Merge branch 'nd/the-index-final'

The assumption to work on the single "in-core index" instance has
been reduced from the library-ish part of the codebase.

* nd/the-index-final:
  cache.h: flip NO_THE_INDEX_COMPATIBILITY_MACROS switch
  read-cache.c: remove the_* from index_has_changes()
  merge-recursive.c: remove implicit dependency on the_repository
  merge-recursive.c: remove implicit dependency on the_index
  sha1-name.c: remove implicit dependency on the_index
  read-cache.c: replace update_index_if_able with repo_&
  read-cache.c: kill read_index()
  checkout: avoid the_index when possible
  repository.c: replace hold_locked_index() with repo_hold_locked_index()
  notes-utils.c: remove the_repository references
  grep: use grep_opt->repo instead of explict repo argument

74 files changed, 394 insertions, 296 deletions

diff --git a/apply.c b/apply.c
index 3703bfc..f489a56 100644
--- a/apply.c
+++ b/apply.c
@@ -4020,7 +4020,7 @@ static int read_apply_cache(struct apply_state *state)
 		return read_index_from(state->repo->index, state->index_file,
 				       get_git_dir());
 	else
-		return read_index(state->repo->index);
+		return repo_read_index(state->repo);
 }
 
 /* This function tries to read the object name from the current index */
@@ -4713,7 +4713,8 @@ static int apply_patch(struct apply_state *state,
 						  state->index_file,
 						  LOCK_DIE_ON_ERROR);
 		else
-			hold_locked_index(&state->lock_file, LOCK_DIE_ON_ERROR);
+			repo_hold_locked_index(state->repo, &state->lock_file,
+					       LOCK_DIE_ON_ERROR);
 	}
 
 	if (state->check_index && read_apply_cache(state) < 0) {
diff --git a/attr.c b/attr.c
index 0cba789..fdd110b 100644
--- a/attr.c
+++ b/attr.c
@@ -7,7 +7,6 @@
  * an insanely large number of attributes.
  */
 
-#define NO_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "exec-cmd.h"
diff --git a/blame.c b/blame.c
index 4386143..da57233 100644
--- a/blame.c
+++ b/blame.c
@@ -188,7 +188,7 @@ static struct commit *fake_working_tree_commit(struct repository *r,
 	unsigned mode;
 	struct strbuf msg = STRBUF_INIT;
 
-	read_index(r->index);
+	repo_read_index(r);
 	time(&now);
 	commit = alloc_commit_node(r);
 	commit->object.parsed = 1;
@@ -270,7 +270,7 @@ static struct commit *fake_working_tree_commit(struct repository *r,
 	 * want to run "diff-index --cached".
 	 */
 	discard_index(r->index);
-	read_index(r->index);
+	repo_read_index(r);
 
 	len = strlen(path);
 	if (!mode) {
diff --git a/builtin/add.c b/builtin/add.c
index 7c2a7c5..db2dfa4 100644
--- a/builtin/add.c
+++ b/builtin/add.c
@@ -3,6 +3,7 @@
  *
  * Copyright (C) 2006 Linus Torvalds
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "builtin.h"
diff --git a/builtin/am.c b/builtin/am.c
index 0cc3997..58a2aef 100644
--- a/builtin/am.c
+++ b/builtin/am.c
@@ -3,6 +3,7 @@
  *
  * Based on git-am.sh by Junio C Hamano.
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "builtin.h"
@@ -511,7 +512,7 @@ static int copy_notes_for_rebase(const struct am_state *state)
 	}
 
 finish:
-	finish_copy_notes_for_rewrite(c, msg);
+	finish_copy_notes_for_rewrite(the_repository, c, msg);
 	fclose(fp);
 	strbuf_release(&sb);
 	return ret;
@@ -1529,7 +1530,7 @@ static int fall_back_threeway(const struct am_state *state, const char *index_pa
 	 * changes.
 	 */
 
-	init_merge_options(&o);
+	init_merge_options(&o, the_repository);
 
 	o.branch1 = "HEAD";
 	their_tree_name = xstrfmt("%.*s", linelen(state->msg), state->msg);
@@ -1703,7 +1704,7 @@ static void am_run(struct am_state *state, int resume)
 
 	refresh_and_write_cache();
 
-	if (index_has_changes(&the_index, NULL, &sb)) {
+	if (repo_index_has_changes(the_repository, NULL, &sb)) {
 		write_state_bool(state, "dirtyindex", 1);
 		die(_("Dirty index: cannot apply patches (dirty: %s)"), sb.buf);
 	}
@@ -1761,7 +1762,7 @@ static void am_run(struct am_state *state, int resume)
 			 * the result may have produced the same tree as ours.
 			 */
 			if (!apply_status &&
-			    !index_has_changes(&the_index, NULL, NULL)) {
+			    !repo_index_has_changes(the_repository, NULL, NULL)) {
 				say(state, stdout, _("No changes -- Patch already applied."));
 				goto next;
 			}
@@ -1815,7 +1816,7 @@ static void am_resolve(struct am_state *state)
 
 	say(state, stdout, _("Applying: %.*s"), linelen(state->msg), state->msg);
 
-	if (!index_has_changes(&the_index, NULL, NULL)) {
+	if (!repo_index_has_changes(the_repository, NULL, NULL)) {
 		printf_ln(_("No changes - did you forget to use 'git add'?\n"
 			"If there is nothing left to stage, chances are that something else\n"
 			"already introduced the same changes; you might want to skip this patch."));
@@ -2271,7 +2272,7 @@ int cmd_am(int argc, const char **argv, const char *prefix)
 	/* Ensure a valid committer ident can be constructed */
 	git_committer_info(IDENT_STRICT);
 
-	if (read_index_preload(&the_index, NULL, 0) < 0)
+	if (repo_read_index_preload(the_repository, NULL, 0) < 0)
 		die(_("failed to read the index"));
 
 	if (in_progress) {
diff --git a/builtin/blame.c b/builtin/blame.c
index 6d798f9..0074ed3 100644
--- a/builtin/blame.c
+++ b/builtin/blame.c
@@ -1007,7 +1007,8 @@ parse_done:
 		long bottom, top;
 		if (parse_range_arg(range_list.items[range_i].string,
 				    nth_line_cb, &sb, lno, anchor,
-				    &bottom, &top, sb.path, &the_index))
+				    &bottom, &top, sb.path,
+				    the_repository->index))
 			usage(blame_usage);
 		if ((!lno && (top || bottom)) || lno < bottom)
 			die(Q_("file %s has only %lu line",
diff --git a/builtin/cat-file.c b/builtin/cat-file.c
index cebc6d7..8487cd7 100644
--- a/builtin/cat-file.c
+++ b/builtin/cat-file.c
@@ -3,6 +3,7 @@
  *
  * Copyright (C) Linus Torvalds, 2005
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "builtin.h"
@@ -73,7 +74,8 @@ static int cat_one_file(int opt, const char *exp_type, const char *obj_name,
 	if (unknown_type)
 		flags |= OBJECT_INFO_ALLOW_UNKNOWN_TYPE;
 
-	if (get_oid_with_context(obj_name, GET_OID_RECORD_PATH,
+	if (get_oid_with_context(the_repository, obj_name,
+				 GET_OID_RECORD_PATH,
 				 &oid, &obj_context))
 		die("Not a valid object name %s", obj_name);
 
@@ -382,7 +384,8 @@ static void batch_one_object(const char *obj_name,
 	int flags = opt->follow_symlinks ? GET_OID_FOLLOW_SYMLINKS : 0;
 	enum get_oid_result result;
 
-	result = get_oid_with_context(obj_name, flags, &data->oid, &ctx);
+	result = get_oid_with_context(the_repository, obj_name,
+				      flags, &data->oid, &ctx);
 	if (result != FOUND) {
 		switch (result) {
 		case MISSING_OBJECT:
diff --git a/builtin/check-attr.c b/builtin/check-attr.c
index 30a2f84..dd83397 100644
--- a/builtin/check-attr.c
+++ b/builtin/check-attr.c
@@ -1,3 +1,4 @@
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "cache.h"
 #include "config.h"
diff --git a/builtin/check-ignore.c b/builtin/check-ignore.c
index ec9a959..5990973 100644
--- a/builtin/check-ignore.c
+++ b/builtin/check-ignore.c
@@ -1,3 +1,4 @@
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "cache.h"
 #include "config.h"
diff --git a/builtin/checkout-index.c b/builtin/checkout-index.c
index a2a726a..1ac1cc2 100644
--- a/builtin/checkout-index.c
+++ b/builtin/checkout-index.c
@@ -4,6 +4,7 @@
  * Copyright (C) 2005 Linus Torvalds
  *
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "config.h"
 #include "lockfile.h"
diff --git a/builtin/checkout.c b/builtin/checkout.c
index 9f8f346..ece4eb1 100644
--- a/builtin/checkout.c
+++ b/builtin/checkout.c
@@ -1,3 +1,4 @@
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "config.h"
 #include "checkout.h"
@@ -288,7 +289,7 @@ static int checkout_paths(const struct checkout_opts *opts,
 		return run_add_interactive(revision, "--patch=checkout",
 					   &opts->pathspec);
 
-	hold_locked_index(&lock_file, LOCK_DIE_ON_ERROR);
+	repo_hold_locked_index(the_repository, &lock_file, LOCK_DIE_ON_ERROR);
 	if (read_cache_preload(&opts->pathspec) < 0)
 		return error(_("index file corrupt"));
 
@@ -701,7 +702,7 @@ static int merge_working_tree(const struct checkout_opts *opts,
 			 * a pain; plumb in an option to set
 			 * o.renormalize?
 			 */
-			init_merge_options(&o);
+			init_merge_options(&o, the_repository);
 			o.verbosity = 0;
 			work = write_tree_from_memory(&o);
 
diff --git a/builtin/clean.c b/builtin/clean.c
index bbcdeb2..aaba4af 100644
--- a/builtin/clean.c
+++ b/builtin/clean.c
@@ -6,6 +6,7 @@
  * Based on git-clean.sh by Pavel Roskin
  */
 
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "cache.h"
 #include "config.h"
diff --git a/builtin/clone.c b/builtin/clone.c
index 739de68..50bde99 100644
--- a/builtin/clone.c
+++ b/builtin/clone.c
@@ -8,6 +8,7 @@
  * Clone a repository into a different directory that does not yet exist.
  */
 
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "config.h"
 #include "lockfile.h"
diff --git a/builtin/commit.c b/builtin/commit.c
index 7d2e0b6..2986553 100644
--- a/builtin/commit.c
+++ b/builtin/commit.c
@@ -5,6 +5,7 @@
  * Based on git-commit.sh by Junio C Hamano and Linus Torvalds
  */
 
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "lockfile.h"
@@ -1368,7 +1369,7 @@ int cmd_status(int argc, const char **argv, const char *prefix)
 	if (status_format != STATUS_FORMAT_PORCELAIN &&
 	    status_format != STATUS_FORMAT_PORCELAIN_V2)
 		progress_flag = REFRESH_PROGRESS;
-	read_index(&the_index);
+	repo_read_index(the_repository);
 	refresh_index(&the_index,
 		      REFRESH_QUIET|REFRESH_UNMERGED|progress_flag,
 		      &s.pathspec, NULL, NULL);
@@ -1397,7 +1398,7 @@ int cmd_status(int argc, const char **argv, const char *prefix)
 	wt_status_collect(&s);
 
 	if (0 <= fd)
-		update_index_if_able(&the_index, &index_lock);
+		repo_update_index_if_able(the_repository, &index_lock);
 
 	if (s.relative_paths)
 		s.prefix = prefix;
@@ -1675,7 +1676,7 @@ int cmd_commit(int argc, const char **argv, const char *prefix)
 	run_command_v_opt(argv_gc_auto, RUN_GIT_CMD);
 	run_commit_hook(use_editor, get_index_file(), "post-commit", NULL);
 	if (amend && !no_post_rewrite) {
-		commit_post_rewrite(current_head, &oid);
+		commit_post_rewrite(the_repository, current_head, &oid);
 	}
 	if (!quiet) {
 		unsigned int flags = 0;
diff --git a/builtin/describe.c b/builtin/describe.c
index cc11844..02ec564 100644
--- a/builtin/describe.c
+++ b/builtin/describe.c
@@ -1,3 +1,4 @@
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "lockfile.h"
@@ -634,7 +635,7 @@ int cmd_describe(int argc, const char **argv, const char *prefix)
 				      NULL, NULL, NULL);
 			fd = hold_locked_index(&index_lock, 0);
 			if (0 <= fd)
-				update_index_if_able(&the_index, &index_lock);
+				repo_update_index_if_able(the_repository, &index_lock);
 
 			repo_init_revisions(the_repository, &revs, prefix);
 			argv_array_pushv(&args, diff_index_args);
diff --git a/builtin/diff-files.c b/builtin/diff-files.c
index 48cfcb9..86ae474 100644
--- a/builtin/diff-files.c
+++ b/builtin/diff-files.c
@@ -3,6 +3,7 @@
  *
  * Copyright (C) Linus Torvalds, 2005
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "diff.h"
diff --git a/builtin/diff-index.c b/builtin/diff-index.c
index fcccd1f..93ec642 100644
--- a/builtin/diff-index.c
+++ b/builtin/diff-index.c
@@ -1,3 +1,4 @@
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "diff.h"
diff --git a/builtin/diff-tree.c b/builtin/diff-tree.c
index ef99612..a90681b 100644
--- a/builtin/diff-tree.c
+++ b/builtin/diff-tree.c
@@ -1,3 +1,4 @@
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "diff.h"
@@ -165,7 +166,7 @@ int cmd_diff_tree(int argc, const char **argv, const char *prefix)
 
 		if (opt->diffopt.detect_rename) {
 			if (!the_index.cache)
-				read_index(&the_index);
+				repo_read_index(the_repository);
 			opt->diffopt.setup |= DIFF_SETUP_USE_SIZE_CACHE;
 		}
 		while (fgets(line, sizeof(line), stdin)) {
diff --git a/builtin/diff.c b/builtin/diff.c
index f0393bb..74351a5 100644
--- a/builtin/diff.c
+++ b/builtin/diff.c
@@ -3,6 +3,7 @@
  *
  * Copyright (c) 2006 Junio C Hamano
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "lockfile.h"
@@ -212,7 +213,7 @@ static void refresh_index_quietly(void)
 	discard_cache();
 	read_cache();
 	refresh_cache(REFRESH_QUIET|REFRESH_UNMERGED);
-	update_index_if_able(&the_index, &lock_file);
+	repo_update_index_if_able(the_repository, &lock_file);
 }
 
 static int builtin_diff_files(struct rev_info *revs, int argc, const char **argv)
diff --git a/builtin/difftool.c b/builtin/difftool.c
index 71318c2..a3ea60e 100644
--- a/builtin/difftool.c
+++ b/builtin/difftool.c
@@ -11,6 +11,7 @@
  *
  * Copyright (C) 2016 Johannes Schindelin
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "builtin.h"
diff --git a/builtin/fsck.c b/builtin/fsck.c
index 9c4c11d..bb4227b 100644
--- a/builtin/fsck.c
+++ b/builtin/fsck.c
@@ -1,3 +1,4 @@
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "cache.h"
 #include "repository.h"
diff --git a/builtin/grep.c b/builtin/grep.c
index dd52ea9..580fd38 100644
--- a/builtin/grep.c
+++ b/builtin/grep.c
@@ -3,6 +3,7 @@
  *
  * Copyright (c) 2006 Junio C Hamano
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "repository.h"
 #include "config.h"
@@ -393,21 +394,22 @@ static void run_pager(struct grep_opt *opt, const char *prefix)
 		exit(status);
 }
 
-static int grep_cache(struct grep_opt *opt, struct repository *repo,
+static int grep_cache(struct grep_opt *opt,
 		      const struct pathspec *pathspec, int cached);
 static int grep_tree(struct grep_opt *opt, const struct pathspec *pathspec,
 		     struct tree_desc *tree, struct strbuf *base, int tn_len,
-		     int check_attr, struct repository *repo);
+		     int check_attr);
 
-static int grep_submodule(struct grep_opt *opt, struct repository *superproject,
+static int grep_submodule(struct grep_opt *opt,
 			  const struct pathspec *pathspec,
 			  const struct object_id *oid,
 			  const char *filename, const char *path)
 {
 	struct repository subrepo;
+	struct repository *superproject = opt->repo;
 	const struct submodule *sub = submodule_from_path(superproject,
 							  &null_oid, path);
-
+	struct grep_opt subopt;
 	int hit;
 
 	/*
@@ -443,6 +445,9 @@ static int grep_submodule(struct grep_opt *opt, struct repository *superproject,
 	add_to_alternates_memory(subrepo.objects->odb->path);
 	grep_read_unlock();
 
+	memcpy(&subopt, opt, sizeof(subopt));
+	subopt.repo = &subrepo;
+
 	if (oid) {
 		struct object *object;
 		struct tree_desc tree;
@@ -464,21 +469,22 @@ static int grep_submodule(struct grep_opt *opt, struct repository *superproject,
 		strbuf_addch(&base, '/');
 
 		init_tree_desc(&tree, data, size);
-		hit = grep_tree(opt, pathspec, &tree, &base, base.len,
-				object->type == OBJ_COMMIT, &subrepo);
+		hit = grep_tree(&subopt, pathspec, &tree, &base, base.len,
+				object->type == OBJ_COMMIT);
 		strbuf_release(&base);
 		free(data);
 	} else {
-		hit = grep_cache(opt, &subrepo, pathspec, 1);
+		hit = grep_cache(&subopt, pathspec, 1);
 	}
 
 	repo_clear(&subrepo);
 	return hit;
 }
 
-static int grep_cache(struct grep_opt *opt, struct repository *repo,
+static int grep_cache(struct grep_opt *opt,
 		      const struct pathspec *pathspec, int cached)
 {
+	struct repository *repo = opt->repo;
 	int hit = 0;
 	int nr;
 	struct strbuf name = STRBUF_INIT;
@@ -516,7 +522,7 @@ static int grep_cache(struct grep_opt *opt, struct repository *repo,
 			}
 		} else if (recurse_submodules && S_ISGITLINK(ce->ce_mode) &&
 			   submodule_path_match(repo->index, pathspec, name.buf, NULL)) {
-			hit |= grep_submodule(opt, repo, pathspec, NULL, ce->name, ce->name);
+			hit |= grep_submodule(opt, pathspec, NULL, ce->name, ce->name);
 		} else {
 			continue;
 		}
@@ -538,8 +544,9 @@ static int grep_cache(struct grep_opt *opt, struct repository *repo,
 
 static int grep_tree(struct grep_opt *opt, const struct pathspec *pathspec,
 		     struct tree_desc *tree, struct strbuf *base, int tn_len,
-		     int check_attr, struct repository *repo)
+		     int check_attr)
 {
+	struct repository *repo = opt->repo;
 	int hit = 0;
 	enum interesting match = entry_not_interesting;
 	struct name_entry entry;
@@ -586,10 +593,10 @@ static int grep_tree(struct grep_opt *opt, const struct pathspec *pathspec,
 			strbuf_addch(base, '/');
 			init_tree_desc(&sub, data, size);
 			hit |= grep_tree(opt, pathspec, &sub, base, tn_len,
-					 check_attr, repo);
+					 check_attr);
 			free(data);
 		} else if (recurse_submodules && S_ISGITLINK(entry.mode)) {
-			hit |= grep_submodule(opt, repo, pathspec, &entry.oid,
+			hit |= grep_submodule(opt, pathspec, &entry.oid,
 					      base->buf, base->buf + tn_len);
 		}
 
@@ -631,7 +638,7 @@ static int grep_object(struct grep_opt *opt, const struct pathspec *pathspec,
 		}
 		init_tree_desc(&tree, data, size);
 		hit = grep_tree(opt, pathspec, &tree, &base, base.len,
-				obj->type == OBJ_COMMIT, the_repository);
+				obj->type == OBJ_COMMIT);
 		strbuf_release(&base);
 		free(data);
 		return hit;
@@ -648,12 +655,12 @@ static int grep_objects(struct grep_opt *opt, const struct pathspec *pathspec,
 
 	for (i = 0; i < nr; i++) {
 		struct object *real_obj;
-		real_obj = deref_tag(the_repository, list->objects[i].item,
+		real_obj = deref_tag(opt->repo, list->objects[i].item,
 				     NULL, 0);
 
 		/* load the gitmodules file for this rev */
 		if (recurse_submodules) {
-			submodule_free(the_repository);
+			submodule_free(opt->repo);
 			gitmodules_config_oid(&real_obj->oid);
 		}
 		if (grep_object(opt, pathspec, real_obj, list->objects[i].name,
@@ -678,9 +685,9 @@ static int grep_directory(struct grep_opt *opt, const struct pathspec *pathspec,
 	if (exc_std)
 		setup_standard_excludes(&dir);
 
-	fill_directory(&dir, &the_index, pathspec);
+	fill_directory(&dir, opt->repo->index, pathspec);
 	for (i = 0; i < dir.nr; i++) {
-		if (!dir_path_match(&the_index, dir.entries[i], pathspec, 0, NULL))
+		if (!dir_path_match(opt->repo->index, dir.entries[i], pathspec, 0, NULL))
 			continue;
 		hit |= grep_file(opt, dir.entries[i]->name);
 		if (hit && opt->status_only)
@@ -1018,7 +1025,8 @@ int cmd_grep(int argc, const char **argv, const char *prefix)
 			break;
 		}
 
-		if (get_oid_with_context(arg, GET_OID_RECORD_PATH,
+		if (get_oid_with_context(the_repository, arg,
+					 GET_OID_RECORD_PATH,
 					 &oid, &oc)) {
 			if (seen_dashdash)
 				die(_("unable to resolve revision: %s"), arg);
@@ -1121,7 +1129,7 @@ int cmd_grep(int argc, const char **argv, const char *prefix)
 		if (!cached)
 			setup_work_tree();
 
-		hit = grep_cache(&opt, the_repository, &pathspec, cached);
+		hit = grep_cache(&opt, &pathspec, cached);
 	} else {
 		if (cached)
 			die(_("both --cached and trees are given"));
diff --git a/builtin/hash-object.c b/builtin/hash-object.c
index d6f06ea..e055c11 100644
--- a/builtin/hash-object.c
+++ b/builtin/hash-object.c
@@ -40,7 +40,8 @@ static void hash_fd(int fd, const char *type, const char *path, unsigned flags,
 	if (fstat(fd, &st) < 0 ||
 	    (literally
 	     ? hash_literally(&oid, fd, type, flags)
-	     : index_fd(&the_index, &oid, fd, &st, type_from_string(type), path, flags)))
+	     : index_fd(the_repository->index, &oid, fd, &st,
+			type_from_string(type), path, flags)))
 		die((flags & HASH_WRITE_OBJECT)
 		    ? "Unable to add %s to database"
 		    : "Unable to hash %s", path);
diff --git a/builtin/log.c b/builtin/log.c
index c91a59d..5786926 100644
--- a/builtin/log.c
+++ b/builtin/log.c
@@ -4,6 +4,7 @@
  * (C) Copyright 2006 Linus Torvalds
  *		 2006 Junio Hamano
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "refs.h"
@@ -509,7 +510,8 @@ static int show_blob_object(const struct object_id *oid, struct rev_info *rev, c
 	    !rev->diffopt.flags.allow_textconv)
 		return stream_blob_to_fd(1, oid, NULL, 0);
 
-	if (get_oid_with_context(obj_name, GET_OID_RECORD_PATH,
+	if (get_oid_with_context(the_repository, obj_name,
+				 GET_OID_RECORD_PATH,
 				 &oidc, &obj_context))
 		die(_("Not a valid object name %s"), obj_name);
 	if (!obj_context.path ||
diff --git a/builtin/ls-files.c b/builtin/ls-files.c
index cde87cb..29a8762 100644
--- a/builtin/ls-files.c
+++ b/builtin/ls-files.c
@@ -5,7 +5,6 @@
  *
  * Copyright (C) Linus Torvalds, 2005
  */
-#define NO_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "repository.h"
 #include "config.h"
diff --git a/builtin/merge-index.c b/builtin/merge-index.c
index c99443b..38ea6ad 100644
--- a/builtin/merge-index.c
+++ b/builtin/merge-index.c
@@ -1,3 +1,4 @@
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "run-command.h"
 
diff --git a/builtin/merge-ours.c b/builtin/merge-ours.c
index 0b07263..4594507 100644
--- a/builtin/merge-ours.c
+++ b/builtin/merge-ours.c
@@ -7,6 +7,7 @@
  *
  * Pretend we resolved the heads, but declare our tree trumps everybody else.
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "git-compat-util.h"
 #include "builtin.h"
 #include "diff.h"
diff --git a/builtin/merge-recursive.c b/builtin/merge-recursive.c
index 7545136..5b910e3 100644
--- a/builtin/merge-recursive.c
+++ b/builtin/merge-recursive.c
@@ -29,7 +29,7 @@ int cmd_merge_recursive(int argc, const char **argv, const char *prefix)
 	char *better1, *better2;
 	struct commit *result;
 
-	init_merge_options(&o);
+	init_merge_options(&o, the_repository);
 	if (argv[0] && ends_with(argv[0], "-subtree"))
 		o.subtree_shift = "";
 
diff --git a/builtin/merge-tree.c b/builtin/merge-tree.c
index 5541ad0..34ca025 100644
--- a/builtin/merge-tree.c
+++ b/builtin/merge-tree.c
@@ -1,3 +1,4 @@
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "tree-walk.h"
 #include "xdiff-interface.h"
@@ -76,7 +77,8 @@ static void *result(struct merge_list *entry, unsigned long *size)
 	their = NULL;
 	if (entry)
 		their = entry->blob;
-	return merge_blobs(&the_index, path, base, our, their, size);
+	return merge_blobs(the_repository->index, path,
+			   base, our, their, size);
 }
 
 static void *origin(struct merge_list *entry, unsigned long *size)
diff --git a/builtin/merge.c b/builtin/merge.c
index dc0b7cc..e47d77b 100644
--- a/builtin/merge.c
+++ b/builtin/merge.c
@@ -6,6 +6,7 @@
  * Based on git-merge.sh by Junio C Hamano.
  */
 
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "parse-options.h"
@@ -702,7 +703,7 @@ static int try_merge_strategy(const char *strategy, struct commit_list *common,
 			return 2;
 		}
 
-		init_merge_options(&o);
+		init_merge_options(&o, the_repository);
 		if (!strcmp(strategy, "subtree"))
 			o.subtree_shift = "";
 
diff --git a/builtin/mv.c b/builtin/mv.c
index 80bb967..be15ba7 100644
--- a/builtin/mv.c
+++ b/builtin/mv.c
@@ -3,6 +3,7 @@
  *
  * Copyright (C) 2006 Johannes Schindelin
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "config.h"
 #include "pathspec.h"
diff --git a/builtin/notes.c b/builtin/notes.c
index 4996a67..02e97f5 100644
--- a/builtin/notes.c
+++ b/builtin/notes.c
@@ -330,10 +330,10 @@ static int notes_copy_from_stdin(int force, const char *rewrite_cmd)
 	}
 
 	if (!rewrite_cmd) {
-		commit_notes(t, msg);
+		commit_notes(the_repository, t, msg);
 		free_notes(t);
 	} else {
-		finish_copy_notes_for_rewrite(c, msg);
+		finish_copy_notes_for_rewrite(the_repository, c, msg);
 	}
 	strbuf_release(&buf);
 	return ret;
@@ -469,12 +469,14 @@ static int add(int argc, const char **argv, const char *prefix)
 		write_note_data(&d, &new_note);
 		if (add_note(t, &object, &new_note, combine_notes_overwrite))
 			BUG("combine_notes_overwrite failed");
-		commit_notes(t, "Notes added by 'git notes add'");
+		commit_notes(the_repository, t,
+			     "Notes added by 'git notes add'");
 	} else {
 		fprintf(stderr, _("Removing note for object %s\n"),
 			oid_to_hex(&object));
 		remove_note(t, object.hash);
-		commit_notes(t, "Notes removed by 'git notes add'");
+		commit_notes(the_repository, t,
+			     "Notes removed by 'git notes add'");
 	}
 
 	free_note_data(&d);
@@ -552,7 +554,8 @@ static int copy(int argc, const char **argv, const char *prefix)
 
 	if (add_note(t, &object, from_note, combine_notes_overwrite))
 		BUG("combine_notes_overwrite failed");
-	commit_notes(t, "Notes added by 'git notes copy'");
+	commit_notes(the_repository, t,
+		     "Notes added by 'git notes copy'");
 out:
 	free_notes(t);
 	return retval;
@@ -636,7 +639,7 @@ static int append_edit(int argc, const char **argv, const char *prefix)
 		remove_note(t, object.hash);
 		logmsg = xstrfmt("Notes removed by 'git notes %s'", argv[0]);
 	}
-	commit_notes(t, logmsg);
+	commit_notes(the_repository, t, logmsg);
 
 	free(logmsg);
 	free_note_data(&d);
@@ -937,7 +940,8 @@ static int remove_cmd(int argc, const char **argv, const char *prefix)
 		strbuf_release(&sb);
 	}
 	if (!retval)
-		commit_notes(t, "Notes removed by 'git notes remove'");
+		commit_notes(the_repository, t,
+			     "Notes removed by 'git notes remove'");
 	free_notes(t);
 	return retval;
 }
@@ -965,7 +969,8 @@ static int prune(int argc, const char **argv, const char *prefix)
 	prune_notes(t, (verbose ? NOTES_PRUNE_VERBOSE : 0) |
 		(show_only ? NOTES_PRUNE_VERBOSE|NOTES_PRUNE_DRYRUN : 0) );
 	if (!show_only)
-		commit_notes(t, "Notes removed by 'git notes prune'");
+		commit_notes(the_repository, t,
+			     "Notes removed by 'git notes prune'");
 	free_notes(t);
 	return 0;
 }
diff --git a/builtin/pack-objects.c b/builtin/pack-objects.c
index 8eb5391..ffef8dc 100644
--- a/builtin/pack-objects.c
+++ b/builtin/pack-objects.c
@@ -970,7 +970,7 @@ static int no_try_delta(const char *path)
 
 	if (!check)
 		check = attr_check_initl("delta", NULL);
-	git_check_attr(&the_index, path, check);
+	git_check_attr(the_repository->index, path, check);
 	if (ATTR_FALSE(check->items[0].value))
 		return 1;
 	return 0;
diff --git a/builtin/pull.c b/builtin/pull.c
index 74808b9..701d147 100644
--- a/builtin/pull.c
+++ b/builtin/pull.c
@@ -5,6 +5,7 @@
  *
  * Fetch one or more remote refs and merge it/them into the current HEAD.
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "builtin.h"
diff --git a/builtin/read-tree.c b/builtin/read-tree.c
index ac255ad..9083dcf 100644
--- a/builtin/read-tree.c
+++ b/builtin/read-tree.c
@@ -4,6 +4,7 @@
  * Copyright (C) Linus Torvalds, 2005
  */
 
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "lockfile.h"
diff --git a/builtin/rebase--interactive.c b/builtin/rebase--interactive.c
index c2c2d51..888390f 100644
--- a/builtin/rebase--interactive.c
+++ b/builtin/rebase--interactive.c
@@ -1,3 +1,4 @@
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "cache.h"
 #include "config.h"
diff --git a/builtin/rebase.c b/builtin/rebase.c
index 8d49e53..0b03931 100644
--- a/builtin/rebase.c
+++ b/builtin/rebase.c
@@ -4,6 +4,7 @@
  * Copyright (c) 2018 Pratik Karki
  */
 
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "run-command.h"
 #include "exec-cmd.h"
@@ -419,7 +420,7 @@ static int reset_head(struct object_id *oid, const char *action,
 	if (!detach_head)
 		unpack_tree_opts.reset = 1;
 
-	if (read_index_unmerged(the_repository->index) < 0) {
+	if (repo_read_index_unmerged(the_repository) < 0) {
 		ret = error(_("could not read index"));
 		goto leave_reset_head;
 	}
@@ -1233,13 +1234,12 @@ int cmd_rebase(int argc, const char **argv, const char *prefix)
 			die(_("Cannot read HEAD"));
 
 		fd = hold_locked_index(&lock_file, 0);
-		if (read_index(the_repository->index) < 0)
+		if (repo_read_index(the_repository) < 0)
 			die(_("could not read index"));
 		refresh_index(the_repository->index, REFRESH_QUIET, NULL, NULL,
 			      NULL);
 		if (0 <= fd)
-			update_index_if_able(the_repository->index,
-					     &lock_file);
+			repo_update_index_if_able(the_repository, &lock_file);
 		rollback_lock_file(&lock_file);
 
 		if (has_unstaged_changes(the_repository, 1)) {
@@ -1591,7 +1591,7 @@ int cmd_rebase(int argc, const char **argv, const char *prefix)
 			get_fork_point(options.upstream_name, head);
 	}
 
-	if (read_index(the_repository->index) < 0)
+	if (repo_read_index(the_repository) < 0)
 		die(_("could not read index"));
 
 	if (options.autostash) {
@@ -1601,7 +1601,7 @@ int cmd_rebase(int argc, const char **argv, const char *prefix)
 		fd = hold_locked_index(&lock_file, 0);
 		refresh_cache(REFRESH_QUIET);
 		if (0 <= fd)
-			update_index_if_able(&the_index, &lock_file);
+			repo_update_index_if_able(the_repository, &lock_file);
 		rollback_lock_file(&lock_file);
 
 		if (has_unstaged_changes(the_repository, 1) ||
@@ -1646,7 +1646,7 @@ int cmd_rebase(int argc, const char **argv, const char *prefix)
 			putchar('\n');
 
 			if (discard_index(the_repository->index) < 0 ||
-				read_index(the_repository->index) < 0)
+				repo_read_index(the_repository) < 0)
 				die(_("could not read index"));
 		}
 	}
diff --git a/builtin/replace.c b/builtin/replace.c
index affcdfb..5b80b7f 100644
--- a/builtin/replace.c
+++ b/builtin/replace.c
@@ -295,7 +295,7 @@ static int import_object(struct object_id *oid, enum object_type type,
 			close(fd);
 			return -1;
 		}
-		if (index_fd(&the_index, oid, fd, &st, type, NULL, flags) < 0)
+		if (index_fd(the_repository->index, oid, fd, &st, type, NULL, flags) < 0)
 			return error(_("unable to write object to database"));
 		/* index_fd close()s fd for us */
 	}
diff --git a/builtin/reset.c b/builtin/reset.c
index 59898c9..4d18a46 100644
--- a/builtin/reset.c
+++ b/builtin/reset.c
@@ -7,6 +7,7 @@
  *
  * Copyright (c) 2005, 2006 Linus Torvalds and Junio C Hamano
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "config.h"
 #include "lockfile.h"
diff --git a/builtin/rev-parse.c b/builtin/rev-parse.c
index 10d4dab..f8bbe6d 100644
--- a/builtin/rev-parse.c
+++ b/builtin/rev-parse.c
@@ -3,6 +3,7 @@
  *
  * Copyright (C) Linus Torvalds, 2005
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "commit.h"
@@ -933,7 +934,8 @@ int cmd_rev_parse(int argc, const char **argv, const char *prefix)
 			name++;
 			type = REVERSED;
 		}
-		if (!get_oid_with_context(name, flags, &oid, &unused)) {
+		if (!get_oid_with_context(the_repository, name,
+					  flags, &oid, &unused)) {
 			if (verify)
 				revs_count++;
 			else
diff --git a/builtin/rm.c b/builtin/rm.c
index 17086d3..db85b33 100644
--- a/builtin/rm.c
+++ b/builtin/rm.c
@@ -3,6 +3,7 @@
  *
  * Copyright (C) Linus Torvalds 2006
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "config.h"
 #include "lockfile.h"
diff --git a/builtin/submodule--helper.c b/builtin/submodule--helper.c
index 0e140f1..b80fc4b 100644
--- a/builtin/submodule--helper.c
+++ b/builtin/submodule--helper.c
@@ -1,3 +1,4 @@
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "repository.h"
 #include "cache.h"
diff --git a/builtin/update-index.c b/builtin/update-index.c
index e19da77..02ace60 100644
--- a/builtin/update-index.c
+++ b/builtin/update-index.c
@@ -3,6 +3,7 @@
  *
  * Copyright (C) Linus Torvalds, 2005
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "lockfile.h"
diff --git a/builtin/write-tree.c b/builtin/write-tree.c
index cdcbf82..3d46d22 100644
--- a/builtin/write-tree.c
+++ b/builtin/write-tree.c
@@ -3,6 +3,7 @@
  *
  * Copyright (C) Linus Torvalds, 2005
  */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
 #include "cache.h"
 #include "config.h"
diff --git a/cache-tree.h b/cache-tree.h
index 3262091..757bbc4 100644
--- a/cache-tree.h
+++ b/cache-tree.h
@@ -51,7 +51,7 @@ void prime_cache_tree(struct repository *, struct index_state *, struct tree *);
 
 int cache_tree_matches_traversal(struct cache_tree *, struct name_entry *ent, struct traverse_info *info);
 
-#ifndef NO_THE_INDEX_COMPATIBILITY_MACROS
+#ifdef USE_THE_INDEX_COMPATIBILITY_MACROS
 static inline int write_cache_as_tree(struct object_id *oid, int flags, const char *prefix)
 {
 	return write_index_as_tree(oid, &the_index, get_index_file(), flags, prefix);
diff --git a/cache.h b/cache.h
index bcf9fd4..c653668 100644
--- a/cache.h
+++ b/cache.h
@@ -348,8 +348,6 @@ struct index_state {
 	struct mem_pool *ce_mem_pool;
 };
 
-extern struct index_state the_index;
-
 /* Name hashing */
 extern int test_lazy_init_name_hash(struct index_state *istate, int try_threaded);
 extern void add_name_hash(struct index_state *istate, struct cache_entry *ce);
@@ -411,18 +409,20 @@ struct cache_entry *dup_cache_entry(const struct cache_entry *ce, struct index_s
  */
 void validate_cache_entries(const struct index_state *istate);
 
-#ifndef NO_THE_INDEX_COMPATIBILITY_MACROS
+#ifdef USE_THE_INDEX_COMPATIBILITY_MACROS
+extern struct index_state the_index;
+
 #define active_cache (the_index.cache)
 #define active_nr (the_index.cache_nr)
 #define active_alloc (the_index.cache_alloc)
 #define active_cache_changed (the_index.cache_changed)
 #define active_cache_tree (the_index.cache_tree)
 
-#define read_cache() read_index(&the_index)
+#define read_cache() repo_read_index(the_repository)
 #define read_cache_from(path) read_index_from(&the_index, (path), (get_git_dir()))
-#define read_cache_preload(pathspec) read_index_preload(&the_index, (pathspec), 0)
+#define read_cache_preload(pathspec) repo_read_index_preload(the_repository, (pathspec), 0)
 #define is_cache_unborn() is_index_unborn(&the_index)
-#define read_cache_unmerged() read_index_unmerged(&the_index)
+#define read_cache_unmerged() repo_read_index_unmerged(the_repository)
 #define discard_cache() discard_index(&the_index)
 #define unmerged_cache() unmerged_index(&the_index)
 #define cache_name_pos(name, namelen) index_name_pos(&the_index,(name),(namelen))
@@ -443,6 +443,7 @@ void validate_cache_entries(const struct index_state *istate);
 #define unmerge_cache_entry_at(at) unmerge_index_entry_at(&the_index, at)
 #define unmerge_cache(pathspec) unmerge_index(&the_index, pathspec)
 #define read_blob_data_from_cache(path, sz) read_blob_data_from_index(&the_index, (path), (sz))
+#define hold_locked_index(lock_file, flags) repo_hold_locked_index(the_repository, (lock_file), (flags))
 #endif
 
 #define TYPE_BITS 3
@@ -670,19 +671,14 @@ extern int daemonize(void);
 
 /* Initialize and use the cache information */
 struct lock_file;
-extern int read_index(struct index_state *);
 extern void preload_index(struct index_state *index,
 			  const struct pathspec *pathspec,
 			  unsigned int refresh_flags);
-extern int read_index_preload(struct index_state *,
-			      const struct pathspec *pathspec,
-			      unsigned int refresh_flags);
 extern int do_read_index(struct index_state *istate, const char *path,
 			 int must_exist); /* for testting only! */
 extern int read_index_from(struct index_state *, const char *path,
 			   const char *gitdir);
 extern int is_index_unborn(struct index_state *);
-extern int read_index_unmerged(struct index_state *);
 
 /* For use with `write_locked_index()`. */
 #define COMMIT_LOCK		(1 << 0)
@@ -720,9 +716,9 @@ extern int unmerged_index(const struct index_state *);
  * provided, the space-separated list of files that differ will be appended
  * to it.
  */
-extern int index_has_changes(struct index_state *istate,
-			     struct tree *tree,
-			     struct strbuf *sb);
+extern int repo_index_has_changes(struct repository *repo,
+				  struct tree *tree,
+				  struct strbuf *sb);
 
 extern int verify_path(const char *path, unsigned mode);
 extern int strcmp_offset(const char *s1, const char *s2, size_t *first_change);
@@ -838,13 +834,6 @@ extern void fill_stat_cache_info(struct cache_entry *ce, struct stat *st);
 extern int refresh_index(struct index_state *, unsigned int flags, const struct pathspec *pathspec, char *seen, const char *header_msg);
 extern struct cache_entry *refresh_cache_entry(struct index_state *, struct cache_entry *, unsigned int);
 
-/*
- * Opportunistically update the index but do not complain if we can't.
- * The lockfile is always committed or rolled back.
- */
-extern void update_index_if_able(struct index_state *, struct lock_file *);
-
-extern int hold_locked_index(struct lock_file *, int);
 extern void set_alternate_index_output(const char *);
 
 extern int verify_index_checksum;
@@ -1370,8 +1359,9 @@ 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);
-extern enum get_oid_result get_oid_with_context(const char *str, unsigned flags, struct object_id *oid, struct object_context *oc);
-
+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);
 
 typedef int each_abbrev_fn(const struct object_id *oid, void *);
 extern int for_each_abbrev(const char *prefix, each_abbrev_fn, void *);
diff --git a/convert.c b/convert.c
index 0d89ae7..489510c 100644
--- a/convert.c
+++ b/convert.c
@@ -1,4 +1,3 @@
-#define NO_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "object-store.h"
diff --git a/dir.c b/dir.c
index 2128448..b2cabad 100644
--- a/dir.c
+++ b/dir.c
@@ -7,7 +7,6 @@
  * Copyright (C) Linus Torvalds, 2005-2006
  *		 Junio Hamano, 2005-2006
  */
-#define NO_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "dir.h"
diff --git a/git.c b/git.c
index 0ce0e13..2dd5886 100644
--- a/git.c
+++ b/git.c
@@ -418,9 +418,9 @@ static int run_builtin(struct cmd_struct *p, int argc, const char **argv)
 
 	trace_argv_printf(argv, "trace: built-in: git");
 
-	validate_cache_entries(&the_index);
+	validate_cache_entries(the_repository->index);
 	status = p->fn(argc, argv, prefix);
-	validate_cache_entries(&the_index);
+	validate_cache_entries(the_repository->index);
 
 	if (status)
 		return status;
diff --git a/list-objects-filter-options.c b/list-objects-filter-options.c
index 9efb3e9..b71bd1f 100644
--- a/list-objects-filter-options.c
+++ b/list-objects-filter-options.c
@@ -71,7 +71,7 @@ static int gently_parse_list_objects_filter(
 		 * command, but DO NOT complain if we don't have the blob or
 		 * ref locally.
 		 */
-		if (!get_oid_with_context(v0, GET_OID_BLOB,
+		if (!get_oid_with_context(the_repository, v0, GET_OID_BLOB,
 					  &sparse_oid, &oc))
 			filter_options->sparse_oid_value = oiddup(&sparse_oid);
 		filter_options->choice = LOFC_SPARSE_OID;
diff --git a/merge-recursive.c b/merge-recursive.c
index 59ba4b4..4851825 100644
--- a/merge-recursive.c
+++ b/merge-recursive.c
@@ -146,7 +146,8 @@ static int err(struct merge_options *o, const char *err, ...)
 	return -1;
 }
 
-static struct tree *shift_tree_object(struct tree *one, struct tree *two,
+static struct tree *shift_tree_object(struct repository *repo,
+				      struct tree *one, struct tree *two,
 				      const char *subtree_shift)
 {
 	struct object_id shifted;
@@ -159,12 +160,14 @@ static struct tree *shift_tree_object(struct tree *one, struct tree *two,
 	}
 	if (oideq(&two->object.oid, &shifted))
 		return two;
-	return lookup_tree(the_repository, &shifted);
+	return lookup_tree(repo, &shifted);
 }
 
-static struct commit *make_virtual_commit(struct tree *tree, const char *comment)
+static struct commit *make_virtual_commit(struct repository *repo,
+					  struct tree *tree,
+					  const char *comment)
 {
-	struct commit *commit = alloc_commit_node(the_repository);
+	struct commit *commit = alloc_commit_node(repo);
 
 	set_merge_remote_desc(commit, comment, (struct object *)commit);
 	commit->maybe_tree = tree;
@@ -343,22 +346,24 @@ static int add_cacheinfo(struct merge_options *o,
 			 unsigned int mode, const struct object_id *oid,
 			 const char *path, int stage, int refresh, int options)
 {
+	struct index_state *istate = o->repo->index;
 	struct cache_entry *ce;
 	int ret;
 
-	ce = make_cache_entry(&the_index, mode, oid ? oid : &null_oid, path, stage, 0);
+	ce = make_cache_entry(istate, mode, oid ? oid : &null_oid, path, stage, 0);
 	if (!ce)
 		return err(o, _("add_cacheinfo failed for path '%s'; merge aborting."), path);
 
-	ret = add_cache_entry(ce, options);
+	ret = add_index_entry(istate, ce, options);
 	if (refresh) {
 		struct cache_entry *nce;
 
-		nce = refresh_cache_entry(&the_index, ce, CE_MATCH_REFRESH | CE_MATCH_IGNORE_MISSING);
+		nce = refresh_cache_entry(istate, ce,
+					  CE_MATCH_REFRESH | CE_MATCH_IGNORE_MISSING);
 		if (!nce)
 			return err(o, _("add_cacheinfo failed to refresh for path '%s'; merge aborting."), path);
 		if (nce != ce)
-			ret = add_cache_entry(nce, options);
+			ret = add_index_entry(istate, nce, options);
 	}
 	return ret;
 }
@@ -386,7 +391,7 @@ static int unpack_trees_start(struct merge_options *o,
 	o->unpack_opts.merge = 1;
 	o->unpack_opts.head_idx = 2;
 	o->unpack_opts.fn = threeway_merge;
-	o->unpack_opts.src_index = &the_index;
+	o->unpack_opts.src_index = o->repo->index;
 	o->unpack_opts.dst_index = &tmp_index;
 	o->unpack_opts.aggressive = !merge_detect_rename(o);
 	setup_unpack_trees_porcelain(&o->unpack_opts, "merge");
@@ -396,16 +401,16 @@ static int unpack_trees_start(struct merge_options *o,
 	init_tree_desc_from_tree(t+2, merge);
 
 	rc = unpack_trees(3, t, &o->unpack_opts);
-	cache_tree_free(&active_cache_tree);
+	cache_tree_free(&o->repo->index->cache_tree);
 
 	/*
-	 * Update the_index to match the new results, AFTER saving a copy
+	 * Update o->repo->index to match the new results, AFTER saving a copy
 	 * in o->orig_index.  Update src_index to point to the saved copy.
 	 * (verify_uptodate() checks src_index, and the original index is
 	 * the one that had the necessary modification timestamps.)
 	 */
-	o->orig_index = the_index;
-	the_index = tmp_index;
+	o->orig_index = *o->repo->index;
+	*o->repo->index = tmp_index;
 	o->unpack_opts.src_index = &o->orig_index;
 
 	return rc;
@@ -420,12 +425,13 @@ static void unpack_trees_finish(struct merge_options *o)
 struct tree *write_tree_from_memory(struct merge_options *o)
 {
 	struct tree *result = NULL;
+	struct index_state *istate = o->repo->index;
 
-	if (unmerged_cache()) {
+	if (unmerged_index(istate)) {
 		int i;
 		fprintf(stderr, "BUG: There are unmerged index entries:\n");
-		for (i = 0; i < active_nr; i++) {
-			const struct cache_entry *ce = active_cache[i];
+		for (i = 0; i < istate->cache_nr; i++) {
+			const struct cache_entry *ce = istate->cache[i];
 			if (ce_stage(ce))
 				fprintf(stderr, "BUG: %d %.*s\n", ce_stage(ce),
 					(int)ce_namelen(ce), ce->name);
@@ -433,16 +439,16 @@ struct tree *write_tree_from_memory(struct merge_options *o)
 		BUG("unmerged index entries in merge-recursive.c");
 	}
 
-	if (!active_cache_tree)
-		active_cache_tree = cache_tree();
+	if (!istate->cache_tree)
+		istate->cache_tree = cache_tree();
 
-	if (!cache_tree_fully_valid(active_cache_tree) &&
-	    cache_tree_update(&the_index, 0) < 0) {
+	if (!cache_tree_fully_valid(istate->cache_tree) &&
+	    cache_tree_update(istate, 0) < 0) {
 		err(o, _("error building trees"));
 		return NULL;
 	}
 
-	result = lookup_tree(the_repository, &active_cache_tree->oid);
+	result = lookup_tree(o->repo, &istate->cache_tree->oid);
 
 	return result;
 }
@@ -513,17 +519,17 @@ static struct stage_data *insert_stage_data(const char *path,
  * Create a dictionary mapping file names to stage_data objects. The
  * dictionary contains one entry for every path with a non-zero stage entry.
  */
-static struct string_list *get_unmerged(void)
+static struct string_list *get_unmerged(struct index_state *istate)
 {
 	struct string_list *unmerged = xcalloc(1, sizeof(struct string_list));
 	int i;
 
 	unmerged->strdup_strings = 1;
 
-	for (i = 0; i < active_nr; i++) {
+	for (i = 0; i < istate->cache_nr; i++) {
 		struct string_list_item *item;
 		struct stage_data *e;
-		const struct cache_entry *ce = active_cache[i];
+		const struct cache_entry *ce = istate->cache[i];
 		if (!ce_stage(ce))
 			continue;
 
@@ -683,7 +689,7 @@ static int update_stages(struct merge_options *opt, const char *path,
 	int clear = 1;
 	int options = ADD_CACHE_OK_TO_ADD | ADD_CACHE_SKIP_DFCHECK;
 	if (clear)
-		if (remove_file_from_cache(path))
+		if (remove_file_from_index(opt->repo->index, path))
 			return -1;
 	if (o)
 		if (add_cacheinfo(opt, o->mode, &o->oid, path, 1, 0, options))
@@ -718,13 +724,14 @@ static int remove_file(struct merge_options *o, int clean,
 	int update_working_directory = !o->call_depth && !no_wd;
 
 	if (update_cache) {
-		if (remove_file_from_cache(path))
+		if (remove_file_from_index(o->repo->index, path))
 			return -1;
 	}
 	if (update_working_directory) {
 		if (ignore_case) {
 			struct cache_entry *ce;
-			ce = cache_file_exists(path, strlen(path), ignore_case);
+			ce = index_file_exists(o->repo->index, path, strlen(path),
+					       ignore_case);
 			if (ce && ce_stage(ce) == 0 && strcmp(path, ce->name))
 				return 0;
 		}
@@ -774,7 +781,8 @@ static char *unique_path(struct merge_options *o, const char *path, const char *
  * check the working directory.  If empty_ok is non-zero, also return
  * 0 in the case where the working-tree dir exists but is empty.
  */
-static int dir_in_way(const char *path, int check_working_copy, int empty_ok)
+static int dir_in_way(struct index_state *istate, const char *path,
+		      int check_working_copy, int empty_ok)
 {
 	int pos;
 	struct strbuf dirpath = STRBUF_INIT;
@@ -783,12 +791,12 @@ static int dir_in_way(const char *path, int check_working_copy, int empty_ok)
 	strbuf_addstr(&dirpath, path);
 	strbuf_addch(&dirpath, '/');
 
-	pos = cache_name_pos(dirpath.buf, dirpath.len);
+	pos = index_name_pos(istate, dirpath.buf, dirpath.len);
 
 	if (pos < 0)
 		pos = -1 - pos;
-	if (pos < active_nr &&
-	    !strncmp(dirpath.buf, active_cache[pos]->name, dirpath.len)) {
+	if (pos < istate->cache_nr &&
+	    !strncmp(dirpath.buf, istate->cache[pos]->name, dirpath.len)) {
 		strbuf_release(&dirpath);
 		return 1;
 	}
@@ -831,8 +839,10 @@ static int was_tracked(struct merge_options *o, const char *path)
 	return 0;
 }
 
-static int would_lose_untracked(const char *path)
+static int would_lose_untracked(struct merge_options *o, const char *path)
 {
+	struct index_state *istate = o->repo->index;
+
 	/*
 	 * This may look like it can be simplified to:
 	 *   return !was_tracked(o, path) && file_exists(path)
@@ -850,19 +860,19 @@ static int would_lose_untracked(const char *path)
 	 * update_file()/would_lose_untracked(); see every comment in this
 	 * file which mentions "update_stages".
 	 */
-	int pos = cache_name_pos(path, strlen(path));
+	int pos = index_name_pos(istate, path, strlen(path));
 
 	if (pos < 0)
 		pos = -1 - pos;
-	while (pos < active_nr &&
-	       !strcmp(path, active_cache[pos]->name)) {
+	while (pos < istate->cache_nr &&
+	       !strcmp(path, istate->cache[pos]->name)) {
 		/*
 		 * If stage #0, it is definitely tracked.
 		 * If it has stage #2 then it was tracked
 		 * before this merge started.  All other
 		 * cases the path was not tracked.
 		 */
-		switch (ce_stage(active_cache[pos])) {
+		switch (ce_stage(istate->cache[pos])) {
 		case 0:
 		case 2:
 			return 0;
@@ -922,7 +932,7 @@ static int make_room_for_path(struct merge_options *o, const char *path)
 	 * Do not unlink a file in the work tree if we are not
 	 * tracking it.
 	 */
-	if (would_lose_untracked(path))
+	if (would_lose_untracked(o, path))
 		return err(o, _("refusing to lose untracked file at '%s'"),
 			   path);
 
@@ -972,7 +982,7 @@ static int update_file_flags(struct merge_options *o,
 		}
 		if (S_ISREG(mode)) {
 			struct strbuf strbuf = STRBUF_INIT;
-			if (convert_to_working_tree(&the_index, path, buf, size, &strbuf)) {
+			if (convert_to_working_tree(o->repo->index, path, buf, size, &strbuf)) {
 				free(buf);
 				size = strbuf.len;
 				buf = strbuf_detach(&strbuf, NULL);
@@ -1092,7 +1102,7 @@ static int merge_3way(struct merge_options *o,
 
 	merge_status = ll_merge(result_buf, a->path, &orig, base_name,
 				&src1, name1, &src2, name2,
-				&the_index, &ll_opts);
+				o->repo->index, &ll_opts);
 
 	free(base_name);
 	free(name1);
@@ -1103,7 +1113,8 @@ static int merge_3way(struct merge_options *o,
 	return merge_status;
 }
 
-static int find_first_merges(struct object_array *result, const char *path,
+static int find_first_merges(struct repository *repo,
+			     struct object_array *result, const char *path,
 			     struct commit *a, struct commit *b)
 {
 	int i, j;
@@ -1123,7 +1134,7 @@ static int find_first_merges(struct object_array *result, const char *path,
 	/* get all revisions that merge commit a */
 	xsnprintf(merged_revision, sizeof(merged_revision), "^%s",
 		  oid_to_hex(&a->object.oid));
-	repo_init_revisions(the_repository, &revs, NULL);
+	repo_init_revisions(repo, &revs, NULL);
 	rev_opts.submodule = path;
 	/* FIXME: can't handle linked worktrees in submodules yet */
 	revs.single_worktree = path != NULL;
@@ -1201,9 +1212,9 @@ static int merge_submodule(struct merge_options *o,
 		return 0;
 	}
 
-	if (!(commit_base = lookup_commit_reference(the_repository, base)) ||
-	    !(commit_a = lookup_commit_reference(the_repository, a)) ||
-	    !(commit_b = lookup_commit_reference(the_repository, b))) {
+	if (!(commit_base = lookup_commit_reference(o->repo, base)) ||
+	    !(commit_a = lookup_commit_reference(o->repo, a)) ||
+	    !(commit_b = lookup_commit_reference(o->repo, b))) {
 		output(o, 1, _("Failed to merge submodule %s (commits not present)"), path);
 		return 0;
 	}
@@ -1253,7 +1264,8 @@ static int merge_submodule(struct merge_options *o,
 		return 0;
 
 	/* find commit which merges them */
-	parent_count = find_first_merges(&merges, path, commit_a, commit_b);
+	parent_count = find_first_merges(o->repo, &merges, path,
+					 commit_a, commit_b);
 	switch (parent_count) {
 	case 0:
 		output(o, 1, _("Failed to merge submodule %s (merge following commits not found)"), path);
@@ -1401,7 +1413,7 @@ static int handle_rename_via_dir(struct merge_options *o,
 	 */
 	const struct diff_filespec *dest = pair->two;
 
-	if (!o->call_depth && would_lose_untracked(dest->path)) {
+	if (!o->call_depth && would_lose_untracked(o, dest->path)) {
 		char *alt_path = unique_path(o, dest->path, rename_branch);
 
 		output(o, 1, _("Error: Refusing to lose untracked file at %s; "
@@ -1439,8 +1451,8 @@ static int handle_change_delete(struct merge_options *o,
 	const char *update_path = path;
 	int ret = 0;
 
-	if (dir_in_way(path, !o->call_depth, 0) ||
-	    (!o->call_depth && would_lose_untracked(path))) {
+	if (dir_in_way(o->repo->index, path, !o->call_depth, 0) ||
+	    (!o->call_depth && would_lose_untracked(o, path))) {
 		update_path = alt_path = unique_path(o, path, change_branch);
 	}
 
@@ -1450,7 +1462,7 @@ static int handle_change_delete(struct merge_options *o,
 		 * correct; since there is no true "middle point" between
 		 * them, simply reuse the base version for virtual merge base.
 		 */
-		ret = remove_file_from_cache(path);
+		ret = remove_file_from_index(o->repo->index, path);
 		if (!ret)
 			ret = update_file(o, 0, o_oid, o_mode, update_path);
 	} else {
@@ -1526,7 +1538,7 @@ static int handle_rename_delete(struct merge_options *o,
 		return -1;
 
 	if (o->call_depth)
-		return remove_file_from_cache(dest->path);
+		return remove_file_from_index(o->repo->index, dest->path);
 	else
 		return update_stages(o, dest->path, NULL,
 				     rename_branch == o->branch1 ? dest : NULL,
@@ -1607,10 +1619,10 @@ static int handle_file_collision(struct merge_options *o,
 	/* Remove rename sources if rename/add or rename/rename(2to1) */
 	if (prev_path1)
 		remove_file(o, 1, prev_path1,
-			    o->call_depth || would_lose_untracked(prev_path1));
+			    o->call_depth || would_lose_untracked(o, prev_path1));
 	if (prev_path2)
 		remove_file(o, 1, prev_path2,
-			    o->call_depth || would_lose_untracked(prev_path2));
+			    o->call_depth || would_lose_untracked(o, prev_path2));
 
 	/*
 	 * Remove the collision path, if it wouldn't cause dirty contents
@@ -1621,7 +1633,7 @@ static int handle_file_collision(struct merge_options *o,
 		output(o, 1, _("Refusing to lose dirty file at %s"),
 		       collide_path);
 		update_path = alt_path = unique_path(o, collide_path, "merged");
-	} else if (would_lose_untracked(collide_path)) {
+	} else if (would_lose_untracked(o, collide_path)) {
 		/*
 		 * Only way we get here is if both renames were from
 		 * a directory rename AND user had an untracked file
@@ -1717,12 +1729,12 @@ static char *find_path_for_conflict(struct merge_options *o,
 				    const char *branch2)
 {
 	char *new_path = NULL;
-	if (dir_in_way(path, !o->call_depth, 0)) {
+	if (dir_in_way(o->repo->index, path, !o->call_depth, 0)) {
 		new_path = unique_path(o, path, branch1);
 		output(o, 1, _("%s is a directory in %s adding "
 			       "as %s instead"),
 		       path, branch2, new_path);
-	} else if (would_lose_untracked(path)) {
+	} else if (would_lose_untracked(o, path)) {
 		new_path = unique_path(o, path, branch1);
 		output(o, 1, _("Refusing to lose untracked file"
 			       " at %s; adding as %s instead"),
@@ -1783,14 +1795,14 @@ static int handle_rename_rename_1to2(struct merge_options *o,
 				return -1;
 		}
 		else
-			remove_file_from_cache(a->path);
+			remove_file_from_index(o->repo->index, a->path);
 		add = filespec_from_entry(&other, ci->dst_entry2, 3 ^ 1);
 		if (add) {
 			if (update_file(o, 0, &add->oid, add->mode, b->path))
 				return -1;
 		}
 		else
-			remove_file_from_cache(b->path);
+			remove_file_from_index(o->repo->index, b->path);
 	} else {
 		/*
 		 * For each destination path, we need to see if there is a
@@ -1887,7 +1899,7 @@ static struct diff_queue_struct *get_diffpairs(struct merge_options *o,
 	struct diff_queue_struct *ret;
 	struct diff_options opts;
 
-	repo_diff_setup(the_repository, &opts);
+	repo_diff_setup(o->repo, &opts);
 	opts.flags.recursive = 1;
 	opts.flags.rename_empty = 0;
 	opts.detect_rename = merge_detect_rename(o);
@@ -3042,8 +3054,8 @@ static int blob_unchanged(struct merge_options *opt,
 	 * performed.  Comparison can be skipped if both files are
 	 * unchanged since their sha1s have already been compared.
 	 */
-	if (renormalize_buffer(&the_index, path, o.buf, o.len, &o) |
-	    renormalize_buffer(&the_index, path, a.buf, a.len, &a))
+	if (renormalize_buffer(opt->repo->index, path, o.buf, o.len, &o) |
+	    renormalize_buffer(opt->repo->index, path, a.buf, a.len, &a))
 		ret = (o.len == a.len && !memcmp(o.buf, a.buf, o.len));
 
 error_return:
@@ -3124,7 +3136,7 @@ static int handle_content_merge(struct merge_options *o,
 		a.path = (char *)path1;
 		b.path = (char *)path2;
 
-		if (dir_in_way(path, !o->call_depth,
+		if (dir_in_way(o->repo->index, path, !o->call_depth,
 			       S_ISGITLINK(pair1->two->mode)))
 			df_conflict_remains = 1;
 	}
@@ -3158,8 +3170,8 @@ static int handle_content_merge(struct merge_options *o,
 		pos = index_name_pos(&o->orig_index, path, strlen(path));
 		ce = o->orig_index.cache[pos];
 		if (ce_skip_worktree(ce)) {
-			pos = index_name_pos(&the_index, path, strlen(path));
-			ce = the_index.cache[pos];
+			pos = index_name_pos(o->repo->index, path, strlen(path));
+			ce = o->repo->index->cache[pos];
 			ce->ce_flags |= CE_SKIP_WORKTREE;
 		}
 		return mfi.clean;
@@ -3178,7 +3190,7 @@ static int handle_content_merge(struct merge_options *o,
 	if (df_conflict_remains || is_dirty) {
 		char *new_path;
 		if (o->call_depth) {
-			remove_file_from_cache(path);
+			remove_file_from_index(o->repo->index, path);
 		} else {
 			if (!mfi.clean) {
 				if (update_stages(o, path, &one, &a, &b))
@@ -3338,7 +3350,7 @@ static int process_entry(struct merge_options *o,
 			oid = b_oid;
 			conf = _("directory/file");
 		}
-		if (dir_in_way(path,
+		if (dir_in_way(o->repo->index, path,
 			       !o->call_depth && !S_ISGITLINK(a_mode),
 			       0)) {
 			char *new_path = unique_path(o, path, add_branch);
@@ -3349,7 +3361,7 @@ static int process_entry(struct merge_options *o,
 			if (update_file(o, 0, oid, mode, new_path))
 				clean_merge = -1;
 			else if (o->call_depth)
-				remove_file_from_cache(path);
+				remove_file_from_index(o->repo->index, path);
 			free(new_path);
 		} else {
 			output(o, 2, _("Adding %s"), path);
@@ -3397,18 +3409,19 @@ int merge_trees(struct merge_options *o,
 		struct tree *common,
 		struct tree **result)
 {
+	struct index_state *istate = o->repo->index;
 	int code, clean;
 	struct strbuf sb = STRBUF_INIT;
 
-	if (!o->call_depth && index_has_changes(&the_index, head, &sb)) {
+	if (!o->call_depth && repo_index_has_changes(o->repo, head, &sb)) {
 		err(o, _("Your local changes to the following files would be overwritten by merge:\n  %s"),
 		    sb.buf);
 		return -1;
 	}
 
 	if (o->subtree_shift) {
-		merge = shift_tree_object(head, merge, o->subtree_shift);
-		common = shift_tree_object(head, common, o->subtree_shift);
+		merge = shift_tree_object(o->repo, head, merge, o->subtree_shift);
+		common = shift_tree_object(o->repo, head, common, o->subtree_shift);
 	}
 
 	if (oid_eq(&common->object.oid, &merge->object.oid)) {
@@ -3428,7 +3441,7 @@ int merge_trees(struct merge_options *o,
 		return -1;
 	}
 
-	if (unmerged_cache()) {
+	if (unmerged_index(istate)) {
 		struct string_list *entries;
 		struct rename_info re_info;
 		int i;
@@ -3443,7 +3456,7 @@ int merge_trees(struct merge_options *o,
 		get_files_dirs(o, head);
 		get_files_dirs(o, merge);
 
-		entries = get_unmerged();
+		entries = get_unmerged(o->repo->index);
 		clean = detect_and_process_renames(o, common, head, merge,
 						   entries, &re_info);
 		record_df_conflict_files(o, entries);
@@ -3544,8 +3557,8 @@ int merge_recursive(struct merge_options *o,
 		/* if there is no common ancestor, use an empty tree */
 		struct tree *tree;
 
-		tree = lookup_tree(the_repository, the_repository->hash_algo->empty_tree);
-		merged_common_ancestors = make_virtual_commit(tree, "ancestor");
+		tree = lookup_tree(o->repo, o->repo->hash_algo->empty_tree);
+		merged_common_ancestors = make_virtual_commit(o->repo, tree, "ancestor");
 	}
 
 	for (iter = ca; iter; iter = iter->next) {
@@ -3559,7 +3572,7 @@ int merge_recursive(struct merge_options *o,
 		 * overwritten it: the committed "conflicts" were
 		 * already resolved.
 		 */
-		discard_cache();
+		discard_index(o->repo->index);
 		saved_b1 = o->branch1;
 		saved_b2 = o->branch2;
 		o->branch1 = "Temporary merge branch 1";
@@ -3575,9 +3588,9 @@ int merge_recursive(struct merge_options *o,
 			return err(o, _("merge returned no commit"));
 	}
 
-	discard_cache();
+	discard_index(o->repo->index);
 	if (!o->call_depth)
-		read_cache();
+		repo_read_index(o->repo);
 
 	o->ancestor = "merged common ancestors";
 	clean = merge_trees(o, get_commit_tree(h1), get_commit_tree(h2),
@@ -3589,7 +3602,7 @@ int merge_recursive(struct merge_options *o,
 	}
 
 	if (o->call_depth) {
-		*result = make_virtual_commit(mrtree, "merged tree");
+		*result = make_virtual_commit(o->repo, mrtree, "merged tree");
 		commit_list_insert(h1, &(*result)->parents);
 		commit_list_insert(h2, &(*result)->parents->next);
 	}
@@ -3602,17 +3615,17 @@ int merge_recursive(struct merge_options *o,
 	return clean;
 }
 
-static struct commit *get_ref(const struct object_id *oid, const char *name)
+static struct commit *get_ref(struct repository *repo, const struct object_id *oid,
+			      const char *name)
 {
 	struct object *object;
 
-	object = deref_tag(the_repository, parse_object(the_repository, oid),
-			   name,
-			   strlen(name));
+	object = deref_tag(repo, parse_object(repo, oid),
+			   name, strlen(name));
 	if (!object)
 		return NULL;
 	if (object->type == OBJ_TREE)
-		return make_virtual_commit((struct tree*)object, name);
+		return make_virtual_commit(repo, (struct tree*)object, name);
 	if (object->type != OBJ_COMMIT)
 		return NULL;
 	if (parse_commit((struct commit *)object))
@@ -3629,22 +3642,22 @@ int merge_recursive_generic(struct merge_options *o,
 {
 	int clean;
 	struct lock_file lock = LOCK_INIT;
-	struct commit *head_commit = get_ref(head, o->branch1);
-	struct commit *next_commit = get_ref(merge, o->branch2);
+	struct commit *head_commit = get_ref(o->repo, head, o->branch1);
+	struct commit *next_commit = get_ref(o->repo, merge, o->branch2);
 	struct commit_list *ca = NULL;
 
 	if (base_list) {
 		int i;
 		for (i = 0; i < num_base_list; ++i) {
 			struct commit *base;
-			if (!(base = get_ref(base_list[i], oid_to_hex(base_list[i]))))
+			if (!(base = get_ref(o->repo, base_list[i], oid_to_hex(base_list[i]))))
 				return err(o, _("Could not parse object '%s'"),
 					   oid_to_hex(base_list[i]));
 			commit_list_insert(base, &ca);
 		}
 	}
 
-	hold_locked_index(&lock, LOCK_DIE_ON_ERROR);
+	repo_hold_locked_index(o->repo, &lock, LOCK_DIE_ON_ERROR);
 	clean = merge_recursive(o, head_commit, next_commit, ca,
 				result);
 	if (clean < 0) {
@@ -3652,7 +3665,7 @@ int merge_recursive_generic(struct merge_options *o,
 		return clean;
 	}
 
-	if (write_locked_index(&the_index, &lock,
+	if (write_locked_index(o->repo->index, &lock,
 			       COMMIT_LOCK | SKIP_IF_UNCHANGED))
 		return err(o, _("Unable to write index."));
 
@@ -3676,10 +3689,12 @@ static void merge_recursive_config(struct merge_options *o)
 	git_config(git_xmerge_config, NULL);
 }
 
-void init_merge_options(struct merge_options *o)
+void init_merge_options(struct merge_options *o,
+			struct repository *repo)
 {
 	const char *merge_verbosity;
 	memset(o, 0, sizeof(struct merge_options));
+	o->repo = repo;
 	o->verbosity = 2;
 	o->buffer_output = 1;
 	o->diff_rename_limit = -1;
diff --git a/merge-recursive.h b/merge-recursive.h
index e6a0828..c2b7bb6 100644
--- a/merge-recursive.h
+++ b/merge-recursive.h
@@ -6,6 +6,8 @@
 
 struct commit;
 
+struct repository;
+
 struct merge_options {
 	const char *ancestor;
 	const char *branch1;
@@ -34,6 +36,7 @@ struct merge_options {
 	struct string_list df_conflict_file_set;
 	struct unpack_trees_options unpack_opts;
 	struct index_state orig_index;
+	struct repository *repo;
 };
 
 /*
@@ -92,7 +95,8 @@ int merge_recursive_generic(struct merge_options *o,
 			    const struct object_id **ca,
 			    struct commit **result);
 
-void init_merge_options(struct merge_options *o);
+void init_merge_options(struct merge_options *o,
+			struct repository *repo);
 struct tree *write_tree_from_memory(struct merge_options *o);
 
 int parse_merge_opt(struct merge_options *out, const char *s);
diff --git a/merge.c b/merge.c
index 91008f7..7c1d756 100644
--- a/merge.c
+++ b/merge.c
@@ -37,7 +37,7 @@ int try_merge_command(struct repository *r,
 	argv_array_clear(&args);
 
 	discard_index(r->index);
-	if (read_index(r->index) < 0)
+	if (repo_read_index(r) < 0)
 		die(_("failed to read the cache"));
 	resolve_undo_clear_index(r->index);
 
@@ -58,7 +58,7 @@ int checkout_fast_forward(struct repository *r,
 
 	refresh_index(r->index, REFRESH_QUIET, NULL, NULL, NULL);
 
-	if (hold_locked_index(&lock_file, LOCK_REPORT_ON_ERROR) < 0)
+	if (repo_hold_locked_index(r, &lock_file, LOCK_REPORT_ON_ERROR) < 0)
 		return -1;
 
 	memset(&trees, 0, sizeof(trees));
diff --git a/name-hash.c b/name-hash.c
index 623ca69..b4861bc 100644
--- a/name-hash.c
+++ b/name-hash.c
@@ -5,7 +5,6 @@
  *
  * Copyright (C) 2008 Linus Torvalds
  */
-#define NO_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "thread-utils.h"
 
diff --git a/notes-merge.c b/notes-merge.c
index 72688d3..280aa8e 100644
--- a/notes-merge.c
+++ b/notes-merge.c
@@ -649,7 +649,7 @@ int notes_merge(struct notes_merge_options *o,
 		struct commit_list *parents = NULL;
 		commit_list_insert(remote, &parents); /* LIFO order */
 		commit_list_insert(local, &parents);
-		create_notes_commit(local_tree, parents, o->commit_msg.buf,
+		create_notes_commit(o->repo, local_tree, parents, o->commit_msg.buf,
 				    o->commit_msg.len, result_oid);
 	}
 
@@ -724,7 +724,7 @@ int notes_merge_commit(struct notes_merge_options *o,
 		strbuf_setlen(&path, baselen);
 	}
 
-	create_notes_commit(partial_tree, partial_commit->parents, msg,
+	create_notes_commit(o->repo, partial_tree, partial_commit->parents, msg,
 			    strlen(msg), result_oid);
 	unuse_commit_buffer(partial_commit, buffer);
 	if (o->verbosity >= 4)
diff --git a/notes-utils.c b/notes-utils.c
index 14ea031..a819410 100644
--- a/notes-utils.c
+++ b/notes-utils.c
@@ -5,7 +5,9 @@
 #include "notes-utils.h"
 #include "repository.h"
 
-void create_notes_commit(struct notes_tree *t, struct commit_list *parents,
+void create_notes_commit(struct repository *r,
+			 struct notes_tree *t,
+			 struct commit_list *parents,
 			 const char *msg, size_t msg_len,
 			 struct object_id *result_oid)
 {
@@ -20,8 +22,7 @@ void create_notes_commit(struct notes_tree *t, struct commit_list *parents,
 		/* Deduce parent commit from t->ref */
 		struct object_id parent_oid;
 		if (!read_ref(t->ref, &parent_oid)) {
-			struct commit *parent = lookup_commit(the_repository,
-							      &parent_oid);
+			struct commit *parent = lookup_commit(r, &parent_oid);
 			if (parse_commit(parent))
 				die("Failed to find/parse commit %s", t->ref);
 			commit_list_insert(parent, &parents);
@@ -34,7 +35,7 @@ void create_notes_commit(struct notes_tree *t, struct commit_list *parents,
 		die("Failed to commit notes tree to database");
 }
 
-void commit_notes(struct notes_tree *t, const char *msg)
+void commit_notes(struct repository *r, struct notes_tree *t, const char *msg)
 {
 	struct strbuf buf = STRBUF_INIT;
 	struct object_id commit_oid;
@@ -50,7 +51,7 @@ void commit_notes(struct notes_tree *t, const char *msg)
 	strbuf_addstr(&buf, msg);
 	strbuf_complete_line(&buf);
 
-	create_notes_commit(t, NULL, buf.buf, buf.len, &commit_oid);
+	create_notes_commit(r, t, NULL, buf.buf, buf.len, &commit_oid);
 	strbuf_insert(&buf, 0, "notes: ", 7); /* commit message starts at index 7 */
 	update_ref(buf.buf, t->update_ref, &commit_oid, NULL, 0,
 		   UPDATE_REFS_DIE_ON_ERR);
@@ -171,11 +172,13 @@ int copy_note_for_rewrite(struct notes_rewrite_cfg *c,
 	return ret;
 }
 
-void finish_copy_notes_for_rewrite(struct notes_rewrite_cfg *c, const char *msg)
+void finish_copy_notes_for_rewrite(struct repository *r,
+				   struct notes_rewrite_cfg *c,
+				   const char *msg)
 {
 	int i;
 	for (i = 0; c->trees[i]; i++) {
-		commit_notes(c->trees[i], msg);
+		commit_notes(r, c->trees[i], msg);
 		free_notes(c->trees[i]);
 	}
 	free(c->trees);
diff --git a/notes-utils.h b/notes-utils.h
index 5408306..d9b3c09 100644
--- a/notes-utils.h
+++ b/notes-utils.h
@@ -5,6 +5,7 @@
 
 struct commit_list;
 struct object_id;
+struct repository;
 
 /*
  * Create new notes commit from the given notes tree
@@ -17,11 +18,13 @@ struct object_id;
  *
  * The resulting commit SHA1 is stored in result_sha1.
  */
-void create_notes_commit(struct notes_tree *t, struct commit_list *parents,
+void create_notes_commit(struct repository *r,
+			 struct notes_tree *t,
+			 struct commit_list *parents,
 			 const char *msg, size_t msg_len,
 			 struct object_id *result_oid);
 
-void commit_notes(struct notes_tree *t, const char *msg);
+void commit_notes(struct repository *r, struct notes_tree *t, const char *msg);
 
 enum notes_merge_strategy {
 		NOTES_MERGE_RESOLVE_MANUAL = 0,
@@ -45,6 +48,8 @@ int parse_notes_merge_strategy(const char *v, enum notes_merge_strategy *s);
 struct notes_rewrite_cfg *init_copy_notes_for_rewrite(const char *cmd);
 int copy_note_for_rewrite(struct notes_rewrite_cfg *c,
 			  const struct object_id *from_obj, const struct object_id *to_obj);
-void finish_copy_notes_for_rewrite(struct notes_rewrite_cfg *c, const char *msg);
+void finish_copy_notes_for_rewrite(struct repository *r,
+				   struct notes_rewrite_cfg *c,
+				   const char *msg);
 
 #endif
diff --git a/pathspec.c b/pathspec.c
index e85298f..12c2b32 100644
--- a/pathspec.c
+++ b/pathspec.c
@@ -1,4 +1,3 @@
-#define NO_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "dir.h"
diff --git a/preload-index.c b/preload-index.c
index c7dc3f2..e73600e 100644
--- a/preload-index.c
+++ b/preload-index.c
@@ -8,6 +8,7 @@
 #include "config.h"
 #include "progress.h"
 #include "thread-utils.h"
+#include "repository.h"
 
 /*
  * Mostly randomly chosen maximum thread counts: we
@@ -146,12 +147,12 @@ void preload_index(struct index_state *index,
 	trace_performance_leave("preload index");
 }
 
-int read_index_preload(struct index_state *index,
-		       const struct pathspec *pathspec,
-		       unsigned int refresh_flags)
+int repo_read_index_preload(struct repository *repo,
+			    const struct pathspec *pathspec,
+			    unsigned int refresh_flags)
 {
-	int retval = read_index(index);
+	int retval = repo_read_index(repo);
 
-	preload_index(index, pathspec, refresh_flags);
+	preload_index(repo->index, pathspec, refresh_flags);
 	return retval;
 }
diff --git a/read-cache.c b/read-cache.c
index 9783c49..a66c87b 100644
--- a/read-cache.c
+++ b/read-cache.c
@@ -3,7 +3,6 @@
  *
  * Copyright (C) Linus Torvalds, 2005
  */
-#define NO_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "config.h"
 #include "diff.h"
@@ -95,7 +94,6 @@ static struct mem_pool *find_mem_pool(struct index_state *istate)
 	return *pool_ptr;
 }
 
-struct index_state the_index;
 static const char *alternate_index_output;
 
 static void set_index_entry(struct index_state *istate, int nr, struct cache_entry *ce)
@@ -1733,16 +1731,6 @@ static int read_index_extension(struct index_state *istate,
 	return 0;
 }
 
-int hold_locked_index(struct lock_file *lk, int lock_flags)
-{
-	return hold_lock_file_for_update(lk, get_index_file(), lock_flags);
-}
-
-int read_index(struct index_state *istate)
-{
-	return read_index_from(istate, get_index_file(), get_git_dir());
-}
-
 static struct cache_entry *create_from_disk(struct mem_pool *ce_mem_pool,
 					    unsigned int version,
 					    struct ondisk_cache_entry *ondisk,
@@ -2375,22 +2363,20 @@ int unmerged_index(const struct index_state *istate)
 	return 0;
 }
 
-int index_has_changes(struct index_state *istate,
-		      struct tree *tree,
-		      struct strbuf *sb)
+int repo_index_has_changes(struct repository *repo,
+			   struct tree *tree,
+			   struct strbuf *sb)
 {
+	struct index_state *istate = repo->index;
 	struct object_id cmp;
 	int i;
 
-	if (istate != &the_index) {
-		BUG("index_has_changes cannot yet accept istate != &the_index; do_diff_cache needs updating first.");
-	}
 	if (tree)
 		cmp = tree->object.oid;
 	if (tree || !get_oid_tree("HEAD", &cmp)) {
 		struct diff_options opt;
 
-		repo_diff_setup(the_repository, &opt);
+		repo_diff_setup(repo, &opt);
 		opt.flags.exit_with_status = 1;
 		if (!sb)
 			opt.flags.quick = 1;
@@ -2664,9 +2650,9 @@ out:
 	return 0;
 }
 
-static int verify_index(const struct index_state *istate)
+static int repo_verify_index(struct repository *repo)
 {
-	return verify_index_from(istate, get_index_file());
+	return verify_index_from(repo->index, repo->index_file);
 }
 
 static int has_racy_timestamp(struct index_state *istate)
@@ -2682,11 +2668,13 @@ static int has_racy_timestamp(struct index_state *istate)
 	return 0;
 }
 
-void update_index_if_able(struct index_state *istate, struct lock_file *lockfile)
+void repo_update_index_if_able(struct repository *repo,
+			       struct lock_file *lockfile)
 {
-	if ((istate->cache_changed || has_racy_timestamp(istate)) &&
-	    verify_index(istate))
-		write_locked_index(istate, lockfile, COMMIT_LOCK);
+	if ((repo->index->cache_changed ||
+	     has_racy_timestamp(repo->index)) &&
+	    repo_verify_index(repo))
+		write_locked_index(repo->index, lockfile, COMMIT_LOCK);
 	else
 		rollback_lock_file(lockfile);
 }
@@ -3223,12 +3211,14 @@ out:
  * state can call this and check its return value, instead of calling
  * read_cache().
  */
-int read_index_unmerged(struct index_state *istate)
+int repo_read_index_unmerged(struct repository *repo)
 {
+	struct index_state *istate;
 	int i;
 	int unmerged = 0;
 
-	read_index(istate);
+	repo_read_index(repo);
+	istate = repo->index;
 	for (i = 0; i < istate->cache_nr; i++) {
 		struct cache_entry *ce = istate->cache[i];
 		struct cache_entry *new_ce;
diff --git a/repository.c b/repository.c
index 20c509a..65e6f8b 100644
--- a/repository.c
+++ b/repository.c
@@ -1,13 +1,20 @@
+/*
+ * not really _using_ the compat macros, just make sure the_index
+ * declaration matches the definition in this file.
+ */
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "repository.h"
 #include "object-store.h"
 #include "config.h"
 #include "object.h"
+#include "lockfile.h"
 #include "submodule-config.h"
 
 /* The main repository */
 static struct repository the_repo;
 struct repository *the_repository;
+struct index_state the_index;
 
 void initialize_the_repository(void)
 {
@@ -256,3 +263,12 @@ int repo_read_index(struct repository *repo)
 
 	return read_index_from(repo->index, repo->index_file, repo->gitdir);
 }
+
+int repo_hold_locked_index(struct repository *repo,
+			   struct lock_file *lf,
+			   int flags)
+{
+	if (!repo->index_file)
+		BUG("the repo hasn't been setup");
+	return hold_lock_file_for_update(lf, repo->index_file, flags);
+}
diff --git a/repository.h b/repository.h
index 0e482b7..8981649 100644
--- a/repository.h
+++ b/repository.h
@@ -6,6 +6,8 @@
 struct config_set;
 struct git_hash_algo;
 struct index_state;
+struct lock_file;
+struct pathspec;
 struct raw_object_store;
 struct submodule_cache;
 
@@ -138,5 +140,19 @@ void repo_clear(struct repository *repo);
  * populated then the number of entries will simply be returned.
  */
 int repo_read_index(struct repository *repo);
+int repo_hold_locked_index(struct repository *repo,
+			   struct lock_file *lf,
+			   int flags);
+
+int repo_read_index_preload(struct repository *,
+			    const struct pathspec *pathspec,
+			    unsigned refresh_flags);
+int repo_read_index_unmerged(struct repository *);
+/*
+ * Opportunistically update the index but do not complain if we can't.
+ * The lockfile is always committed or rolled back.
+ */
+void repo_update_index_if_able(struct repository *, struct lock_file *);
+
 
 #endif /* REPOSITORY_H */
diff --git a/rerere.c b/rerere.c
index 1362403..17abb47 100644
--- a/rerere.c
+++ b/rerere.c
@@ -561,7 +561,7 @@ static int find_conflict(struct repository *r, struct string_list *conflict)
 {
 	int i;
 
-	if (read_index(r->index) < 0)
+	if (repo_read_index(r) < 0)
 		return error(_("index file corrupt"));
 
 	for (i = 0; i < r->index->cache_nr;) {
@@ -595,7 +595,7 @@ int rerere_remaining(struct repository *r, struct string_list *merge_rr)
 
 	if (setup_rerere(r, merge_rr, RERERE_READONLY))
 		return 0;
-	if (read_index(r->index) < 0)
+	if (repo_read_index(r) < 0)
 		return error(_("index file corrupt"));
 
 	for (i = 0; i < r->index->cache_nr;) {
@@ -705,7 +705,7 @@ static void update_paths(struct repository *r, struct string_list *update)
 	struct lock_file index_lock = LOCK_INIT;
 	int i;
 
-	hold_locked_index(&index_lock, LOCK_DIE_ON_ERROR);
+	repo_hold_locked_index(r, &index_lock, LOCK_DIE_ON_ERROR);
 
 	for (i = 0; i < update->nr; i++) {
 		struct string_list_item *item = &update->items[i];
@@ -1107,7 +1107,7 @@ int rerere_forget(struct repository *r, struct pathspec *pathspec)
 	struct string_list conflict = STRING_LIST_INIT_DUP;
 	struct string_list merge_rr = STRING_LIST_INIT_DUP;
 
-	if (read_index(r->index) < 0)
+	if (repo_read_index(r) < 0)
 		return error(_("index file corrupt"));
 
 	fd = setup_rerere(r, &merge_rr, RERERE_NOAUTOUPDATE);
diff --git a/revision.c b/revision.c
index 8f886fe..5c7d3c7 100644
--- a/revision.c
+++ b/revision.c
@@ -1397,7 +1397,7 @@ void add_index_objects_to_pending(struct rev_info *revs, unsigned int flags)
 {
 	struct worktree **worktrees, **p;
 
-	read_index(revs->repo->index);
+	repo_read_index(revs->repo);
 	do_add_index_objects_to_pending(revs, revs->repo->index, flags);
 
 	if (revs->single_worktree)
@@ -1544,7 +1544,7 @@ static void prepare_show_merge(struct rev_info *revs)
 	head->object.flags |= SYMMETRIC_LEFT;
 
 	if (!istate->cache_nr)
-		read_index(istate);
+		repo_read_index(revs->repo);
 	for (i = 0; i < istate->cache_nr; i++) {
 		const struct cache_entry *ce = istate->cache[i];
 		if (!ce_stage(ce))
@@ -1603,8 +1603,8 @@ static int handle_dotdot_1(const char *arg, char *dotdot,
 	if (!*b_name)
 		b_name = "HEAD";
 
-	if (get_oid_with_context(a_name, oc_flags, &a_oid, a_oc) ||
-	    get_oid_with_context(b_name, oc_flags, &b_oid, b_oc))
+	if (get_oid_with_context(revs->repo, a_name, oc_flags, &a_oid, a_oc) ||
+	    get_oid_with_context(revs->repo, b_name, oc_flags, &b_oid, b_oc))
 		return -1;
 
 	if (!cant_be_filename) {
@@ -1738,7 +1738,7 @@ int handle_revision_arg(const char *arg_, struct rev_info *revs, int flags, unsi
 	if (revarg_opt & REVARG_COMMITTISH)
 		get_sha1_flags |= GET_OID_COMMITTISH;
 
-	if (get_oid_with_context(arg, get_sha1_flags, &oid, &oc))
+	if (get_oid_with_context(revs->repo, arg, get_sha1_flags, &oid, &oc))
 		return revs->ignore_missing ? 0 : -1;
 	if (!cant_be_filename)
 		verify_non_filename(revs->prefix, arg);
@@ -2471,7 +2471,7 @@ int setup_revisions(int argc, const char **argv, struct rev_info *revs, struct s
 		struct object_id oid;
 		struct object *object;
 		struct object_context oc;
-		if (get_oid_with_context(revs->def, 0, &oid, &oc))
+		if (get_oid_with_context(revs->repo, revs->def, 0, &oid, &oc))
 			diagnose_missing_default(revs->def);
 		object = get_reference(revs, revs->def, &oid, 0);
 		add_pending_object_with_mode(revs, object, revs->def, oc.mode);
diff --git a/sequencer.c b/sequencer.c
index a6333ab..972402e 100644
--- a/sequencer.c
+++ b/sequencer.c
@@ -447,9 +447,9 @@ static struct tree *empty_tree(struct repository *r)
 	return lookup_tree(r, the_hash_algo->empty_tree);
 }
 
-static int error_dirty_index(struct index_state *istate, struct replay_opts *opts)
+static int error_dirty_index(struct repository *repo, struct replay_opts *opts)
 {
-	if (read_index_unmerged(istate))
+	if (repo_read_index_unmerged(repo))
 		return error_resolve_conflict(_(action_name(opts)));
 
 	error(_("your local changes would be overwritten by %s."),
@@ -484,7 +484,7 @@ static int fast_forward_to(struct repository *r,
 	struct strbuf sb = STRBUF_INIT;
 	struct strbuf err = STRBUF_INIT;
 
-	read_index(r->index);
+	repo_read_index(r);
 	if (checkout_fast_forward(r, from, to, 1))
 		return -1; /* the callee should have complained already */
 
@@ -541,12 +541,12 @@ static int do_recursive_merge(struct repository *r,
 	char **xopt;
 	struct lock_file index_lock = LOCK_INIT;
 
-	if (hold_locked_index(&index_lock, LOCK_REPORT_ON_ERROR) < 0)
+	if (repo_hold_locked_index(r, &index_lock, LOCK_REPORT_ON_ERROR) < 0)
 		return -1;
 
-	read_index(r->index);
+	repo_read_index(r);
 
-	init_merge_options(&o);
+	init_merge_options(&o, r);
 	o.ancestor = base ? base_label : "(empty tree)";
 	o.branch1 = "HEAD";
 	o.branch2 = next ? next_label : "(empty tree)";
@@ -1116,7 +1116,8 @@ static int run_rewrite_hook(const struct object_id *oldoid,
 	return finish_command(&proc);
 }
 
-void commit_post_rewrite(const struct commit *old_head,
+void commit_post_rewrite(struct repository *r,
+			 const struct commit *old_head,
 			 const struct object_id *new_head)
 {
 	struct notes_rewrite_cfg *cfg;
@@ -1125,7 +1126,7 @@ void commit_post_rewrite(const struct commit *old_head,
 	if (cfg) {
 		/* we are amending, so old_head is not NULL */
 		copy_note_for_rewrite(cfg, &old_head->object.oid, new_head);
-		finish_copy_notes_for_rewrite(cfg, "Notes added by 'git commit --amend'");
+		finish_copy_notes_for_rewrite(r, cfg, "Notes added by 'git commit --amend'");
 	}
 	run_rewrite_hook(&old_head->object.oid, new_head);
 }
@@ -1406,7 +1407,7 @@ static int try_to_commit(struct repository *r,
 	}
 
 	if (flags & AMEND_MSG)
-		commit_post_rewrite(current_head, oid);
+		commit_post_rewrite(r, current_head, oid);
 
 out:
 	free_commit_extra_headers(extra);
@@ -1768,7 +1769,7 @@ static int do_pick_commit(struct repository *r,
 			oidcpy(&head, the_hash_algo->empty_tree);
 		if (index_differs_from(r, unborn ? empty_tree_oid_hex() : "HEAD",
 				       NULL, 0))
-			return error_dirty_index(r->index, opts);
+			return error_dirty_index(r, opts);
 	}
 	discard_index(r->index);
 
@@ -1998,8 +1999,8 @@ static int read_and_refresh_cache(struct repository *r,
 				  struct replay_opts *opts)
 {
 	struct lock_file index_lock = LOCK_INIT;
-	int index_fd = hold_locked_index(&index_lock, 0);
-	if (read_index(r->index) < 0) {
+	int index_fd = repo_hold_locked_index(r, &index_lock, 0);
+	if (repo_read_index(r) < 0) {
 		rollback_lock_file(&index_lock);
 		return error(_("git %s: failed to read the index"),
 			_(action_name(opts)));
@@ -2865,7 +2866,7 @@ static int do_exec(struct repository *r, const char *command_line)
 					  child_env.argv);
 
 	/* force re-reading of the cache */
-	if (discard_index(r->index) < 0 || read_index(r->index) < 0)
+	if (discard_index(r->index) < 0 || repo_read_index(r) < 0)
 		return error(_("could not read index"));
 
 	dirty = require_clean_work_tree(r, "rebase", NULL, 1, 1);
@@ -2989,7 +2990,7 @@ static int do_reset(struct repository *r,
 	struct unpack_trees_options unpack_tree_opts;
 	int ret = 0;
 
-	if (hold_locked_index(&lock, LOCK_REPORT_ON_ERROR) < 0)
+	if (repo_hold_locked_index(r, &lock, LOCK_REPORT_ON_ERROR) < 0)
 		return -1;
 
 	if (len == 10 && !strncmp("[new root]", name, len)) {
@@ -3034,7 +3035,7 @@ static int do_reset(struct repository *r,
 	unpack_tree_opts.merge = 1;
 	unpack_tree_opts.update = 1;
 
-	if (read_index_unmerged(r->index)) {
+	if (repo_read_index_unmerged(r)) {
 		rollback_lock_file(&lock);
 		strbuf_release(&ref_name);
 		return error_resolve_conflict(_(action_name(opts)));
@@ -3107,7 +3108,7 @@ static int do_merge(struct repository *r,
 	static struct lock_file lock;
 	const char *p;
 
-	if (hold_locked_index(&lock, LOCK_REPORT_ON_ERROR) < 0) {
+	if (repo_hold_locked_index(r, &lock, LOCK_REPORT_ON_ERROR) < 0) {
 		ret = -1;
 		goto leave_merge;
 	}
@@ -3288,7 +3289,7 @@ static int do_merge(struct repository *r,
 
 		/* force re-reading of the cache */
 		if (!ret && (discard_index(r->index) < 0 ||
-			     read_index(r->index) < 0))
+			     repo_read_index(r) < 0))
 			ret = error(_("could not read index"));
 		goto leave_merge;
 	}
@@ -3310,8 +3311,8 @@ static int do_merge(struct repository *r,
 		commit_list_insert(j->item, &reversed);
 	free_commit_list(bases);
 
-	read_index(r->index);
-	init_merge_options(&o);
+	repo_read_index(r);
+	init_merge_options(&o, r);
 	o.branch1 = "HEAD";
 	o.branch2 = ref_name.buf;
 	o.buffer_output = 2;
@@ -3987,7 +3988,7 @@ int sequencer_continue(struct repository *r, struct replay_opts *opts)
 				goto release_todo_list;
 		}
 		if (index_differs_from(r, "HEAD", NULL, 0)) {
-			res = error_dirty_index(r->index, opts);
+			res = error_dirty_index(r, opts);
 			goto release_todo_list;
 		}
 		todo_list.current++;
diff --git a/sequencer.h b/sequencer.h
index 53b8679..93e8913 100644
--- a/sequencer.h
+++ b/sequencer.h
@@ -126,7 +126,8 @@ int update_head_with_reflog(const struct commit *old_head,
 			    const struct object_id *new_head,
 			    const char *action, const struct strbuf *msg,
 			    struct strbuf *err);
-void commit_post_rewrite(const struct commit *current_head,
+void commit_post_rewrite(struct repository *r,
+			 const struct commit *current_head,
 			 const struct object_id *new_head);
 
 int prepare_branch_to_be_rebased(struct replay_opts *opts, const char *commit);
diff --git a/sha1-name.c b/sha1-name.c
index 4acd406..d1cc77c 100644
--- a/sha1-name.c
+++ b/sha1-name.c
@@ -1515,7 +1515,7 @@ int strbuf_check_branch_ref(struct strbuf *sb, const char *name)
 int get_oid(const char *name, struct object_id *oid)
 {
 	struct object_context unused;
-	return get_oid_with_context(name, 0, oid, &unused);
+	return get_oid_with_context(the_repository, name, 0, oid, &unused);
 }
 
 
@@ -1532,35 +1532,40 @@ int get_oid(const char *name, struct object_id *oid)
 int get_oid_committish(const char *name, struct object_id *oid)
 {
 	struct object_context unused;
-	return get_oid_with_context(name, GET_OID_COMMITTISH,
+	return get_oid_with_context(the_repository,
+				    name, GET_OID_COMMITTISH,
 				    oid, &unused);
 }
 
 int get_oid_treeish(const char *name, struct object_id *oid)
 {
 	struct object_context unused;
-	return get_oid_with_context(name, GET_OID_TREEISH,
+	return get_oid_with_context(the_repository,
+				    name, GET_OID_TREEISH,
 				    oid, &unused);
 }
 
 int get_oid_commit(const char *name, struct object_id *oid)
 {
 	struct object_context unused;
-	return get_oid_with_context(name, GET_OID_COMMIT,
+	return get_oid_with_context(the_repository,
+				    name, GET_OID_COMMIT,
 				    oid, &unused);
 }
 
 int get_oid_tree(const char *name, struct object_id *oid)
 {
 	struct object_context unused;
-	return get_oid_with_context(name, GET_OID_TREE,
+	return get_oid_with_context(the_repository,
+				    name, GET_OID_TREE,
 				    oid, &unused);
 }
 
 int get_oid_blob(const char *name, struct object_id *oid)
 {
 	struct object_context unused;
-	return get_oid_with_context(name, GET_OID_BLOB,
+	return get_oid_with_context(the_repository,
+				    name, GET_OID_BLOB,
 				    oid, &unused);
 }
 
@@ -1599,7 +1604,8 @@ static void diagnose_invalid_oid_path(const char *prefix,
 }
 
 /* Must be called only when :stage:filename doesn't exist. */
-static void diagnose_invalid_index_path(int stage,
+static void diagnose_invalid_index_path(struct index_state *istate,
+					int stage,
 					const char *prefix,
 					const char *filename)
 {
@@ -1612,11 +1618,11 @@ static void diagnose_invalid_index_path(int stage,
 		prefix = "";
 
 	/* Wrong stage number? */
-	pos = cache_name_pos(filename, namelen);
+	pos = index_name_pos(istate, filename, namelen);
 	if (pos < 0)
 		pos = -pos - 1;
-	if (pos < active_nr) {
-		ce = active_cache[pos];
+	if (pos < istate->cache_nr) {
+		ce = istate->cache[pos];
 		if (ce_namelen(ce) == namelen &&
 		    !memcmp(ce->name, filename, namelen))
 			die("Path '%s' is in the index, but not at stage %d.\n"
@@ -1628,11 +1634,11 @@ static void diagnose_invalid_index_path(int stage,
 	/* Confusion between relative and absolute filenames? */
 	strbuf_addstr(&fullname, prefix);
 	strbuf_addstr(&fullname, filename);
-	pos = cache_name_pos(fullname.buf, fullname.len);
+	pos = index_name_pos(istate, fullname.buf, fullname.len);
 	if (pos < 0)
 		pos = -pos - 1;
-	if (pos < active_nr) {
-		ce = active_cache[pos];
+	if (pos < istate->cache_nr) {
+		ce = istate->cache[pos];
 		if (ce_namelen(ce) == fullname.len &&
 		    !memcmp(ce->name, fullname.buf, fullname.len))
 			die("Path '%s' is in the index, but not '%s'.\n"
@@ -1666,11 +1672,12 @@ static char *resolve_relative_path(const char *rel)
 			   rel);
 }
 
-static enum get_oid_result get_oid_with_context_1(const char *name,
-						  unsigned flags,
-						  const char *prefix,
-						  struct object_id *oid,
-						  struct object_context *oc)
+static enum get_oid_result get_oid_with_context_1(struct repository *repo,
+				  const char *name,
+				  unsigned flags,
+				  const char *prefix,
+				  struct object_id *oid,
+				  struct object_context *oc)
 {
 	int ret, bracket_depth;
 	int namelen = strlen(name);
@@ -1725,13 +1732,13 @@ static enum get_oid_result get_oid_with_context_1(const char *name,
 		if (flags & GET_OID_RECORD_PATH)
 			oc->path = xstrdup(cp);
 
-		if (!active_cache)
-			read_cache();
-		pos = cache_name_pos(cp, namelen);
+		if (!repo->index->cache)
+			repo_read_index(the_repository);
+		pos = index_name_pos(repo->index, cp, namelen);
 		if (pos < 0)
 			pos = -pos - 1;
-		while (pos < active_nr) {
-			ce = active_cache[pos];
+		while (pos < repo->index->cache_nr) {
+			ce = repo->index->cache[pos];
 			if (ce_namelen(ce) != namelen ||
 			    memcmp(ce->name, cp, namelen))
 				break;
@@ -1744,7 +1751,7 @@ static enum get_oid_result get_oid_with_context_1(const char *name,
 			pos++;
 		}
 		if (only_to_die && name[1] && name[1] != '/')
-			diagnose_invalid_index_path(stage, prefix, cp);
+			diagnose_invalid_index_path(repo->index, stage, prefix, cp);
 		free(new_path);
 		return -1;
 	}
@@ -1809,12 +1816,15 @@ void maybe_die_on_misspelt_object_name(const char *name, const char *prefix)
 {
 	struct object_context oc;
 	struct object_id oid;
-	get_oid_with_context_1(name, GET_OID_ONLY_TO_DIE, prefix, &oid, &oc);
+	get_oid_with_context_1(the_repository, name, GET_OID_ONLY_TO_DIE,
+			       prefix, &oid, &oc);
 }
 
-int get_oid_with_context(const char *str, unsigned flags, struct object_id *oid, struct object_context *oc)
+int get_oid_with_context(struct repository *repo, const char *str,
+			 unsigned flags, struct object_id *oid,
+			 struct object_context *oc)
 {
 	if (flags & GET_OID_FOLLOW_SYMLINKS && flags & GET_OID_ONLY_TO_DIE)
 		BUG("incompatible flags for get_sha1_with_context");
-	return get_oid_with_context_1(str, flags, NULL, oid, oc);
+	return get_oid_with_context_1(repo, str, flags, NULL, oid, oc);
 }
diff --git a/submodule.c b/submodule.c
index a5f2694..934ecfa 100644
--- a/submodule.c
+++ b/submodule.c
@@ -1,4 +1,3 @@
-#define NO_THE_INDEX_COMPATIBILITY_MACROS
 
 #include "cache.h"
 #include "repository.h"
diff --git a/t/helper/test-dump-fsmonitor.c b/t/helper/test-dump-fsmonitor.c
index 08e3684..2786f47 100644
--- a/t/helper/test-dump-fsmonitor.c
+++ b/t/helper/test-dump-fsmonitor.c
@@ -3,11 +3,11 @@
 
 int cmd__dump_fsmonitor(int ac, const char **av)
 {
-	struct index_state *istate = &the_index;
+	struct index_state *istate = the_repository->index;
 	int i;
 
 	setup_git_directory();
-	if (do_read_index(istate, get_index_file(), 0) < 0)
+	if (do_read_index(istate, the_repository->index_file, 0) < 0)
 		die("unable to read index file");
 	if (!istate->fsmonitor_last_update) {
 		printf("no fsmonitor\n");
diff --git a/t/helper/test-dump-untracked-cache.c b/t/helper/test-dump-untracked-cache.c
index 52870eb..cf0f2c7 100644
--- a/t/helper/test-dump-untracked-cache.c
+++ b/t/helper/test-dump-untracked-cache.c
@@ -1,3 +1,4 @@
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "test-tool.h"
 #include "cache.h"
 #include "dir.h"
diff --git a/t/helper/test-tool.h b/t/helper/test-tool.h
index ca5c88e..a396c10 100644
--- a/t/helper/test-tool.h
+++ b/t/helper/test-tool.h
@@ -1,6 +1,7 @@
 #ifndef TEST_TOOL_H
 #define TEST_TOOL_H
 
+#define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "git-compat-util.h"
 
 int cmd__chmtime(int argc, const char **argv);
diff --git a/tree.c b/tree.c
index 9f0457c..f416afc 100644
--- a/tree.c
+++ b/tree.c
@@ -1,4 +1,3 @@
-#define NO_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "cache-tree.h"
 #include "tree.h"
diff --git a/unpack-trees.c b/unpack-trees.c
index 01c2175..3563daa 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -1,4 +1,3 @@
-#define NO_THE_INDEX_COMPATIBILITY_MACROS
 #include "cache.h"
 #include "argv-array.h"
 #include "repository.h"
diff --git a/wt-status.c b/wt-status.c
index 0fe3bcd..1f564b1 100644
--- a/wt-status.c
+++ b/wt-status.c
@@ -2375,10 +2375,10 @@ int require_clean_work_tree(struct repository *r,
 	struct lock_file lock_file = LOCK_INIT;
 	int err = 0, fd;
 
-	fd = hold_locked_index(&lock_file, 0);
+	fd = repo_hold_locked_index(r, &lock_file, 0);
 	refresh_index(r->index, REFRESH_QUIET, NULL, NULL, NULL);
 	if (0 <= fd)
-		update_index_if_able(r->index, &lock_file);
+		repo_update_index_if_able(r, &lock_file);
 	rollback_lock_file(&lock_file);
 
 	if (has_unstaged_changes(r, ignore_submodules)) {