ds->candidate, ds->cb_data);
 		ds->disambiguate_fn_used = 1;
 		ds->candidate_checked = 1;
 	}
@@ -71,7 +73,7 @@
 	}
 
 	/* if we reach this point, we know ds->candidate satisfies fn */
-	if (ds->fn(current, ds->cb_data)) {
+	if (ds->fn(ds->repo, current, ds->cb_data)) {
 		/*
 		 * if both current and candidate satisfy fn, we cannot
 		 * disambiguate.
@@ -89,9 +91,7 @@
 {
 	struct object_directory *odb;
 
-	for (odb = the_repository->objects->odb;
-	     odb && !ds->ambiguous;
-	     odb = odb->next) {
+	for (odb = ds->repo->objects->odb; odb && !ds->ambiguous; odb = odb->next) {
 		int pos;
 		struct oid_array *loose_objects;
 
@@ -182,10 +182,10 @@
 	struct multi_pack_index *m;
 	struct packed_git *p;
 
-	for (m = get_multi_pack_index(the_repository); m && !ds->ambiguous;
+	for (m = get_multi_pack_index(ds->repo); m && !ds->ambiguous;
 	     m = m->next)
 		unique_in_midx(m, ds);
-	for (p = get_packed_git(the_repository); p && !ds->ambiguous;
+	for (p = get_packed_git(ds->repo); p && !ds->ambiguous;
 	     p = p->next)
 		unique_in_pack(p, ds);
 }
@@ -215,7 +215,7 @@
 		 * same repository!
 		 */
 		ds->candidate_ok = (!ds->disambiguate_fn_used ||
-				    ds->fn(&ds->candidate, ds->cb_data));
+				    ds->fn(ds->repo, &ds->candidate, ds->cb_data));
 
 	if (!ds->candidate_ok)
 		return SHORT_NAME_AMBIGUOUS;
@@ -224,59 +224,67 @@
 	return 0;
 }
 
-static int disambiguate_commit_only(const struct object_id *oid, void *cb_data_unused)
+static int disambiguate_commit_only(struct repository *r,
+				    const struct object_id *oid,
+				    void *cb_data_unused)
 {
-	int kind = oid_object_info(the_repository, oid, NULL);
+	int kind = oid_object_info(r, oid, NULL);
 	return kind == OBJ_COMMIT;
 }
 
-static int disambiguate_committish_only(const struct object_id *oid, void *cb_data_unused)
+static int disambiguate_committish_only(struct repository *r,
+					const struct object_id *oid,
+					void *cb_data_unused)
 {
 	struct object *obj;
 	int kind;
 
-	kind = oid_object_info(the_repository, oid, NULL);
+	kind = oid_object_info(r, oid, NULL);
 	if (kind == OBJ_COMMIT)
 		return 1;
 	if (kind != OBJ_TAG)
 		return 0;
 
 	/* We need to do this the hard way... */
-	obj = deref_tag(the_repository, parse_object(the_repository, oid),
-			NULL, 0);
+	obj = deref_tag(r, parse_object(r, oid), NULL, 0);
 	if (obj && obj->type == OBJ_COMMIT)
 		return 1;
 	return 0;
 }
 
-static int disambiguate_tree_only(const struct object_id *oid, void *cb_data_unused)
+static int disambiguate_tree_only(struct repository *r,
+				  const struct object_id *oid,
+				  void *cb_data_unused)
 {
-	int kind = oid_object_info(the_repository, oid, NULL);
+	int kind = oid_object_info(r, oid, NULL);
 	return kind == OBJ_TREE;
 }
 
-static int disambiguate_treeish_only(const struct object_id *oid, void *cb_data_unused)
+static int disambiguate_treeish_only(struct repository *r,
+				     const struct object_id *oid,
+				     void *cb_data_unused)
 {
 	struct object *obj;
 	int kind;
 
-	kind = oid_object_info(the_repository, oid, NULL);
+	kind = oid_object_info(r, oid, NULL);
 	if (kind == OBJ_TREE || kind == OBJ_COMMIT)
 		return 1;
 	if (kind != OBJ_TAG)
 		return 0;
 
 	/* We need to do this the hard way... */
-	obj = deref_tag(the_repository, parse_object(the_repository, oid),
-			NULL, 0);
+	obj = deref_tag(r, parse_object(r, oid), NULL, 0);
 	if (obj && (obj->type == OBJ_TREE || obj->type == OBJ_COMMIT))
 		return 1;
 	return 0;
 }
 
-static int disambiguate_blob_only(const struct object_id *oid, void *cb_data_unused)
+static int disambiguate_blob_only(struct repository *r,
+				  const struct object_id *oid,
+				  void *cb_data_unused)
 {
-	int kind = oid_object_info(the_repository, oid, NULL);
+	int kind = oid_object_info(r, oid, NULL);
 	return kind == OBJ_BLOB;
 }
 
@@ -310,7 +318,8 @@
 	return error("unknown hint type for '%s': %s", var, value);
 }
 
-static int init_object_disambiguation(const char *name, int len,
+static int init_object_disambiguation(struct repository *r,
+				      const char *name, int len,
 				      struct disambiguate_state *ds)
 {
 	int i;
@@ -341,7 +350,8 @@
 
 	ds->len = len;
 	ds->hex_pfx[len] = '\0';
-	prepare_alt_odb(the_repository);
+	ds->repo = r;
+	prepare_alt_odb(r);
 	return 0;
 }
 
@@ -351,25 +361,25 @@
 	struct strbuf desc = STRBUF_INIT;
 	int type;
 
-	if (ds->fn && !ds->fn(oid, ds->cb_data))
+	if (ds->fn && !ds->fn(ds->repo, oid, ds->cb_data))
 		return 0;
 
-	type = oid_object_info(the_repository, oid, NULL);
+	type = oid_object_info(ds->repo, oid, NULL);
 	if (type == OBJ_COMMIT) {
-		struct commit *commit = lookup_commit(the_repository, oid);
+		struct commit *commit = lookup_commit(ds->repo, oid);
 		if (commit) {
 			struct pretty_print_context pp = {0};
 			pp.date_mode.type = DATE_SHORT;
 			format_commit_message(commit, " %ad - %s", &desc, &pp);
 		}
 	} else if (type == OBJ_TAG) {
-		struct tag *tag = lookup_tag(the_repository, oid);
+		struct tag *tag = lookup_tag(ds->repo, oid);
 		if (!parse_tag(tag) && tag->tag)
 			strbuf_addf(&desc, " %s", tag->tag);
 	}
 
 	advise("  %s %s%s",
-	       find_unique_abbrev(oid, DEFAULT_ABBREV),
+	       repo_find_unique_abbrev(ds->repo, oid, DEFAULT_ABBREV),
 	       type_name(type) ? type_name(type) : "unknown type",
 	       desc.buf);
 
@@ -383,10 +393,18 @@
 	return 0;
 }
 
+static int repo_collect_ambiguous(struct repository *r,
+				  const struct object_id *oid,
+				  void *data)
+{
+	return collect_ambiguous(oid, data);
+}
+
+static struct repository *sort_ambiguous_repo;
 static int sort_ambiguous(const void *a, const void *b)
 {
-	int a_type = oid_object_info(the_repository, a, NULL);
-	int b_type = oid_object_info(the_repository, b, NULL);
+	int a_type = oid_object_info(sort_ambiguous_repo, a, NULL);
+	int b_type = oid_object_info(sort_ambiguous_repo, b, NULL);
 	int a_type_sort;
 	int b_type_sort;
 
@@ -411,7 +429,16 @@
 	return a_type_sort > b_type_sort ? 1 : -1;
 }
 
-static enum get_oid_result get_short_oid(const char *name, int len,
+static void sort_ambiguous_oid_array(struct repository *r, struct oid_array *a)
+{
+	/* mutex will be needed if this code is to be made thread safe */
+	sort_ambiguous_repo = r;
+	QSORT(a->oid, a->nr, sort_ambiguous);
+	sort_ambiguous_repo = NULL;
+}
+
+static enum get_oid_result get_short_oid(struct repository *r,
+					 const char *name, int len,
 					 struct object_id *oid,
 					 unsigned flags)
 {
@@ -419,7 +446,7 @@
 	struct disambiguate_state ds;
 	int quietly = !!(flags & GET_OID_QUIETLY);
 
-	if (init_object_disambiguation(name, len, &ds) < 0)
+	if (init_object_disambiguation(r, name, len, &ds) < 0)
 		return -1;
 
 	if (HAS_MULTI_BITS(flags & GET_OID_DISAMBIGUATORS))
@@ -469,8 +496,8 @@
 			ds.fn = NULL;
 
 		advise(_("The candidates are:"));
-		for_each_abbrev(ds.hex_pfx, collect_ambiguous, &collect);
-		QSORT(collect.oid, collect.nr, sort_ambiguous);
+		repo_for_each_abbrev(r, ds.hex_pfx, collect_ambiguous, &collect);
+		sort_ambiguous_oid_array(r, &collect);
 
 		if (oid_array_for_each(&collect, show_ambiguous_object, &ds))
 			BUG("show_ambiguous_object shouldn't return non-zero");
@@ -480,17 +507,18 @@
 	return status;
 }
 
-int for_each_abbrev(const char *prefix, each_abbrev_fn fn, void *cb_data)
+int repo_for_each_abbrev(struct repository *r, const char *prefix,
+			 each_abbrev_fn fn, void *cb_data)
 {
 	struct oid_array collect = OID_ARRAY_INIT;
 	struct disambiguate_state ds;
 	int ret;
 
-	if (init_object_disambiguation(prefix, strlen(prefix), &ds) < 0)
+	if (init_object_disambiguation(r, prefix, strlen(prefix), &ds) < 0)
 		return -1;
 
 	ds.always_call_fn = 1;
-	ds.fn = collect_ambiguous;
+	ds.fn = repo_collect_ambiguous;
 	ds.cb_data = &collect;
 	find_short_object_filename(&ds);
 	find_short_packed_object(&ds);
@@ -517,6 +545,7 @@
 	unsigned int init_len;
 	unsigned int cur_len;
 	char *hex;
+	struct repository *repo;
 	const struct object_id *oid;
 };
 
@@ -545,6 +574,13 @@
 	return 0;
 }
 
+static int repo_extend_abbrev_len(struct repository *r,
+				  const struct object_id *oid,
+				  void *cb_data)
+{
+	return extend_abbrev_len(oid, cb_data);
+}
+
 static void find_abbrev_len_for_midx(struct multi_pack_index *m,
 				     struct min_abbrev_data *mad)
 {
@@ -622,21 +658,22 @@
 	struct multi_pack_index *m;
 	struct packed_git *p;
 
-	for (m = get_multi_pack_index(the_repository); m; m = m->next)
+	for (m = get_multi_pack_index(mad->repo); m; m = m->next)
 		find_abbrev_len_for_midx(m, mad);
-	for (p = get_packed_git(the_repository); p; p = p->next)
+	for (p = get_packed_git(mad->repo); p; p = p->next)
 		find_abbrev_len_for_pack(p, mad);
 }
 
-int find_unique_abbrev_r(char *hex, const struct object_id *oid, int len)
+int repo_find_unique_abbrev_r(struct repository *r, char *hex,
+			      const struct object_id *oid, int len)
 {
 	struct disambiguate_state ds;
 	struct min_abbrev_data mad;
 	struct object_id oid_ret;
-	const unsigned hexsz = the_hash_algo->hexsz;
+	const unsigned hexsz = r->hash_algo->hexsz;
 
 	if (len < 0) {
-		unsigned long count = approximate_object_count();
+		unsigned long count = repo_approximate_object_count(r);
 		/*
 		 * Add one because the MSB only tells us the highest bit set,
 		 * not including the value of all the _other_ bits (so "15"
@@ -661,6 +698,7 @@
 	if (len == hexsz || !len)
 		return hexsz;
 
+	mad.repo = r;
 	mad.init_len = len;
 	mad.cur_len = len;
 	mad.hex = hex;
@@ -668,10 +706,10 @@
 
 	find_abbrev_len_packed(&mad);
 
-	if (init_object_disambiguation(hex, mad.cur_len, &ds) < 0)
+	if (init_object_disambiguation(r, hex, mad.cur_len, &ds) < 0)
 		return -1;
 
-	ds.fn = extend_abbrev_len;
+	ds.fn = repo_extend_abbrev_len;
 	ds.always_call_fn = 1;
 	ds.cb_data = (void *)&mad;
 
@@ -682,13 +720,15 @@
 	return mad.cur_len;
 }
 
-const char *find_unique_abbrev(const struct object_id *oid, int len)
+const char *repo_find_unique_abbrev(struct repository *r,
+				    const struct object_id *oid,
+				    int len)
 {
 	static int bufno;
 	static char hexbuffer[4][GIT_MAX_HEXSZ + 1];
 	char *hex = hexbuffer[bufno];
 	bufno = (bufno + 1) % ARRAY_SIZE(hexbuffer);
-	find_unique_abbrev_r(hex, oid, len);
+	repo_find_unique_abbrev_r(r, hex, oid, len);
 	return hex;
 }
 
@@ -743,11 +783,11 @@
 	return at_mark(string, len, suffix, ARRAY_SIZE(suffix));
 }
 
-static enum get_oid_result get_oid_1(const char *name, int len, struct object_id *oid, unsigned lookup_flags);
-static int interpret_nth_prior_checkout(const char *name, int namelen, struct strbuf *buf);
+static enum get_oid_result get_oid_1(struct repository *r, const char *name, int len, struct object_id *oid, unsigned lookup_flags);
+static int interpret_nth_prior_checkout(struct repository *r, const char *name, int namelen, struct strbuf *buf);
 
-static int get_oid_basic(const char *str, int len, struct object_id *oid,
-			  unsigned int flags)
+static int get_oid_basic(struct repository *r, const char *str, int len,
+			 struct object_id *oid, unsigned int flags)
 {
 	static const char *warn_msg = "refname '%.*s' is ambiguous.";
 	static const char *object_name_msg = N_(
@@ -765,9 +805,9 @@
 	int refs_found = 0;
 	int at, reflog_len, nth_prior = 0;
 
-	if (len == the_hash_algo->hexsz && !get_oid_hex(str, oid)) {
+	if (len == r->hash_algo->hexsz && !get_oid_hex(str, oid)) {
 		if (warn_ambiguous_refs && warn_on_object_refname_ambiguity) {
-			refs_found = dwim_ref(str, len, &tmp_oid, &real_ref);
+			refs_found = repo_dwim_ref(r, str, len, &tmp_oid, &real_ref);
 			if (refs_found > 0) {
 				warning(warn_msg, len, str);
 				if (advice_object_name_warning)
@@ -808,8 +848,8 @@
 		struct strbuf buf = STRBUF_INIT;
 		int detached;
 
-		if (interpret_nth_prior_checkout(str, len, &buf) > 0) {
-			detached = (buf.len == the_hash_algo->hexsz && !get_oid_hex(buf.buf, oid));
+		if (interpret_nth_prior_checkout(r, str, len, &buf) > 0) {
+			detached = (buf.len == r->hash_algo->hexsz && !get_oid_hex(buf.buf, oid));
 			strbuf_release(&buf);
 			if (detached)
 				return 0;
@@ -818,18 +858,18 @@
 
 	if (!len && reflog_len)
 		/* allow "@{...}" to mean the current branch reflog */
-		refs_found = dwim_ref("HEAD", 4, oid, &real_ref);
+		refs_found = repo_dwim_ref(r, "HEAD", 4, oid, &real_ref);
 	else if (reflog_len)
-		refs_found = dwim_log(str, len, oid, &real_ref);
+		refs_found = repo_dwim_log(r, str, len, oid, &real_ref);
 	else
-		refs_found = dwim_ref(str, len, oid, &real_ref);
+		refs_found = repo_dwim_ref(r, str, len, oid, &real_ref);
 
 	if (!refs_found)
 		return -1;
 
 	if (warn_ambiguous_refs && !(flags & GET_OID_QUIETLY) &&
 	    (refs_found > 1 ||
-	     !get_short_oid(str, len, &tmp_oid, GET_OID_QUIETLY)))
+	     !get_short_oid(r, str, len, &tmp_oid, GET_OID_QUIETLY)))
 		warning(warn_msg, len, str);
 
 	if (reflog_len) {
@@ -861,7 +901,8 @@
 				return -1;
 			}
 		}
-		if (read_ref_at(real_ref, flags, at_time, nth, oid, NULL,
+		if (read_ref_at(get_main_ref_store(r),
+				real_ref, flags, at_time, nth, oid, NULL,
 				&co_time, &co_tz, &co_cnt)) {
 			if (!len) {
 				if (starts_with(real_ref, "refs/heads/")) {
@@ -893,18 +934,19 @@
 	return 0;
 }
 
-static enum get_oid_result get_parent(const char *name, int len,
+static enum get_oid_result get_parent(struct repository *r,
+				      const char *name, int len,
 				      struct object_id *result, int idx)
 {
 	struct object_id oid;
-	enum get_oid_result ret = get_oid_1(name, len, &oid,
+	enum get_oid_result ret = get_oid_1(r, name, len, &oid,
 					    GET_OID_COMMITTISH);
 	struct commit *commit;
 	struct commit_list *p;
 
 	if (ret)
 		return ret;
-	commit = lookup_commit_reference(the_repository, &oid);
+	commit = lookup_commit_reference(r, &oid);
 	if (parse_commit(commit))
 		return MISSING_OBJECT;
 	if (!idx) {
@@ -922,7 +964,8 @@
 	return MISSING_OBJECT;
 }
 
-static enum get_oid_result get_nth_ancestor(const char *name, int len,
+static enum get_oid_result get_nth_ancestor(struct repository *r,
+					    const char *name, int len,
 					    struct object_id *result,
 					    int generation)
 {
@@ -930,10 +973,10 @@
 	struct commit *commit;
 	int ret;
 
-	ret = get_oid_1(name, len, &oid, GET_OID_COMMITTISH);
+	ret = get_oid_1(r, name, len, &oid, GET_OID_COMMITTISH);
 	if (ret)
 		return ret;
-	commit = lookup_commit_reference(the_repository, &oid);
+	commit = lookup_commit_reference(r, &oid);
 	if (!commit)
 		return MISSING_OBJECT;
 
@@ -946,20 +989,20 @@
 	return FOUND;
 }
 
-struct object *peel_to_type(const char *name, int namelen,
-			    struct object *o, enum object_type expected_type)
+struct object *repo_peel_to_type(struct repository *r, const char *name, int namelen,
+				 struct object *o, enum object_type expected_type)
 {
 	if (name && !namelen)
 		namelen = strlen(name);
 	while (1) {
-		if (!o || (!o->parsed && !parse_object(the_repository, &o->oid)))
+		if (!o || (!o->parsed && !parse_object(r, &o->oid)))
 			return NULL;
 		if (expected_type == OBJ_ANY || o->type == expected_type)
 			return o;
 		if (o->type == OBJ_TAG)
 			o = ((struct tag*) o)->tagged;
 		else if (o->type == OBJ_COMMIT)
-			o = &(get_commit_tree(((struct commit *)o))->object);
+			o = &(repo_get_commit_tree(r, ((struct commit *)o))->object);
 		else {
 			if (name)
 				error("%.*s: expected %s type, but the object "
@@ -971,8 +1014,8 @@
 	}
 }
 
-static int peel_onion(const char *name, int len, struct object_id *oid,
-		      unsigned lookup_flags)
+static int peel_onion(struct repository *r, const char *name, int len,
+		      struct object_id *oid, unsigned lookup_flags)
 {
 	struct object_id outer;
 	const char *sp;
@@ -1022,15 +1065,15 @@
 	else if (expected_type == OBJ_TREE)
 		lookup_flags |= GET_OID_TREEISH;
 
-	if (get_oid_1(name, sp - name - 2, &outer, lookup_flags))
+	if (get_oid_1(r, name, sp - name - 2, &outer, lookup_flags))
 		return -1;
 
-	o = parse_object(the_repository, &outer);
+	o = parse_object(r, &outer);
 	if (!o)
 		return -1;
 	if (!expected_type) {
-		o = deref_tag(the_repository, o, name, sp - name - 2);
-		if (!o || (!o->parsed && !parse_object(the_repository, &o->oid)))
+		o = deref_tag(r, o, name, sp - name - 2);
+		if (!o || (!o->parsed && !parse_object(r, &o->oid)))
 			return -1;
 		oidcpy(oid, &o->oid);
 		return 0;
@@ -1041,7 +1084,7 @@
 	 * if we do not get the needed object, we should
 	 * barf.
 	 */
-	o = peel_to_type(name, len, o, expected_type);
+	o = repo_peel_to_type(r, name, len, o, expected_type);
 	if (!o)
 		return -1;
 
@@ -1061,14 +1104,16 @@
 
 		prefix = xstrndup(sp + 1, name + len - 1 - (sp + 1));
 		commit_list_insert((struct commit *)o, &list);
-		ret = get_oid_oneline(prefix, oid, list);
+		ret = get_oid_oneline(r, prefix, oid, list);
 		free(prefix);
 		return ret;
 	}
 	return 0;
 }
 
-static int get_describe_name(const char *name, int len, struct object_id *oid)
+static int get_describe_name(struct repository *r,
+			     const char *name, int len,
+			     struct object_id *oid)
 {
 	const char *cp;
 	unsigned flags = GET_OID_QUIETLY | GET_OID_COMMIT;
@@ -1082,14 +1127,16 @@
 			if (ch == 'g' && cp[-1] == '-') {
 				cp++;
 				len -= cp - name;
-				return get_short_oid(cp, len, oid, flags);
+				return get_short_oid(r,
+						     cp, len, oid, flags);
 			}
 		}
 	}
 	return -1;
 }
 
-static enum get_oid_result get_oid_1(const char *name, int len,
+static enum get_oid_result get_oid_1(struct repository *r,
+				     const char *name, int len,
 				     struct object_id *oid,
 				     unsigned lookup_flags)
 {
@@ -1118,25 +1165,25 @@
 		if (!num && len1 == len - 1)
 			num = 1;
 		if (has_suffix == '^')
-			return get_parent(name, len1, oid, num);
+			return get_parent(r, name, len1, oid, num);
 		/* else if (has_suffix == '~') -- goes without saying */
-		return get_nth_ancestor(name, len1, oid, num);
+		return get_nth_ancestor(r, name, len1, oid, num);
 	}
 
-	ret = peel_onion(name, len, oid, lookup_flags);
+	ret = peel_onion(r, name, len, oid, lookup_flags);
 	if (!ret)
 		return FOUND;
 
-	ret = get_oid_basic(name, len, oid, lookup_flags);
+	ret = get_oid_basic(r, name, len, oid, lookup_flags);
 	if (!ret)
 		return FOUND;
 
 	/* It could be describe output that is "SOMETHING-gXXXX" */
-	ret = get_describe_name(name, len, oid);
+	ret = get_describe_name(r, name, len, oid);
 	if (!ret)
 		return FOUND;
 
-	return get_short_oid(name, len, oid, lookup_flags);
+	return get_short_oid(r, name, len, oid, lookup_flags);
 }
 
 /*
@@ -1155,15 +1202,21 @@
 /* Remember to update object flag allocation in object.h */
 #define ONELINE_SEEN (1u<<20)
 
+struct handle_one_ref_cb {
+	struct repository *repo;
+	struct commit_list **list;
+};
+
 static int handle_one_ref(const char *path, const struct object_id *oid,
 			  int flag, void *cb_data)
 {
-	struct commit_list **list = cb_data;
-	struct object *object = parse_object(the_repository, oid);
+	struct handle_one_ref_cb *cb = cb_data;
+	struct commit_list **list = cb->list;
+	struct object *object = parse_object(cb->repo, oid);
 	if (!object)
 		return 0;
 	if (object->type == OBJ_TAG) {
-		object = deref_tag(the_repository, object, path,
+		object = deref_tag(cb->repo, object, path,
 				   strlen(path));
 		if (!object)
 			return 0;
@@ -1174,8 +1227,9 @@
 	return 0;
 }
 
-static int get_oid_oneline(const char *prefix, struct object_id *oid,
-			    struct commit_list *list)
+static int get_oid_oneline(struct repository *r,
+			   const char *prefix, struct object_id *oid,
+			   struct commit_list *list)
 {
 	struct commit_list *backup = NULL, *l;
 	int found = 0;
@@ -1206,7 +1260,7 @@
 		int matches;
 
 		commit = pop_most_recent_commit(&list, ONELINE_SEEN);
-		if (!parse_object(the_repository, &commit->object.oid))
+		if (!parse_object(r, &commit->object.oid))
 			continue;
 		buf = get_commit_buffer(commit, NULL);
 		p = strstr(buf, "\n\n");
@@ -1258,7 +1312,8 @@
  * Parse @{-N} syntax, return the number of characters parsed
  * if successful; otherwise signal an error with negative value.
  */
-static int interpret_nth_prior_checkout(const char *name, int namelen,
+static int interpret_nth_prior_checkout(struct repository *r,
+					const char *name, int namelen,
 					struct strbuf *buf)
 {
 	long nth;
@@ -1282,18 +1337,22 @@
 	cb.remaining = nth;
 	strbuf_init(&cb.buf, 20);
 
-	retval = 0;
-	if (0 < for_each_reflog_ent_reverse("HEAD", grab_nth_branch_switch, &cb)) {
+	retval = refs_for_each_reflog_ent_reverse(get_main_ref_store(r),
+			"HEAD", grab_nth_branch_switch, &cb);
+	if (0 < retval) {
 		strbuf_reset(buf);
 		strbuf_addbuf(buf, &cb.buf);
 		retval = brace - name + 1;
-	}
+	} else
+		retval = 0;
 
 	strbuf_release(&cb.buf);
 	return retval;
 }
 
-int get_oid_mb(const char *name, struct object_id *oid)
+int repo_get_oid_mb(struct repository *r,
+		    const char *name,
+		    struct object_id *oid)
 {
 	struct commit *one, *two;
 	struct commit_list *mbs;
@@ -1303,27 +1362,29 @@
 
 	dots = strstr(name, "...");
 	if (!dots)
-		return get_oid(name, oid);
+		return repo_get_oid(r, name, oid);
 	if (dots == name)
-		st = get_oid("HEAD", &oid_tmp);
+		st = repo_get_oid(r, "HEAD", &oid_tmp);
 	else {
 		struct strbuf sb;
 		strbuf_init(&sb, dots - name);
 		strbuf_add(&sb, name, dots - name);
-		st = get_oid_committish(sb.buf, &oid_tmp);
+		st = repo_get_oid_committish(r, sb.buf, &oid_tmp);
 		strbuf_release(&sb);
 	}
 	if (st)
 		return st;
-	one = lookup_commit_reference_gently(the_repository, &oid_tmp, 0);
+	one = lookup_commit_reference_gently(r, &oid_tmp, 0);
 	if (!one)
 		return -1;
 
-	if (get_oid_committish(dots[3] ? (dots + 3) : "HEAD", &oid_tmp))
+	if (repo_get_oid_committish(r, dots[3] ? (dots + 3) : "HEAD", &oid_tmp))
 		return -1;
-	two = lookup_commit_reference_gently(the_repository, &oid_tmp, 0);
+	two = lookup_commit_reference_gently(r, &oid_tmp, 0);
 	if (!two)
 		return -1;
+	if (r != the_repository)
+		BUG("sorry get_merge_bases() can't take struct repository yet");
 	mbs = get_merge_bases(one, two);
 	if (!mbs || mbs->next)
 		st = -1;
@@ -1357,7 +1418,8 @@
 	return 1;
 }
 
-static int reinterpret(const char *name, int namelen, int len,
+static int reinterpret(struct repository *r,
+		       const char *name, int namelen, int len,
 		       struct strbuf *buf, unsigned allowed)
 {
 	/* we have extra data, which might need further processing */
@@ -1366,7 +1428,7 @@
 	int ret;
 
 	strbuf_add(buf, name + len, namelen - len);
-	ret = interpret_branch_name(buf->buf, buf->len, &tmp, allowed);
+	ret = repo_interpret_branch_name(r, buf->buf, buf->len, &tmp, allowed);
 	/* that data was not interpreted, remove our cruft */
 	if (ret < 0) {
 		strbuf_setlen(buf, used);
@@ -1379,9 +1441,9 @@
 	return ret - used + len;
 }
 
-static void set_shortened_ref(struct strbuf *buf, const char *ref)
+static void set_shortened_ref(struct repository *r, struct strbuf *buf, const char *ref)
 {
-	char *s = shorten_unambiguous_ref(ref, 0);
+	char *s = refs_shorten_unambiguous_ref(get_main_ref_store(r), ref, 0);
 	strbuf_reset(buf);
 	strbuf_addstr(buf, s);
 	free(s);
@@ -1402,7 +1464,8 @@
 	return 0;
 }
 
-static int interpret_branch_mark(const char *name, int namelen,
+static int interpret_branch_mark(struct repository *r,
+				 const char *name, int namelen,
 				 int at, struct strbuf *buf,
 				 int (*get_mark)(const char *, int),
 				 const char *(*get_data)(struct branch *,
@@ -1435,12 +1498,14 @@
 	if (!branch_interpret_allowed(value, allowed))
 		return -1;
 
-	set_shortened_ref(buf, value);
+	set_shortened_ref(r, buf, value);
 	return len + at;
 }
 
-int interpret_branch_name(const char *name, int namelen, struct strbuf *buf,
-			  unsigned allowed)
+int repo_interpret_branch_name(struct repository *r,
+			       const char *name, int namelen,
+			       struct strbuf *buf,
+			       unsigned allowed)
 {
 	char *at;
 	const char *start;
@@ -1450,14 +1515,14 @@
 		namelen = strlen(name);
 
 	if (!allowed || (allowed & INTERPRET_BRANCH_LOCAL)) {
-		len = interpret_nth_prior_checkout(name, namelen, buf);
+		len = interpret_nth_prior_checkout(r, name, namelen, buf);
 		if (!len) {
 			return len; /* syntax Ok, not enough switches */
 		} else if (len > 0) {
 			if (len == namelen)
 				return len; /* consumed all */
 			else
-				return reinterpret(name, namelen, len, buf, allowed);
+				return reinterpret(r, name, namelen, len, buf, allowed);
 		}
 	}
 
@@ -1468,17 +1533,17 @@
 		if (!allowed || (allowed & INTERPRET_BRANCH_HEAD)) {
 			len = interpret_empty_at(name, namelen, at - name, buf);
 			if (len > 0)
-				return reinterpret(name, namelen, len, buf,
+				return reinterpret(r, name, namelen, len, buf,
 						   allowed);
 		}
 
-		len = interpret_branch_mark(name, namelen, at - name, buf,
+		len = interpret_branch_mark(r, name, namelen, at - name, buf,
 					    upstream_mark, branch_get_upstream,
 					    allowed);
 		if (len > 0)
 			return len;
 
-		len = interpret_branch_mark(name, namelen, at - name, buf,
+		len = interpret_branch_mark(r, name, namelen, at - name, buf,
 					    push_mark, branch_get_push,
 					    allowed);
 		if (len > 0)
@@ -1524,10 +1589,10 @@
  * This is like "get_oid_basic()", except it allows "object ID expressions",
  * notably "xyz^" for "parent of xyz"
  */
-int get_oid(const char *name, struct object_id *oid)
+int repo_get_oid(struct repository *r, const char *name, struct object_id *oid)
 {
 	struct object_context unused;
-	return get_oid_with_context(the_repository, name, 0, oid, &unused);
+	return get_oid_with_context(r, name, 0, oid, &unused);
 }
 
 /*
@@ -1560,43 +1625,48 @@
  * commit-ish. It is merely to give a hint to the disambiguation
  * machinery.
  */
-int get_oid_committish(const char *name, struct object_id *oid)
+int repo_get_oid_committish(struct repository *r,
+			    const char *name,
+			    struct object_id *oid)
 {
 	struct object_context unused;
-	return get_oid_with_context(the_repository,
-				    name, GET_OID_COMMITTISH,
+	return get_oid_with_context(r, name, GET_OID_COMMITTISH,
 				    oid, &unused);
 }
 
-int get_oid_treeish(const char *name, struct object_id *oid)
+int repo_get_oid_treeish(struct repository *r,
+			 const char *name,
+			 struct object_id *oid)
 {
 	struct object_context unused;
-	return get_oid_with_context(the_repository,
-				    name, GET_OID_TREEISH,
+	return get_oid_with_context(r, name, GET_OID_TREEISH,
 				    oid, &unused);
 }
 
-int get_oid_commit(const char *name, struct object_id *oid)
+int repo_get_oid_commit(struct repository *r,
+			const char *name,
+			struct object_id *oid)
 {
 	struct object_context unused;
-	return get_oid_with_context(the_repository,
-				    name, GET_OID_COMMIT,
+	return get_oid_with_context(r, name, GET_OID_COMMIT,
 				    oid, &unused);
 }
 
-int get_oid_tree(const char *name, struct object_id *oid)
+int repo_get_oid_tree(struct repository *r,
+		      const char *name,
+		      struct object_id *oid)
 {
 	struct object_context unused;
-	return get_oid_with_context(the_repository,
-				    name, GET_OID_TREE,
+	return get_oid_with_context(r, name, GET_OID_TREE,
 				    oid, &unused);
 }
 
-int get_oid_blob(const char *name, struct object_id *oid)
+int repo_get_oid_blob(struct repository *r,
+		      const char *name,
+		      struct object_id *oid)
 {
 	struct object_context unused;
-	return get_oid_with_context(the_repository,
-				    name, GET_OID_BLOB,
+	return get_oid_with_context(r, name, GET_OID_BLOB,
 				    oid, &unused);
 }
 
@@ -1635,11 +1705,12 @@
 }
 
 /* Must be called only when :stage:filename doesn't exist. */
-static void diagnose_invalid_index_path(struct index_state *istate,
+static void diagnose_invalid_index_path(struct repository *r,
 					int stage,
 					const char *prefix,
 					const char *filename)
 {
+	struct index_state *istate = r->index;
 	const struct cache_entry *ce;
 	int pos;
 	unsigned namelen = strlen(filename);
@@ -1679,7 +1750,7 @@
 			    ce_stage(ce), filename);
 	}
 
-	if (file_exists(filename))
+	if (repo_file_exists(r, filename))
 		die("Path '%s' exists on disk, but not in the index.", filename);
 	if (is_missing_file_error(errno))
 		die("Path '%s' does not exist (neither on disk nor in the index).",
@@ -1689,12 +1760,12 @@
 }
 
 
-static char *resolve_relative_path(const char *rel)
+static char *resolve_relative_path(struct repository *r, const char *rel)
 {
 	if (!starts_with(rel, "./") && !starts_with(rel, "../"))
 		return NULL;
 
-	if (!is_inside_work_tree())
+	if (r != the_repository || !is_inside_work_tree())
 		die("relative path syntax can't be used outside working tree.");
 
 	/* die() inside prefix_path() if resolved path is outside worktree */
@@ -1721,7 +1792,7 @@
 	memset(oc, 0, sizeof(*oc));
 	oc->mode = S_IFINVALID;
 	strbuf_init(&oc->symlink_path, 0);
-	ret = get_oid_1(name, namelen, oid, flags);
+	ret = get_oid_1(repo, name, namelen, oid, flags);
 	if (!ret)
 		return ret;
 	/*
@@ -1737,12 +1808,15 @@
 		char *new_path = NULL;
 		int pos;
 		if (!only_to_die && namelen > 2 && name[1] == '/') {
+			struct handle_one_ref_cb cb;
 			struct commit_list *list = NULL;
 
-			for_each_ref(handle_one_ref, &list);
-			head_ref(handle_one_ref, &list);
+			cb.repo = repo;
+			cb.list = &list;
+			refs_for_each_ref(repo->refs, handle_one_ref, &cb);
+			refs_head_ref(repo->refs, handle_one_ref, &cb);
 			commit_list_sort_by_date(&list);
-			return get_oid_oneline(name + 2, oid, list);
+			return get_oid_oneline(repo, name + 2, oid, list);
 		}
 		if (namelen < 3 ||
 		    name[2] != ':' ||
@@ -1752,7 +1826,7 @@
 			stage = name[1] - '0';
 			cp = name + 3;
 		}
-		new_path = resolve_relative_path(cp);
+		new_path = resolve_relative_path(repo, cp);
 		if (!new_path) {
 			namelen = namelen - (cp - name);
 		} else {
@@ -1764,7 +1838,7 @@
 			oc->path = xstrdup(cp);
 
 		if (!repo->index->cache)
-			repo_read_index(the_repository);
+			repo_read_index(repo);
 		pos = index_name_pos(repo->index, cp, namelen);
 		if (pos < 0)
 			pos = -pos - 1;
@@ -1782,7 +1856,7 @@
 			pos++;
 		}
 		if (only_to_die && name[1] && name[1] != '/')
-			diagnose_invalid_index_path(repo->index, stage, prefix, cp);
+			diagnose_invalid_index_path(repo, stage, prefix, cp);
 		free(new_path);
 		return -1;
 	}
@@ -1802,13 +1876,21 @@
 		sub_flags &= ~GET_OID_DISAMBIGUATORS;
 		sub_flags |= GET_OID_TREEISH;
 
-		if (!get_oid_1(name, len, &tree_oid, sub_flags)) {
+		if (!get_oid_1(repo, name, len, &tree_oid, sub_flags)) {
 			const char *filename = cp+1;
 			char *new_filename = NULL;
 
-			new_filename = resolve_relative_path(filename);
+			new_filename = resolve_relative_path(repo, filename);
 			if (new_filename)
 				filename = new_filename;
+			/*
+			 * NEEDSWORK: Eventually get_tree_entry*() should
+			 * learn to take struct repository directly and we
+			 * would not need to inject submodule odb to the
+			 * in-core odb.
+			 */
+			if (repo != the_repository)
+				add_to_alternates_memory(repo->objects->odb->path);
 			if (flags & GET_OID_FOLLOW_SYMLINKS) {
 				ret = get_tree_entry_follow_symlinks(&tree_oid,
 					filename, oid, &oc->symlink_path,
@@ -1843,11 +1925,13 @@
  * exist in 'HEAD'" when given "HEAD:doc", or it may return in which case
  * you have a chance to diagnose the error further.
  */
-void maybe_die_on_misspelt_object_name(const char *name, const char *prefix)
+void maybe_die_on_misspelt_object_name(struct repository *r,
+				       const char *name,
+				       const char *prefix)
 {
 	struct object_context oc;
 	struct object_id oid;
-	get_oid_with_context_1(the_repository, name, GET_OID_ONLY_TO_DIE,
+	get_oid_with_context_1(r, name, GET_OID_ONLY_TO_DIE,
 			       prefix, &oid, &oc);
 }
 
diff --git a/submodule-config.c b/submodule-config.c
index 66653e8..4264ee2 100644
--- a/submodule-config.c
+++ b/submodule-config.c
@@ -625,23 +625,16 @@
 		const struct config_options opts = { 0 };
 		struct object_id oid;
 		char *file;
+		char *oidstr = NULL;
 
 		file = repo_worktree_path(repo, GITMODULES_FILE);
 		if (file_exists(file)) {
 			config_source.file = file;
-		} else if (repo->submodule_prefix) {
-			/*
-			 * When get_oid and config_with_options, used below,
-			 * become able to work on a specific repository, this
-			 * warning branch can be removed.
-			 */
-			warning("nested submodules without %s in the working tree are not supported yet",
-				GITMODULES_FILE);
-			goto out;
-		} else if (get_oid(GITMODULES_INDEX, &oid) >= 0) {
-			config_source.blob = GITMODULES_INDEX;
-		} else if (get_oid(GITMODULES_HEAD, &oid) >= 0) {
-			config_source.blob = GITMODULES_HEAD;
+		} 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)
+				add_to_alternates_memory(repo->objects->odb->path);
 		} else {
 			goto out;
 		}
@@ -649,6 +642,7 @@
 		config_with_options(fn, data, &config_source, &opts);
 
 out:
+		free(oidstr);
 		free(file);
 	}
 }
diff --git a/t/t7814-grep-recurse-submodules.sh b/t/t7814-grep-recurse-submodules.sh
index fa475d5..134a6945 100755
--- a/t/t7814-grep-recurse-submodules.sh
+++ b/t/t7814-grep-recurse-submodules.sh
@@ -380,11 +380,7 @@
 	fi
 '
 
-# Recursing down into nested submodules which do not have .gitmodules in their
-# working tree does not work yet. This is because config_from_gitmodules()
-# uses get_oid() and the latter is still not able to get objects from an
-# arbitrary repository (the nested submodule, in this case).
-test_expect_failure 'grep --recurse-submodules with submodules without .gitmodules in the working tree' '
+test_expect_success 'grep --recurse-submodules with submodules without .gitmodules in the working tree' '
 	test_when_finished "git -C submodule checkout .gitmodules" &&
 	rm submodule/.gitmodules &&
 	git grep --recurse-submodules -e "(.|.)[\d]" >actual &&
diff --git a/upload-pack.c b/upload-pack.c
index cb603a6..d2ea5eb 100644
--- a/upload-pack.c
+++ b/upload-pack.c
@@ -839,7 +839,7 @@
 	if (skip_prefix(line, "deepen-not ", &arg)) {
 		char *ref = NULL;
 		struct object_id oid;
-		if (expand_ref(arg, strlen(arg), &oid, &ref) != 1)
+		if (expand_ref(the_repository, arg, strlen(arg), &oid, &ref) != 1)
 			die("git upload-pack: ambiguous deepen-not: %s", line);
 		string_list_append(deepen_not, ref);
 		free(ref);