Merge branch 'nd/tree-walk-with-repo'

The tree-walk API learned to pass an in-core repository
instance throughout more codepaths.

* nd/tree-walk-with-repo:
  t7814: do not generate same commits in different repos
  Use the right 'struct repository' instead of the_repository
  match-trees.c: remove the_repo from shift_tree*()
  tree-walk.c: remove the_repo from get_tree_entry_follow_symlinks()
  tree-walk.c: remove the_repo from get_tree_entry()
  tree-walk.c: remove the_repo from fill_tree_descriptor()
  sha1-file.c: remove the_repo from read_object_with_reference()

26 files changed, 146 insertions, 98 deletions

diff --git a/archive.c b/archive.c
index 53141c1..a8da0fc 100644
--- a/archive.c
+++ b/archive.c
@@ -418,7 +418,9 @@ static void parse_treeish_arg(const char **argv,
 		unsigned short mode;
 		int err;
 
-		err = get_tree_entry(&tree->object.oid, prefix, &tree_oid,
+		err = get_tree_entry(ar_args->repo,
+				     &tree->object.oid,
+				     prefix, &tree_oid,
 				     &mode);
 		if (err || !S_ISDIR(mode))
 			die(_("current working directory is untracked"));
diff --git a/blame.c b/blame.c
index 7f04580..36a2e7e 100644
--- a/blame.c
+++ b/blame.c
@@ -101,7 +101,7 @@ static void verify_working_tree_path(struct repository *r,
 		struct object_id blob_oid;
 		unsigned short mode;
 
-		if (!get_tree_entry(commit_oid, path, &blob_oid, &mode) &&
+		if (!get_tree_entry(r, commit_oid, path, &blob_oid, &mode) &&
 		    oid_object_info(r, &blob_oid, NULL) == OBJ_BLOB)
 			return;
 	}
@@ -1232,7 +1232,7 @@ static int fill_blob_sha1_and_mode(struct repository *r,
 {
 	if (!is_null_oid(&origin->blob_oid))
 		return 0;
-	if (get_tree_entry(&origin->commit->object.oid, origin->path, &origin->blob_oid, &origin->mode))
+	if (get_tree_entry(r, &origin->commit->object.oid, origin->path, &origin->blob_oid, &origin->mode))
 		goto error_out;
 	if (oid_object_info(r, &origin->blob_oid, NULL) != OBJ_BLOB)
 		goto error_out;
diff --git a/builtin/cat-file.c b/builtin/cat-file.c
index 0f09238..995d47c 100644
--- a/builtin/cat-file.c
+++ b/builtin/cat-file.c
@@ -172,7 +172,8 @@ static int cat_one_file(int opt, const char *exp_type, const char *obj_name,
 			 * fall-back to the usual case.
 			 */
 		}
-		buf = read_object_with_reference(&oid, exp_type, &size, NULL);
+		buf = read_object_with_reference(the_repository,
+						 &oid, exp_type, &size, NULL);
 		break;
 
 	default:
diff --git a/builtin/grep.c b/builtin/grep.c
index 580fd38..5600517 100644
--- a/builtin/grep.c
+++ b/builtin/grep.c
@@ -458,7 +458,8 @@ static int grep_submodule(struct grep_opt *opt,
 		object = parse_object_or_die(oid, oid_to_hex(oid));
 
 		grep_read_lock();
-		data = read_object_with_reference(&object->oid, tree_type,
+		data = read_object_with_reference(&subrepo,
+						  &object->oid, tree_type,
 						  &size, NULL);
 		grep_read_unlock();
 
@@ -623,7 +624,8 @@ static int grep_object(struct grep_opt *opt, const struct pathspec *pathspec,
 		int hit, len;
 
 		grep_read_lock();
-		data = read_object_with_reference(&obj->oid, tree_type,
+		data = read_object_with_reference(opt->repo,
+						  &obj->oid, tree_type,
 						  &size, NULL);
 		grep_read_unlock();
 
diff --git a/builtin/merge-tree.c b/builtin/merge-tree.c
index 34ca025..97b54ca 100644
--- a/builtin/merge-tree.c
+++ b/builtin/merge-tree.c
@@ -205,6 +205,7 @@ static void resolve(const struct traverse_info *info, struct name_entry *ours, s
 static void unresolved_directory(const struct traverse_info *info,
 				 struct name_entry n[3])
 {
+	struct repository *r = the_repository;
 	char *newbase;
 	struct name_entry *p;
 	struct tree_desc t[3];
@@ -220,9 +221,9 @@ static void unresolved_directory(const struct traverse_info *info,
 	newbase = traverse_path(info, p);
 
 #define ENTRY_OID(e) (((e)->mode && S_ISDIR((e)->mode)) ? &(e)->oid : NULL)
-	buf0 = fill_tree_descriptor(t + 0, ENTRY_OID(n + 0));
-	buf1 = fill_tree_descriptor(t + 1, ENTRY_OID(n + 1));
-	buf2 = fill_tree_descriptor(t + 2, ENTRY_OID(n + 2));
+	buf0 = fill_tree_descriptor(r, t + 0, ENTRY_OID(n + 0));
+	buf1 = fill_tree_descriptor(r, t + 1, ENTRY_OID(n + 1));
+	buf2 = fill_tree_descriptor(r, t + 2, ENTRY_OID(n + 2));
 #undef ENTRY_OID
 
 	merge_trees(t, newbase);
@@ -351,14 +352,16 @@ static void merge_trees(struct tree_desc t[3], const char *base)
 	traverse_trees(&the_index, 3, t, &info);
 }
 
-static void *get_tree_descriptor(struct tree_desc *desc, const char *rev)
+static void *get_tree_descriptor(struct repository *r,
+				 struct tree_desc *desc,
+				 const char *rev)
 {
 	struct object_id oid;
 	void *buf;
 
-	if (get_oid(rev, &oid))
+	if (repo_get_oid(r, rev, &oid))
 		die("unknown rev %s", rev);
-	buf = fill_tree_descriptor(desc, &oid);
+	buf = fill_tree_descriptor(r, desc, &oid);
 	if (!buf)
 		die("%s is not a tree", rev);
 	return buf;
@@ -366,15 +369,16 @@ static void *get_tree_descriptor(struct tree_desc *desc, const char *rev)
 
 int cmd_merge_tree(int argc, const char **argv, const char *prefix)
 {
+	struct repository *r = the_repository;
 	struct tree_desc t[3];
 	void *buf1, *buf2, *buf3;
 
 	if (argc != 4)
 		usage(merge_tree_usage);
 
-	buf1 = get_tree_descriptor(t+0, argv[1]);
-	buf2 = get_tree_descriptor(t+1, argv[2]);
-	buf3 = get_tree_descriptor(t+2, argv[3]);
+	buf1 = get_tree_descriptor(r, t+0, argv[1]);
+	buf2 = get_tree_descriptor(r, t+1, argv[2]);
+	buf3 = get_tree_descriptor(r, t+2, argv[3]);
 	merge_trees(t, "");
 	free(buf1);
 	free(buf2);
diff --git a/builtin/pack-objects.c b/builtin/pack-objects.c
index 000dc4b..267c562 100644
--- a/builtin/pack-objects.c
+++ b/builtin/pack-objects.c
@@ -1428,7 +1428,8 @@ static void add_preferred_base(struct object_id *oid)
 	if (window <= num_preferred_base++)
 		return;
 
-	data = read_object_with_reference(oid, tree_type, &size, &tree_oid);
+	data = read_object_with_reference(the_repository, oid,
+					  tree_type, &size, &tree_oid);
 	if (!data)
 		return;
 
diff --git a/builtin/rebase.c b/builtin/rebase.c
index 89fc4b8..95d3422 100644
--- a/builtin/rebase.c
+++ b/builtin/rebase.c
@@ -850,13 +850,13 @@ static int reset_head(struct object_id *oid, const char *action,
 		goto leave_reset_head;
 	}
 
-	if (!reset_hard && !fill_tree_descriptor(&desc[nr++], &head_oid)) {
+	if (!reset_hard && !fill_tree_descriptor(the_repository, &desc[nr++], &head_oid)) {
 		ret = error(_("failed to find tree of %s"),
 			    oid_to_hex(&head_oid));
 		goto leave_reset_head;
 	}
 
-	if (!fill_tree_descriptor(&desc[nr++], oid)) {
+	if (!fill_tree_descriptor(the_repository, &desc[nr++], oid)) {
 		ret = error(_("failed to find tree of %s"), oid_to_hex(oid));
 		goto leave_reset_head;
 	}
diff --git a/builtin/reset.c b/builtin/reset.c
index c2bb35a..fdd5721 100644
--- a/builtin/reset.c
+++ b/builtin/reset.c
@@ -79,13 +79,13 @@ static int reset_index(const struct object_id *oid, int reset_type, int quiet)
 		struct object_id head_oid;
 		if (get_oid("HEAD", &head_oid))
 			return error(_("You do not have a valid HEAD."));
-		if (!fill_tree_descriptor(desc + nr, &head_oid))
+		if (!fill_tree_descriptor(the_repository, desc + nr, &head_oid))
 			return error(_("Failed to find tree of HEAD."));
 		nr++;
 		opts.fn = twoway_merge;
 	}
 
-	if (!fill_tree_descriptor(desc + nr, oid)) {
+	if (!fill_tree_descriptor(the_repository, desc + nr, oid)) {
 		error(_("Failed to find tree of %s."), oid_to_hex(oid));
 		goto out;
 	}
diff --git a/builtin/rm.c b/builtin/rm.c
index be8edc6..2eacda4 100644
--- a/builtin/rm.c
+++ b/builtin/rm.c
@@ -179,7 +179,7 @@ static int check_local_mod(struct object_id *head, int index_only)
 		 * way as changed from the HEAD.
 		 */
 		if (no_head
-		     || get_tree_entry(head, name, &oid, &mode)
+		     || get_tree_entry(the_repository, head, name, &oid, &mode)
 		     || ce->ce_mode != create_ce_mode(mode)
 		     || !oideq(&ce->oid, &oid))
 			staged_changes = 1;
diff --git a/builtin/update-index.c b/builtin/update-index.c
index 3f8cc6c..dff2f4b 100644
--- a/builtin/update-index.c
+++ b/builtin/update-index.c
@@ -601,7 +601,7 @@ static struct cache_entry *read_one_ent(const char *which,
 	struct object_id oid;
 	struct cache_entry *ce;
 
-	if (get_tree_entry(ent, path, &oid, &mode)) {
+	if (get_tree_entry(the_repository, ent, path, &oid, &mode)) {
 		if (which)
 			error("%s: not in %s branch.", path, which);
 		return NULL;
diff --git a/cache.h b/cache.h
index 3167585..b1da1ab 100644
--- a/cache.h
+++ b/cache.h
@@ -1476,7 +1476,8 @@ int df_name_compare(const char *name1, int len1, int mode1, const char *name2, i
 int name_compare(const char *name1, size_t len1, const char *name2, size_t len2);
 int cache_name_stage_compare(const char *name1, int len1, int stage1, const char *name2, int len2, int stage2);
 
-void *read_object_with_reference(const struct object_id *oid,
+void *read_object_with_reference(struct repository *r,
+				 const struct object_id *oid,
 				 const char *required_type,
 				 unsigned long *size,
 				 struct object_id *oid_ret);
@@ -1762,8 +1763,8 @@ int add_files_to_cache(const char *prefix, const struct pathspec *pathspec, int
 extern int diff_auto_refresh_index;
 
 /* match-trees.c */
-void shift_tree(const struct object_id *, const struct object_id *, struct object_id *, int);
-void shift_tree_by(const struct object_id *, const struct object_id *, struct object_id *, const char *);
+void shift_tree(struct repository *, const struct object_id *, const struct object_id *, struct object_id *, int);
+void shift_tree_by(struct repository *, const struct object_id *, const struct object_id *, struct object_id *, const char *);
 
 /*
  * whitespace rules.
diff --git a/fast-import.c b/fast-import.c
index 6dfdd68..b44d6a4 100644
--- a/fast-import.c
+++ b/fast-import.c
@@ -2410,7 +2410,8 @@ static void note_change_n(const char *p, struct branch *b, unsigned char *old_fa
 		oidcpy(&commit_oid, &commit_oe->idx.oid);
 	} else if (!get_oid(p, &commit_oid)) {
 		unsigned long size;
-		char *buf = read_object_with_reference(&commit_oid,
+		char *buf = read_object_with_reference(the_repository,
+						       &commit_oid,
 						       commit_type, &size,
 						       &commit_oid);
 		if (!buf || size < the_hash_algo->hexsz + 6)
@@ -2482,7 +2483,8 @@ static void parse_from_existing(struct branch *b)
 		unsigned long size;
 		char *buf;
 
-		buf = read_object_with_reference(&b->oid, commit_type, &size,
+		buf = read_object_with_reference(the_repository,
+						 &b->oid, commit_type, &size,
 						 &b->oid);
 		parse_from_commit(b, buf, size);
 		free(buf);
@@ -2560,7 +2562,8 @@ static struct hash_list *parse_merge(unsigned int *count)
 			oidcpy(&n->oid, &oe->idx.oid);
 		} else if (!get_oid(from, &n->oid)) {
 			unsigned long size;
-			char *buf = read_object_with_reference(&n->oid,
+			char *buf = read_object_with_reference(the_repository,
+							       &n->oid,
 							       commit_type,
 							       &size, &n->oid);
 			if (!buf || size < the_hash_algo->hexsz + 6)
diff --git a/line-log.c b/line-log.c
index 0a17b21..3aff184 100644
--- a/line-log.c
+++ b/line-log.c
@@ -496,12 +496,13 @@ static struct commit *check_single_commit(struct rev_info *revs)
 	return (struct commit *) commit;
 }
 
-static void fill_blob_sha1(struct commit *commit, struct diff_filespec *spec)
+static void fill_blob_sha1(struct repository *r, struct commit *commit,
+			   struct diff_filespec *spec)
 {
 	unsigned short mode;
 	struct object_id oid;
 
-	if (get_tree_entry(&commit->object.oid, spec->path, &oid, &mode))
+	if (get_tree_entry(r, &commit->object.oid, spec->path, &oid, &mode))
 		die("There is no path %s in the commit", spec->path);
 	fill_filespec(spec, &oid, 1, mode);
 
@@ -585,7 +586,7 @@ parse_lines(struct repository *r, struct commit *commit,
 					name_part);
 
 		spec = alloc_filespec(full_name);
-		fill_blob_sha1(commit, spec);
+		fill_blob_sha1(r, commit, spec);
 		fill_line_ends(r, spec, &lines, &ends);
 		cb_data.spec = spec;
 		cb_data.lines = lines;
diff --git a/match-trees.c b/match-trees.c
index 9d1ec8d..f6c194c 100644
--- a/match-trees.c
+++ b/match-trees.c
@@ -248,7 +248,8 @@ static int splice_tree(const struct object_id *oid1, const char *prefix,
  * other hand, it could cover tree one and we might need to pick a
  * subtree of it.
  */
-void shift_tree(const struct object_id *hash1,
+void shift_tree(struct repository *r,
+		const struct object_id *hash1,
 		const struct object_id *hash2,
 		struct object_id *shifted,
 		int depth_limit)
@@ -290,7 +291,7 @@ void shift_tree(const struct object_id *hash1,
 		if (!*del_prefix)
 			return;
 
-		if (get_tree_entry(hash2, del_prefix, shifted, &mode))
+		if (get_tree_entry(r, hash2, del_prefix, shifted, &mode))
 			die("cannot find path %s in tree %s",
 			    del_prefix, oid_to_hex(hash2));
 		return;
@@ -307,7 +308,8 @@ void shift_tree(const struct object_id *hash1,
  * Unfortunately we cannot fundamentally tell which one to
  * be prefixed, as recursive merge can work in either direction.
  */
-void shift_tree_by(const struct object_id *hash1,
+void shift_tree_by(struct repository *r,
+		   const struct object_id *hash1,
 		   const struct object_id *hash2,
 		   struct object_id *shifted,
 		   const char *shift_prefix)
@@ -317,12 +319,12 @@ void shift_tree_by(const struct object_id *hash1,
 	unsigned candidate = 0;
 
 	/* Can hash2 be a tree at shift_prefix in tree hash1? */
-	if (!get_tree_entry(hash1, shift_prefix, &sub1, &mode1) &&
+	if (!get_tree_entry(r, hash1, shift_prefix, &sub1, &mode1) &&
 	    S_ISDIR(mode1))
 		candidate |= 1;
 
 	/* Can hash1 be a tree at shift_prefix in tree hash2? */
-	if (!get_tree_entry(hash2, shift_prefix, &sub2, &mode2) &&
+	if (!get_tree_entry(r, hash2, shift_prefix, &sub2, &mode2) &&
 	    S_ISDIR(mode2))
 		candidate |= 2;
 
diff --git a/merge-recursive.c b/merge-recursive.c
index d2e380b..1230013 100644
--- a/merge-recursive.c
+++ b/merge-recursive.c
@@ -153,9 +153,9 @@ static struct tree *shift_tree_object(struct repository *repo,
 	struct object_id shifted;
 
 	if (!*subtree_shift) {
-		shift_tree(&one->object.oid, &two->object.oid, &shifted, 0);
+		shift_tree(repo, &one->object.oid, &two->object.oid, &shifted, 0);
 	} else {
-		shift_tree_by(&one->object.oid, &two->object.oid, &shifted,
+		shift_tree_by(repo, &one->object.oid, &two->object.oid, &shifted,
 			      subtree_shift);
 	}
 	if (oideq(&two->object.oid, &shifted))
@@ -465,17 +465,18 @@ static void get_files_dirs(struct merge_options *opt, struct tree *tree)
 {
 	struct pathspec match_all;
 	memset(&match_all, 0, sizeof(match_all));
-	read_tree_recursive(the_repository, tree, "", 0, 0,
+	read_tree_recursive(opt->repo, tree, "", 0, 0,
 			    &match_all, save_files_dirs, opt);
 }
 
-static int get_tree_entry_if_blob(const struct object_id *tree,
+static int get_tree_entry_if_blob(struct repository *r,
+				  const struct object_id *tree,
 				  const char *path,
 				  struct diff_filespec *dfs)
 {
 	int ret;
 
-	ret = get_tree_entry(tree, path, &dfs->oid, &dfs->mode);
+	ret = get_tree_entry(r, tree, path, &dfs->oid, &dfs->mode);
 	if (S_ISDIR(dfs->mode)) {
 		oidcpy(&dfs->oid, &null_oid);
 		dfs->mode = 0;
@@ -487,15 +488,16 @@ static int get_tree_entry_if_blob(const struct object_id *tree,
  * Returns an index_entry instance which doesn't have to correspond to
  * a real cache entry in Git's index.
  */
-static struct stage_data *insert_stage_data(const char *path,
+static struct stage_data *insert_stage_data(struct repository *r,
+		const char *path,
 		struct tree *o, struct tree *a, struct tree *b,
 		struct string_list *entries)
 {
 	struct string_list_item *item;
 	struct stage_data *e = xcalloc(1, sizeof(struct stage_data));
-	get_tree_entry_if_blob(&o->object.oid, path, &e->stages[1]);
-	get_tree_entry_if_blob(&a->object.oid, path, &e->stages[2]);
-	get_tree_entry_if_blob(&b->object.oid, path, &e->stages[3]);
+	get_tree_entry_if_blob(r, &o->object.oid, path, &e->stages[1]);
+	get_tree_entry_if_blob(r, &a->object.oid, path, &e->stages[2]);
+	get_tree_entry_if_blob(r, &b->object.oid, path, &e->stages[3]);
 	item = string_list_insert(entries, path);
 	item->util = e;
 	return e;
@@ -1900,12 +1902,14 @@ static struct diff_queue_struct *get_diffpairs(struct merge_options *opt,
 	return ret;
 }
 
-static int tree_has_path(struct tree *tree, const char *path)
+static int tree_has_path(struct repository *r, struct tree *tree,
+			 const char *path)
 {
 	struct object_id hashy;
 	unsigned short mode_o;
 
-	return !get_tree_entry(&tree->object.oid, path,
+	return !get_tree_entry(r,
+			       &tree->object.oid, path,
 			       &hashy, &mode_o);
 }
 
@@ -2056,7 +2060,7 @@ static char *handle_path_level_conflicts(struct merge_options *opt,
 	 */
 	if (collision_ent->reported_already) {
 		clean = 0;
-	} else if (tree_has_path(tree, new_path)) {
+	} else if (tree_has_path(opt->repo, tree, new_path)) {
 		collision_ent->reported_already = 1;
 		strbuf_add_separated_string_list(&collision_paths, ", ",
 						 &collision_ent->source_files);
@@ -2134,7 +2138,7 @@ static void handle_directory_level_conflicts(struct merge_options *opt,
 			string_list_append(&remove_from_merge,
 					   merge_ent->dir)->util = merge_ent;
 			strbuf_release(&merge_ent->new_dir);
-		} else if (tree_has_path(head, head_ent->dir)) {
+		} else if (tree_has_path(opt->repo, head, head_ent->dir)) {
 			/* 2. This wasn't a directory rename after all */
 			string_list_append(&remove_from_head,
 					   head_ent->dir)->util = head_ent;
@@ -2148,7 +2152,7 @@ static void handle_directory_level_conflicts(struct merge_options *opt,
 	hashmap_iter_init(dir_re_merge, &iter);
 	while ((merge_ent = hashmap_iter_next(&iter))) {
 		head_ent = dir_rename_find_entry(dir_re_head, merge_ent->dir);
-		if (tree_has_path(merge, merge_ent->dir)) {
+		if (tree_has_path(opt->repo, merge, merge_ent->dir)) {
 			/* 2. This wasn't a directory rename after all */
 			string_list_append(&remove_from_merge,
 					   merge_ent->dir)->util = merge_ent;
@@ -2477,7 +2481,7 @@ static void apply_directory_rename_modifications(struct merge_options *opt,
 		if (pair->status == 'R')
 			re->dst_entry->processed = 1;
 
-		re->dst_entry = insert_stage_data(new_path,
+		re->dst_entry = insert_stage_data(opt->repo, new_path,
 						  o_tree, a_tree, b_tree,
 						  entries);
 		item = string_list_insert(entries, new_path);
@@ -2500,7 +2504,8 @@ static void apply_directory_rename_modifications(struct merge_options *opt,
 	 * the various handle_rename_*() functions update the index
 	 * explicitly rather than relying on unpack_trees() to have done it.
 	 */
-	get_tree_entry(&tree->object.oid,
+	get_tree_entry(opt->repo,
+		       &tree->object.oid,
 		       pair->two->path,
 		       &re->dst_entry->stages[stage].oid,
 		       &re->dst_entry->stages[stage].mode);
@@ -2585,14 +2590,16 @@ static struct string_list *get_renames(struct merge_options *opt,
 		re->dir_rename_original_dest = NULL;
 		item = string_list_lookup(entries, re->pair->one->path);
 		if (!item)
-			re->src_entry = insert_stage_data(re->pair->one->path,
+			re->src_entry = insert_stage_data(opt->repo,
+					re->pair->one->path,
 					o_tree, a_tree, b_tree, entries);
 		else
 			re->src_entry = item->util;
 
 		item = string_list_lookup(entries, re->pair->two->path);
 		if (!item)
-			re->dst_entry = insert_stage_data(re->pair->two->path,
+			re->dst_entry = insert_stage_data(opt->repo,
+					re->pair->two->path,
 					o_tree, a_tree, b_tree, entries);
 		else
 			re->dst_entry = item->util;
diff --git a/notes.c b/notes.c
index 532ec37..75c028b 100644
--- a/notes.c
+++ b/notes.c
@@ -397,7 +397,7 @@ static void load_subtree(struct notes_tree *t, struct leaf_node *subtree,
 	struct name_entry entry;
 	const unsigned hashsz = the_hash_algo->rawsz;
 
-	buf = fill_tree_descriptor(&desc, &subtree->val_oid);
+	buf = fill_tree_descriptor(the_repository, &desc, &subtree->val_oid);
 	if (!buf)
 		die("Could not read %s for notes-index",
 		     oid_to_hex(&subtree->val_oid));
@@ -1015,7 +1015,7 @@ void init_notes(struct notes_tree *t, const char *notes_ref,
 		return;
 	if (flags & NOTES_INIT_WRITABLE && read_ref(notes_ref, &object_oid))
 		die("Cannot use notes ref %s", notes_ref);
-	if (get_tree_entry(&object_oid, "", &oid, &mode))
+	if (get_tree_entry(the_repository, &object_oid, "", &oid, &mode))
 		die("Failed to read notes tree referenced by %s (%s)",
 		    notes_ref, oid_to_hex(&object_oid));
 
diff --git a/sequencer.c b/sequencer.c
index 66126e0..34ebf8e 100644
--- a/sequencer.c
+++ b/sequencer.c
@@ -3302,7 +3302,7 @@ static int do_reset(struct repository *r,
 		return error_resolve_conflict(_(action_name(opts)));
 	}
 
-	if (!fill_tree_descriptor(&desc, &oid)) {
+	if (!fill_tree_descriptor(r, &desc, &oid)) {
 		error(_("failed to find tree of %s"), oid_to_hex(&oid));
 		rollback_lock_file(&lock);
 		free((void *)desc.buffer);
@@ -3841,7 +3841,7 @@ static int pick_commits(struct repository *r,
 			unlink(rebase_path_author_script());
 			unlink(rebase_path_stopped_sha());
 			unlink(rebase_path_amend());
-			unlink(git_path_merge_head(the_repository));
+			unlink(git_path_merge_head(r));
 			delete_ref(NULL, "REBASE_HEAD", NULL, REF_NO_DEREF);
 
 			if (item->command == TODO_BREAK) {
@@ -4226,7 +4226,7 @@ static int commit_staged_changes(struct repository *r,
 			   opts, flags))
 		return error(_("could not commit staged changes."));
 	unlink(rebase_path_amend());
-	unlink(git_path_merge_head(the_repository));
+	unlink(git_path_merge_head(r));
 	if (final_fixup) {
 		unlink(rebase_path_fixup_msg());
 		unlink(rebase_path_squash_msg());
diff --git a/sha1-file.c b/sha1-file.c
index 888b602..59b2e40 100644
--- a/sha1-file.c
+++ b/sha1-file.c
@@ -1505,7 +1505,8 @@ void *read_object_file_extended(struct repository *r,
 	return NULL;
 }
 
-void *read_object_with_reference(const struct object_id *oid,
+void *read_object_with_reference(struct repository *r,
+				 const struct object_id *oid,
 				 const char *required_type_name,
 				 unsigned long *size,
 				 struct object_id *actual_oid_return)
@@ -1521,7 +1522,7 @@ void *read_object_with_reference(const struct object_id *oid,
 		int ref_length = -1;
 		const char *ref_type = NULL;
 
-		buffer = read_object_file(&actual_oid, &type, &isize);
+		buffer = repo_read_object_file(r, &actual_oid, &type, &isize);
 		if (!buffer)
 			return NULL;
 		if (type == required_type) {
diff --git a/sha1-name.c b/sha1-name.c
index 49855ad..2989e27 100644
--- a/sha1-name.c
+++ b/sha1-name.c
@@ -478,7 +478,7 @@ static enum get_oid_result get_short_oid(struct repository *r,
 	 * or migrated from loose to packed.
 	 */
 	if (status == MISSING_OBJECT) {
-		reprepare_packed_git(the_repository);
+		reprepare_packed_git(r);
 		find_short_object_filename(&ds);
 		find_short_packed_object(&ds);
 		status = finish_object_disambiguation(&ds, oid);
@@ -1389,9 +1389,7 @@ int repo_get_oid_mb(struct repository *r,
 	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);
+	mbs = repo_get_merge_bases(r, one, two);
 	if (!mbs || mbs->next)
 		st = -1;
 	else {
@@ -1677,7 +1675,8 @@ int repo_get_oid_blob(struct repository *r,
 }
 
 /* Must be called only when object_name:filename doesn't exist. */
-static void diagnose_invalid_oid_path(const char *prefix,
+static void diagnose_invalid_oid_path(struct repository *r,
+				      const char *prefix,
 				      const char *filename,
 				      const struct object_id *tree_oid,
 				      const char *object_name,
@@ -1695,7 +1694,7 @@ static void diagnose_invalid_oid_path(const char *prefix,
 	if (is_missing_file_error(errno)) {
 		char *fullname = xstrfmt("%s%s", prefix, filename);
 
-		if (!get_tree_entry(tree_oid, fullname, &oid, &mode)) {
+		if (!get_tree_entry(r, tree_oid, fullname, &oid, &mode)) {
 			die("Path '%s' exists, but not '%s'.\n"
 			    "Did you mean '%.*s:%s' aka '%.*s:./%s'?",
 			    fullname,
@@ -1889,23 +1888,15 @@ static enum get_oid_result get_oid_with_context_1(struct repository *repo,
 			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,
+				ret = get_tree_entry_follow_symlinks(repo, &tree_oid,
 					filename, oid, &oc->symlink_path,
 					&oc->mode);
 			} else {
-				ret = get_tree_entry(&tree_oid, filename, oid,
+				ret = get_tree_entry(repo, &tree_oid, filename, oid,
 						     &oc->mode);
 				if (ret && only_to_die) {
-					diagnose_invalid_oid_path(prefix,
+					diagnose_invalid_oid_path(repo, prefix,
 								   filename,
 								   &tree_oid,
 								   name, len);
diff --git a/shallow.c b/shallow.c
index ce45297..5fa2b15 100644
--- a/shallow.c
+++ b/shallow.c
@@ -248,7 +248,8 @@ static void check_shallow_file_for_update(struct repository *r)
 	if (r->parsed_objects->is_shallow == -1)
 		BUG("shallow must be initialized by now");
 
-	if (!stat_validity_check(r->parsed_objects->shallow_stat, git_path_shallow(the_repository)))
+	if (!stat_validity_check(r->parsed_objects->shallow_stat,
+				 git_path_shallow(r)))
 		die("shallow file has changed since we read it");
 }
 
diff --git a/t/helper/test-match-trees.c b/t/helper/test-match-trees.c
index 96857f2..b9fd427 100644
--- a/t/helper/test-match-trees.c
+++ b/t/helper/test-match-trees.c
@@ -20,7 +20,7 @@ int cmd__match_trees(int ac, const char **av)
 	if (!two)
 		die("not a tree-ish %s", av[2]);
 
-	shift_tree(&one->object.oid, &two->object.oid, &shifted, -1);
+	shift_tree(the_repository, &one->object.oid, &two->object.oid, &shifted, -1);
 	printf("shifted: %s\n", oid_to_hex(&shifted));
 
 	exit(0);
diff --git a/t/t7814-grep-recurse-submodules.sh b/t/t7814-grep-recurse-submodules.sh
index 134a6945..a11366b 100755
--- a/t/t7814-grep-recurse-submodules.sh
+++ b/t/t7814-grep-recurse-submodules.sh
@@ -14,12 +14,14 @@ test_expect_success 'setup directory structure and submodule' '
 	echo "(3|4)" >b/b &&
 	git add a b &&
 	git commit -m "add a and b" &&
+	test_tick &&
 	git init submodule &&
 	echo "(1|2)d(3|4)" >submodule/a &&
 	git -C submodule add a &&
 	git -C submodule commit -m "add a" &&
 	git submodule add ./submodule &&
-	git commit -m "added submodule"
+	git commit -m "added submodule" &&
+	test_tick
 '
 
 test_expect_success 'grep correctly finds patterns in a submodule' '
@@ -65,11 +67,14 @@ test_expect_success 'grep and nested submodules' '
 	echo "(1|2)d(3|4)" >submodule/sub/a &&
 	git -C submodule/sub add a &&
 	git -C submodule/sub commit -m "add a" &&
+	test_tick &&
 	git -C submodule submodule add ./sub &&
 	git -C submodule add sub &&
 	git -C submodule commit -m "added sub" &&
+	test_tick &&
 	git add submodule &&
 	git commit -m "updated submodule" &&
+	test_tick &&
 
 	cat >expect <<-\EOF &&
 	a:(1|2)d(3|4)
@@ -179,15 +184,18 @@ test_expect_success !MINGW 'grep recurse submodule colon in name' '
 	echo "(1|2)d(3|4)" >"parent/fi:le" &&
 	git -C parent add "fi:le" &&
 	git -C parent commit -m "add fi:le" &&
+	test_tick &&
 
 	git init "su:b" &&
 	test_when_finished "rm -rf su:b" &&
 	echo "(1|2)d(3|4)" >"su:b/fi:le" &&
 	git -C "su:b" add "fi:le" &&
 	git -C "su:b" commit -m "add fi:le" &&
+	test_tick &&
 
 	git -C parent submodule add "../su:b" "su:b" &&
 	git -C parent commit -m "add submodule" &&
+	test_tick &&
 
 	cat >expect <<-\EOF &&
 	fi:le:(1|2)d(3|4)
@@ -210,15 +218,18 @@ test_expect_success 'grep history with moved submoules' '
 	echo "(1|2)d(3|4)" >parent/file &&
 	git -C parent add file &&
 	git -C parent commit -m "add file" &&
+	test_tick &&
 
 	git init sub &&
 	test_when_finished "rm -rf sub" &&
 	echo "(1|2)d(3|4)" >sub/file &&
 	git -C sub add file &&
 	git -C sub commit -m "add file" &&
+	test_tick &&
 
 	git -C parent submodule add ../sub dir/sub &&
 	git -C parent commit -m "add submodule" &&
+	test_tick &&
 
 	cat >expect <<-\EOF &&
 	dir/sub/file:(1|2)d(3|4)
@@ -229,6 +240,7 @@ test_expect_success 'grep history with moved submoules' '
 
 	git -C parent mv dir/sub sub-moved &&
 	git -C parent commit -m "moved submodule" &&
+	test_tick &&
 
 	cat >expect <<-\EOF &&
 	file:(1|2)d(3|4)
@@ -251,6 +263,7 @@ test_expect_success 'grep using relative path' '
 	echo "(1|2)d(3|4)" >sub/file &&
 	git -C sub add file &&
 	git -C sub commit -m "add file" &&
+	test_tick &&
 
 	git init parent &&
 	echo "(1|2)d(3|4)" >parent/file &&
@@ -260,6 +273,7 @@ test_expect_success 'grep using relative path' '
 	git -C parent add src/file2 &&
 	git -C parent submodule add ../sub &&
 	git -C parent commit -m "add files and submodule" &&
+	test_tick &&
 
 	# From top works
 	cat >expect <<-\EOF &&
@@ -293,6 +307,7 @@ test_expect_success 'grep from a subdir' '
 	echo "(1|2)d(3|4)" >sub/file &&
 	git -C sub add file &&
 	git -C sub commit -m "add file" &&
+	test_tick &&
 
 	git init parent &&
 	mkdir parent/src &&
@@ -301,6 +316,7 @@ test_expect_success 'grep from a subdir' '
 	git -C parent submodule add ../sub src/sub &&
 	git -C parent submodule add ../sub sub &&
 	git -C parent commit -m "add files and submodules" &&
+	test_tick &&
 
 	# Verify grep from root works
 	cat >expect <<-\EOF &&
diff --git a/tree-diff.c b/tree-diff.c
index f1f641e..33ded7f 100644
--- a/tree-diff.c
+++ b/tree-diff.c
@@ -422,8 +422,8 @@ static struct combine_diff_path *ll_diff_tree_paths(
 	 *   diff_tree_oid(parent, commit) )
 	 */
 	for (i = 0; i < nparent; ++i)
-		tptree[i] = fill_tree_descriptor(&tp[i], parents_oid[i]);
-	ttree = fill_tree_descriptor(&t, oid);
+		tptree[i] = fill_tree_descriptor(opt->repo, &tp[i], parents_oid[i]);
+	ttree = fill_tree_descriptor(opt->repo, &t, oid);
 
 	/* Enable recursion indefinitely */
 	opt->pathspec.recursive = opt->flags.recursive;
diff --git a/tree-walk.c b/tree-walk.c
index ec32a47..c20b62f 100644
--- a/tree-walk.c
+++ b/tree-walk.c
@@ -81,13 +81,15 @@ int init_tree_desc_gently(struct tree_desc *desc, const void *buffer, unsigned l
 	return result;
 }
 
-void *fill_tree_descriptor(struct tree_desc *desc, const struct object_id *oid)
+void *fill_tree_descriptor(struct repository *r,
+			   struct tree_desc *desc,
+			   const struct object_id *oid)
 {
 	unsigned long size = 0;
 	void *buf = NULL;
 
 	if (oid) {
-		buf = read_object_with_reference(oid, tree_type, &size, NULL);
+		buf = read_object_with_reference(r, oid, tree_type, &size, NULL);
 		if (!buf)
 			die("unable to read tree %s", oid_to_hex(oid));
 	}
@@ -500,7 +502,9 @@ struct dir_state {
 	struct object_id oid;
 };
 
-static int find_tree_entry(struct tree_desc *t, const char *name, struct object_id *result, unsigned short *mode)
+static int find_tree_entry(struct repository *r, struct tree_desc *t,
+			   const char *name, struct object_id *result,
+			   unsigned short *mode)
 {
 	int namelen = strlen(name);
 	while (t->size) {
@@ -530,19 +534,23 @@ static int find_tree_entry(struct tree_desc *t, const char *name, struct object_
 			oidcpy(result, &oid);
 			return 0;
 		}
-		return get_tree_entry(&oid, name + entrylen, result, mode);
+		return get_tree_entry(r, &oid, name + entrylen, result, mode);
 	}
 	return -1;
 }
 
-int get_tree_entry(const struct object_id *tree_oid, const char *name, struct object_id *oid, unsigned short *mode)
+int get_tree_entry(struct repository *r,
+		   const struct object_id *tree_oid,
+		   const char *name,
+		   struct object_id *oid,
+		   unsigned short *mode)
 {
 	int retval;
 	void *tree;
 	unsigned long size;
 	struct object_id root;
 
-	tree = read_object_with_reference(tree_oid, tree_type, &size, &root);
+	tree = read_object_with_reference(r, tree_oid, tree_type, &size, &root);
 	if (!tree)
 		return -1;
 
@@ -557,7 +565,7 @@ int get_tree_entry(const struct object_id *tree_oid, const char *name, struct ob
 	} else {
 		struct tree_desc t;
 		init_tree_desc(&t, tree, size);
-		retval = find_tree_entry(&t, name, oid, mode);
+		retval = find_tree_entry(r, &t, name, oid, mode);
 	}
 	free(tree);
 	return retval;
@@ -585,7 +593,10 @@ int get_tree_entry(const struct object_id *tree_oid, const char *name, struct ob
  * See the code for enum get_oid_result for a description of
  * the return values.
  */
-enum get_oid_result get_tree_entry_follow_symlinks(struct object_id *tree_oid, const char *name, struct object_id *result, struct strbuf *result_path, unsigned short *mode)
+enum get_oid_result get_tree_entry_follow_symlinks(struct repository *r,
+		struct object_id *tree_oid, const char *name,
+		struct object_id *result, struct strbuf *result_path,
+		unsigned short *mode)
 {
 	int retval = MISSING_OBJECT;
 	struct dir_state *parents = NULL;
@@ -609,7 +620,8 @@ enum get_oid_result get_tree_entry_follow_symlinks(struct object_id *tree_oid, c
 			void *tree;
 			struct object_id root;
 			unsigned long size;
-			tree = read_object_with_reference(&current_tree_oid,
+			tree = read_object_with_reference(r,
+							  &current_tree_oid,
 							  tree_type, &size,
 							  &root);
 			if (!tree)
@@ -678,7 +690,7 @@ enum get_oid_result get_tree_entry_follow_symlinks(struct object_id *tree_oid, c
 		}
 
 		/* Look up the first (or only) path component in the tree. */
-		find_result = find_tree_entry(&t, namebuf.buf,
+		find_result = find_tree_entry(r, &t, namebuf.buf,
 					      &current_tree_oid, mode);
 		if (find_result) {
 			goto done;
@@ -722,7 +734,8 @@ enum get_oid_result get_tree_entry_follow_symlinks(struct object_id *tree_oid, c
 			 */
 			retval = DANGLING_SYMLINK;
 
-			contents = read_object_file(&current_tree_oid, &type,
+			contents = repo_read_object_file(r,
+						    &current_tree_oid, &type,
 						    &link_len);
 
 			if (!contents)
diff --git a/tree-walk.h b/tree-walk.h
index 161e240..2a5db29 100644
--- a/tree-walk.h
+++ b/tree-walk.h
@@ -45,13 +45,15 @@ int init_tree_desc_gently(struct tree_desc *desc, const void *buf, unsigned long
 int tree_entry(struct tree_desc *, struct name_entry *);
 int tree_entry_gently(struct tree_desc *, struct name_entry *);
 
-void *fill_tree_descriptor(struct tree_desc *desc, const struct object_id *oid);
+void *fill_tree_descriptor(struct repository *r,
+			   struct tree_desc *desc,
+			   const struct object_id *oid);
 
 struct traverse_info;
 typedef int (*traverse_callback_t)(int n, unsigned long mask, unsigned long dirmask, struct name_entry *entry, struct traverse_info *);
 int traverse_trees(struct index_state *istate, int n, struct tree_desc *t, struct traverse_info *info);
 
-enum get_oid_result get_tree_entry_follow_symlinks(struct object_id *tree_oid, const char *name, struct object_id *result, struct strbuf *result_path, unsigned short *mode);
+enum get_oid_result get_tree_entry_follow_symlinks(struct repository *r, struct object_id *tree_oid, const char *name, struct object_id *result, struct strbuf *result_path, unsigned short *mode);
 
 struct traverse_info {
 	const char *traverse_path;
@@ -66,7 +68,7 @@ struct traverse_info {
 	int show_all_errors;
 };
 
-int get_tree_entry(const struct object_id *, const char *, struct object_id *, unsigned short *);
+int get_tree_entry(struct repository *, const struct object_id *, const char *, struct object_id *, unsigned short *);
 char *make_traverse_path(char *path, const struct traverse_info *info, const struct name_entry *n);
 void setup_traverse_info(struct traverse_info *info, const char *base);
 
diff --git a/unpack-trees.c b/unpack-trees.c
index dab7132..62276d4 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -840,7 +840,7 @@ static int traverse_trees_recursive(int n, unsigned long dirmask,
 			const struct object_id *oid = NULL;
 			if (dirmask & 1)
 				oid = &names[i].oid;
-			buf[nr_buf++] = fill_tree_descriptor(t + i, oid);
+			buf[nr_buf++] = fill_tree_descriptor(the_repository, t + i, oid);
 		}
 	}