diff --git a/t/helper/test-ref-store.c b/t/helper/test-ref-store.c
index 48552e6a9e..702ec1f128 100644
--- a/t/helper/test-ref-store.c
+++ b/t/helper/test-ref-store.c
@@ -298,16 +298,19 @@ static int cmd_update_ref(struct ref_store *refs, const char **argv)
 	const char *new_sha1_buf = notnull(*argv++, "new-sha1");
 	const char *old_sha1_buf = notnull(*argv++, "old-sha1");
 	unsigned int flags = arg_flags(*argv++, "flags", transaction_flags);
-	struct object_id old_oid;
+	struct object_id old_oid, *old_oid_ptr = NULL;
 	struct object_id new_oid;
 
-	if (get_oid_hex(old_sha1_buf, &old_oid))
-		die("cannot parse %s as %s", old_sha1_buf, the_hash_algo->name);
+	if (*old_sha1_buf) {
+		if (get_oid_hex(old_sha1_buf, &old_oid))
+			die("cannot parse %s as %s", old_sha1_buf, the_hash_algo->name);
+		old_oid_ptr = &old_oid;
+	}
 	if (get_oid_hex(new_sha1_buf, &new_oid))
 		die("cannot parse %s as %s", new_sha1_buf, the_hash_algo->name);
 
 	return refs_update_ref(refs, msg, refname,
-			       &new_oid, &old_oid,
+			       &new_oid, old_oid_ptr,
 			       flags, UPDATE_REFS_DIE_ON_ERR);
 }
 
diff --git a/t/t1400-update-ref.sh b/t/t1400-update-ref.sh
index 9ac4b7036b..6d1810c358 100755
--- a/t/t1400-update-ref.sh
+++ b/t/t1400-update-ref.sh
@@ -9,8 +9,6 @@ test_description='Test git update-ref and basic ref logging'
 Z=$ZERO_OID
 
 m=refs/heads/main
-n_dir=refs/heads/gu
-n=$n_dir/fixes
 outside=refs/foo
 bare=bare-repo
 
@@ -62,10 +60,10 @@ test_expect_success "delete $m without oldvalue verification" '
 	test_must_fail git show-ref --verify -q $m
 '
 
-test_expect_success "fail to create $n" '
-	test_when_finished "rm -f .git/$n_dir" &&
-	touch .git/$n_dir &&
-	test_must_fail git update-ref $n $A
+test_expect_success "fail to create $n due to file/directory conflict" '
+	test_when_finished "git update-ref -d refs/heads/gu" &&
+	git update-ref refs/heads/gu $A &&
+	test_must_fail git update-ref refs/heads/gu/fixes $A
 '
 
 test_expect_success "create $m (by HEAD)" '
@@ -92,7 +90,8 @@ test_expect_success "deleting current branch adds message to HEAD's log" '
 	git symbolic-ref HEAD $m &&
 	git update-ref -m delete-$m -d $m &&
 	test_must_fail git show-ref --verify -q $m &&
-	grep "delete-$m$" .git/logs/HEAD
+	test-tool ref-store main for-each-reflog-ent HEAD >actual &&
+	grep "delete-$m$" actual
 '
 
 test_expect_success "deleting by HEAD adds message to HEAD's log" '
@@ -101,7 +100,8 @@ test_expect_success "deleting by HEAD adds message to HEAD's log" '
 	git symbolic-ref HEAD $m &&
 	git update-ref -m delete-by-head -d HEAD &&
 	test_must_fail git show-ref --verify -q $m &&
-	grep "delete-by-head$" .git/logs/HEAD
+	test-tool ref-store main for-each-reflog-ent HEAD >actual &&
+	grep "delete-by-head$" actual
 '
 
 test_expect_success 'update-ref does not create reflogs by default' '
@@ -132,7 +132,7 @@ test_expect_success 'creates no reflog in bare repository' '
 
 test_expect_success 'core.logAllRefUpdates=true creates reflog in bare repository' '
 	test_when_finished "git -C $bare config --unset core.logAllRefUpdates && \
-		rm $bare/logs/$m" &&
+		test-tool ref-store main delete-reflog $m" &&
 	git -C $bare config core.logAllRefUpdates true &&
 	git -C $bare update-ref $m $bareB &&
 	git -C $bare rev-parse $bareB >expect &&
@@ -221,27 +221,27 @@ test_expect_success 'delete symref without dereference when the referred ref is
 '
 
 test_expect_success 'update-ref -d is not confused by self-reference' '
+	test_when_finished "test-tool ref-store main delete-refs REF_NO_DEREF refs/heads/self" &&
 	git symbolic-ref refs/heads/self refs/heads/self &&
-	test_when_finished "rm -f .git/refs/heads/self" &&
-	test_path_is_file .git/refs/heads/self &&
+	git symbolic-ref --no-recurse refs/heads/self &&
 	test_must_fail git update-ref -d refs/heads/self &&
-	test_path_is_file .git/refs/heads/self
+	git symbolic-ref --no-recurse refs/heads/self
 '
 
 test_expect_success 'update-ref --no-deref -d can delete self-reference' '
+	test_when_finished "test-tool ref-store main delete-refs REF_NO_DEREF refs/heads/self" &&
 	git symbolic-ref refs/heads/self refs/heads/self &&
-	test_when_finished "rm -f .git/refs/heads/self" &&
-	test_path_is_file .git/refs/heads/self &&
+	git symbolic-ref --no-recurse refs/heads/self &&
 	git update-ref --no-deref -d refs/heads/self &&
 	test_must_fail git show-ref --verify -q refs/heads/self
 '
 
-test_expect_success 'update-ref --no-deref -d can delete reference to bad ref' '
+test_expect_success REFFILES 'update-ref --no-deref -d can delete reference to bad ref' '
 	>.git/refs/heads/bad &&
 	test_when_finished "rm -f .git/refs/heads/bad" &&
 	git symbolic-ref refs/heads/ref-to-bad refs/heads/bad &&
 	test_when_finished "git update-ref -d refs/heads/ref-to-bad" &&
-	test_path_is_file .git/refs/heads/ref-to-bad &&
+	git symbolic-ref --no-recurse refs/heads/ref-to-bad &&
 	git update-ref --no-deref -d refs/heads/ref-to-bad &&
 	test_must_fail git show-ref --verify -q refs/heads/ref-to-bad
 '
@@ -265,7 +265,10 @@ test_expect_success "(not) changed .git/$m" '
 	! test $B = $(git show-ref -s --verify $m)
 '
 
-rm -f .git/logs/refs/heads/main
+test_expect_success "clean up reflog" '
+	test-tool ref-store main delete-reflog $m
+'
+
 test_expect_success "create $m (logged by touch)" '
 	test_config core.logAllRefUpdates false &&
 	GIT_COMMITTER_DATE="2005-05-26 23:30" \
@@ -285,7 +288,7 @@ test_expect_success "set $m (logged by touch)" '
 	test $A = $(git show-ref -s --verify $m)
 '
 
-test_expect_success 'empty directory removal' '
+test_expect_success REFFILES 'empty directory removal' '
 	git branch d1/d2/r1 HEAD &&
 	git branch d1/r2 HEAD &&
 	test_path_is_file .git/refs/heads/d1/d2/r1 &&
@@ -297,7 +300,7 @@ test_expect_success 'empty directory removal' '
 	test_path_is_file .git/logs/refs/heads/d1/r2
 '
 
-test_expect_success 'symref empty directory removal' '
+test_expect_success REFFILES 'symref empty directory removal' '
 	git branch e1/e2/r1 HEAD &&
 	git branch e1/r2 HEAD &&
 	git checkout e1/e2/r1 &&
@@ -318,7 +321,7 @@ $A $B $GIT_COMMITTER_NAME <$GIT_COMMITTER_EMAIL> 1117150260 +0000	Switch
 $B $A $GIT_COMMITTER_NAME <$GIT_COMMITTER_EMAIL> 1117150860 +0000
 EOF
 test_expect_success "verifying $m's log (logged by touch)" '
-	test_when_finished "git update-ref -d $m && rm -rf .git/logs actual expect" &&
+	test_when_finished "git update-ref -d $m && git reflog expire --expire=all --all && rm -rf actual expect" &&
 	test-tool ref-store main for-each-reflog-ent $m >actual &&
 	test_cmp actual expect
 '
@@ -348,7 +351,7 @@ $A $B $GIT_COMMITTER_NAME <$GIT_COMMITTER_EMAIL> 1117150380 +0000	Switch
 $B $A $GIT_COMMITTER_NAME <$GIT_COMMITTER_EMAIL> 1117150980 +0000
 EOF
 test_expect_success "verifying $m's log (logged by config)" '
-	test_when_finished "git update-ref -d $m && rm -rf .git/logs actual expect" &&
+	test_when_finished "git update-ref -d $m && git reflog expire --expire=all --all && rm -rf actual expect" &&
 	test-tool ref-store main for-each-reflog-ent $m >actual &&
 	test_cmp actual expect
 '
@@ -434,7 +437,8 @@ test_expect_success 'Query "main@{2005-05-28}" (past end of history)' '
 	test_grep -F "warning: log for ref $m unexpectedly ended on $ld" e
 '
 
-rm -f .git/$m .git/logs/$m expect
+rm -f expect
+git update-ref -d $m
 
 test_expect_success 'creating initial files' '
 	test_when_finished rm -f M &&
@@ -1635,7 +1639,7 @@ test_expect_success PIPE 'transaction flushes status updates' '
 	test_cmp expected actual
 '
 
-test_expect_success 'directory not created deleting packed ref' '
+test_expect_success REFFILES 'directory not created deleting packed ref' '
 	git branch d1/d2/r1 HEAD &&
 	git pack-refs --all &&
 	test_path_is_missing .git/refs/heads/d1/d2 &&
diff --git a/t/t1430-bad-ref-name.sh b/t/t1430-bad-ref-name.sh
index 68cc9e73d0..0c00118c2b 100755
--- a/t/t1430-bad-ref-name.sh
+++ b/t/t1430-bad-ref-name.sh
@@ -164,9 +164,9 @@ test_expect_success 'rev-parse skips symref pointing to broken name' '
 test_expect_success 'for-each-ref emits warnings for broken names' '
 	test-tool ref-store main update-ref msg "refs/heads/broken...ref" $main_sha1 $ZERO_OID REF_SKIP_REFNAME_VERIFICATION &&
 	test_when_finished "test-tool ref-store main delete-refs REF_NO_DEREF msg refs/heads/broken...ref" &&
-	printf "ref: refs/heads/broken...ref\n" >.git/refs/heads/badname &&
+	test-tool ref-store main create-symref refs/heads/badname refs/heads/broken...ref &&
 	test_when_finished "test-tool ref-store main delete-refs REF_NO_DEREF msg refs/heads/badname" &&
-	printf "ref: refs/heads/main\n" >.git/refs/heads/broken...symref &&
+	test-tool ref-store main create-symref refs/heads/broken...symref refs/heads/main &&
 	test_when_finished "test-tool ref-store main delete-refs REF_NO_DEREF msg refs/heads/broken...symref" &&
 	git for-each-ref >output 2>error &&
 	! grep -e "broken\.\.\.ref" output &&
@@ -257,7 +257,7 @@ test_expect_success 'update-ref -d can delete broken name through symref' '
 '
 
 test_expect_success 'update-ref --no-deref -d can delete symref with broken name' '
-	printf "ref: refs/heads/main\n" >.git/refs/heads/broken...symref &&
+	test-tool ref-store main create-symref refs/heads/broken...symref refs/heads/main &&
 	test_when_finished "test-tool ref-store main delete-refs REF_NO_DEREF msg refs/heads/broken...symref" &&
 	test_ref_exists refs/heads/broken...symref &&
 	git update-ref --no-deref -d refs/heads/broken...symref >output 2>error &&
@@ -267,7 +267,7 @@ test_expect_success 'update-ref --no-deref -d can delete symref with broken name
 '
 
 test_expect_success 'branch -d can delete symref with broken name' '
-	printf "ref: refs/heads/main\n" >.git/refs/heads/broken...symref &&
+	test-tool ref-store main create-symref refs/heads/broken...symref refs/heads/main &&
 	test_when_finished "test-tool ref-store main delete-refs REF_NO_DEREF msg refs/heads/broken...symref" &&
 	test_ref_exists refs/heads/broken...symref &&
 	git branch -d broken...symref >output 2>error &&
@@ -277,7 +277,7 @@ test_expect_success 'branch -d can delete symref with broken name' '
 '
 
 test_expect_success 'update-ref --no-deref -d can delete dangling symref with broken name' '
-	printf "ref: refs/heads/idonotexist\n" >.git/refs/heads/broken...symref &&
+	test-tool ref-store main create-symref refs/heads/broken...symref refs/heads/idonotexist &&
 	test_when_finished "test-tool ref-store main delete-refs REF_NO_DEREF msg refs/heads/broken...symref" &&
 	test_ref_exists refs/heads/broken...symref &&
 	git update-ref --no-deref -d refs/heads/broken...symref >output 2>error &&
@@ -287,7 +287,7 @@ test_expect_success 'update-ref --no-deref -d can delete dangling symref with br
 '
 
 test_expect_success 'branch -d can delete dangling symref with broken name' '
-	printf "ref: refs/heads/idonotexist\n" >.git/refs/heads/broken...symref &&
+	test-tool ref-store main create-symref refs/heads/broken...symref refs/heads/idonotexist &&
 	test_when_finished "test-tool ref-store main delete-refs REF_NO_DEREF msg refs/heads/broken...symref" &&
 	test_ref_exists refs/heads/broken...symref &&
 	git branch -d broken...symref >output 2>error &&
diff --git a/t/t1450-fsck.sh b/t/t1450-fsck.sh
index 0e3e87d37a..8a456b1142 100755
--- a/t/t1450-fsck.sh
+++ b/t/t1450-fsck.sh
@@ -15,6 +15,7 @@ test_expect_success setup '
 	git config --unset i18n.commitencoding &&
 	git checkout HEAD^0 &&
 	test_commit B fileB two &&
+	orig_head=$(git rev-parse HEAD) &&
 	git tag -d A B &&
 	git reflog expire --expire=now --all
 '
@@ -115,15 +116,15 @@ test_expect_success 'zlib corrupt loose object output ' '
 '
 
 test_expect_success 'branch pointing to non-commit' '
-	git rev-parse HEAD^{tree} >.git/refs/heads/invalid &&
+	tree_oid=$(git rev-parse --verify HEAD^{tree}) &&
 	test_when_finished "git update-ref -d refs/heads/invalid" &&
+	test-tool ref-store main update-ref msg refs/heads/invalid $tree_oid $ZERO_OID REF_SKIP_OID_VERIFICATION &&
 	test_must_fail git fsck 2>out &&
 	test_grep "not a commit" out
 '
 
-test_expect_success 'HEAD link pointing at a funny object' '
-	test_when_finished "mv .git/SAVED_HEAD .git/HEAD" &&
-	mv .git/HEAD .git/SAVED_HEAD &&
+test_expect_success REFFILES 'HEAD link pointing at a funny object' '
+	test_when_finished "git update-ref HEAD $orig_head" &&
 	echo $ZERO_OID >.git/HEAD &&
 	# avoid corrupt/broken HEAD from interfering with repo discovery
 	test_must_fail env GIT_DIR=.git git fsck 2>out &&
@@ -131,27 +132,25 @@ test_expect_success 'HEAD link pointing at a funny object' '
 '
 
 test_expect_success 'HEAD link pointing at a funny place' '
-	test_when_finished "mv .git/SAVED_HEAD .git/HEAD" &&
-	mv .git/HEAD .git/SAVED_HEAD &&
-	echo "ref: refs/funny/place" >.git/HEAD &&
+	test_when_finished "git update-ref --no-deref HEAD $orig_head" &&
+	test-tool ref-store main create-symref HEAD refs/funny/place &&
 	# avoid corrupt/broken HEAD from interfering with repo discovery
 	test_must_fail env GIT_DIR=.git git fsck 2>out &&
 	test_grep "HEAD points to something strange" out
 '
 
-test_expect_success 'HEAD link pointing at a funny object (from different wt)' '
-	test_when_finished "mv .git/SAVED_HEAD .git/HEAD" &&
-	test_when_finished "rm -rf .git/worktrees wt" &&
+test_expect_success REFFILES 'HEAD link pointing at a funny object (from different wt)' '
+	test_when_finished "git update-ref HEAD $orig_head" &&
+	test_when_finished "git worktree remove -f wt" &&
 	git worktree add wt &&
-	mv .git/HEAD .git/SAVED_HEAD &&
 	echo $ZERO_OID >.git/HEAD &&
 	# avoid corrupt/broken HEAD from interfering with repo discovery
 	test_must_fail git -C wt fsck 2>out &&
 	test_grep "main-worktree/HEAD: detached HEAD points" out
 '
 
-test_expect_success 'other worktree HEAD link pointing at a funny object' '
-	test_when_finished "rm -rf .git/worktrees other" &&
+test_expect_success REFFILES 'other worktree HEAD link pointing at a funny object' '
+	test_when_finished "git worktree remove -f other" &&
 	git worktree add other &&
 	echo $ZERO_OID >.git/worktrees/other/HEAD &&
 	test_must_fail git fsck 2>out &&
@@ -159,17 +158,18 @@ test_expect_success 'other worktree HEAD link pointing at a funny object' '
 '
 
 test_expect_success 'other worktree HEAD link pointing at missing object' '
-	test_when_finished "rm -rf .git/worktrees other" &&
+	test_when_finished "git worktree remove -f other" &&
 	git worktree add other &&
-	echo "Contents missing from repo" | git hash-object --stdin >.git/worktrees/other/HEAD &&
+	object_id=$(echo "Contents missing from repo" | git hash-object --stdin) &&
+	test-tool -C other ref-store main update-ref msg HEAD $object_id "" REF_NO_DEREF,REF_SKIP_OID_VERIFICATION &&
 	test_must_fail git fsck 2>out &&
 	test_grep "worktrees/other/HEAD: invalid sha1 pointer" out
 '
 
 test_expect_success 'other worktree HEAD link pointing at a funny place' '
-	test_when_finished "rm -rf .git/worktrees other" &&
+	test_when_finished "git worktree remove -f other" &&
 	git worktree add other &&
-	echo "ref: refs/funny/place" >.git/worktrees/other/HEAD &&
+	git -C other symbolic-ref HEAD refs/funny/place &&
 	test_must_fail git fsck 2>out &&
 	test_grep "worktrees/other/HEAD points to something strange" out
 '
@@ -391,7 +391,7 @@ test_expect_success 'tag pointing to nonexistent' '
 
 	tag=$(git hash-object -t tag -w --stdin <invalid-tag) &&
 	test_when_finished "remove_object $tag" &&
-	echo $tag >.git/refs/tags/invalid &&
+	git update-ref refs/tags/invalid $tag &&
 	test_when_finished "git update-ref -d refs/tags/invalid" &&
 	test_must_fail git fsck --tags >out &&
 	test_grep "broken link" out
@@ -411,7 +411,7 @@ test_expect_success 'tag pointing to something else than its type' '
 
 	tag=$(git hash-object -t tag -w --stdin <wrong-tag) &&
 	test_when_finished "remove_object $tag" &&
-	echo $tag >.git/refs/tags/wrong &&
+	git update-ref refs/tags/wrong $tag &&
 	test_when_finished "git update-ref -d refs/tags/wrong" &&
 	test_must_fail git fsck --tags
 '
@@ -428,7 +428,7 @@ test_expect_success 'tag with incorrect tag name & missing tagger' '
 
 	tag=$(git hash-object --literally -t tag -w --stdin <wrong-tag) &&
 	test_when_finished "remove_object $tag" &&
-	echo $tag >.git/refs/tags/wrong &&
+	git update-ref refs/tags/wrong $tag &&
 	test_when_finished "git update-ref -d refs/tags/wrong" &&
 	git fsck --tags 2>out &&
 
@@ -452,7 +452,7 @@ test_expect_success 'tag with bad tagger' '
 
 	tag=$(git hash-object --literally -t tag -w --stdin <wrong-tag) &&
 	test_when_finished "remove_object $tag" &&
-	echo $tag >.git/refs/tags/wrong &&
+	git update-ref refs/tags/wrong $tag &&
 	test_when_finished "git update-ref -d refs/tags/wrong" &&
 	test_must_fail git fsck --tags 2>out &&
 	test_grep "error in tag .*: invalid author/committer" out
@@ -471,7 +471,7 @@ test_expect_success 'tag with NUL in header' '
 
 	tag=$(git hash-object --literally -t tag -w --stdin <tag-NUL-header) &&
 	test_when_finished "remove_object $tag" &&
-	echo $tag >.git/refs/tags/wrong &&
+	git update-ref refs/tags/wrong $tag &&
 	test_when_finished "git update-ref -d refs/tags/wrong" &&
 	test_must_fail git fsck --tags 2>out &&
 	test_grep "error in tag $tag.*unterminated header: NUL at offset" out
diff --git a/t/t2011-checkout-invalid-head.sh b/t/t2011-checkout-invalid-head.sh
index d9997e7b6b..3c8135831b 100755
--- a/t/t2011-checkout-invalid-head.sh
+++ b/t/t2011-checkout-invalid-head.sh
@@ -18,18 +18,18 @@ test_expect_success 'checkout should not start branch from a tree' '
 	test_must_fail git checkout -b newbranch main^{tree}
 '
 
-test_expect_success 'checkout main from invalid HEAD' '
+test_expect_success REFFILES 'checkout main from invalid HEAD' '
 	echo $ZERO_OID >.git/HEAD &&
 	git checkout main --
 '
 
-test_expect_success 'checkout notices failure to lock HEAD' '
+test_expect_success REFFILES 'checkout notices failure to lock HEAD' '
 	test_when_finished "rm -f .git/HEAD.lock" &&
 	>.git/HEAD.lock &&
 	test_must_fail git checkout -b other
 '
 
-test_expect_success 'create ref directory/file conflict scenario' '
+test_expect_success REFFILES 'create ref directory/file conflict scenario' '
 	git update-ref refs/heads/outer/inner main &&
 
 	# do not rely on symbolic-ref to get a known state,
@@ -39,26 +39,26 @@ test_expect_success 'create ref directory/file conflict scenario' '
 	}
 '
 
-test_expect_success 'checkout away from d/f HEAD (unpacked, to branch)' '
+test_expect_success REFFILES 'checkout away from d/f HEAD (unpacked, to branch)' '
 	reset_to_df &&
 	git checkout main
 '
 
-test_expect_success 'checkout away from d/f HEAD (unpacked, to detached)' '
+test_expect_success REFFILES 'checkout away from d/f HEAD (unpacked, to detached)' '
 	reset_to_df &&
 	git checkout --detach main
 '
 
-test_expect_success 'pack refs' '
+test_expect_success REFFILES 'pack refs' '
 	git pack-refs --all --prune
 '
 
-test_expect_success 'checkout away from d/f HEAD (packed, to branch)' '
+test_expect_success REFFILES 'checkout away from d/f HEAD (packed, to branch)' '
 	reset_to_df &&
 	git checkout main
 '
 
-test_expect_success 'checkout away from d/f HEAD (packed, to detached)' '
+test_expect_success REFFILES 'checkout away from d/f HEAD (packed, to detached)' '
 	reset_to_df &&
 	git checkout --detach main
 '
diff --git a/t/t3200-branch.sh b/t/t3200-branch.sh
index c54fd9ea06..c7b4e49465 100755
--- a/t/t3200-branch.sh
+++ b/t/t3200-branch.sh
@@ -28,7 +28,7 @@ test_expect_success 'git branch --help should not have created a bogus branch' '
 	test_ref_missing refs/heads/--help
 '
 
-test_expect_success 'branch -h in broken repository' '
+test_expect_success REFFILES 'branch -h in broken repository' '
 	mkdir broken &&
 	(
 		cd broken &&
@@ -76,14 +76,14 @@ test_expect_success 'git branch HEAD should fail' '
 '
 
 cat >expect <<EOF
-$ZERO_OID $HEAD $GIT_COMMITTER_NAME <$GIT_COMMITTER_EMAIL> 1117150200 +0000	branch: Created from main
+$HEAD refs/heads/d/e/f@{0}: branch: Created from main
 EOF
 test_expect_success 'git branch --create-reflog d/e/f should create a branch and a log' '
 	GIT_COMMITTER_DATE="2005-05-26 23:30" \
 	git -c core.logallrefupdates=false branch --create-reflog d/e/f &&
 	test_ref_exists refs/heads/d/e/f &&
-	test_path_is_file .git/logs/refs/heads/d/e/f &&
-	test_cmp expect .git/logs/refs/heads/d/e/f
+	git reflog show --no-abbrev-commit refs/heads/d/e/f >actual &&
+	test_cmp expect actual
 '
 
 test_expect_success 'git branch -d d/e/f should delete a branch and a log' '
@@ -203,10 +203,9 @@ test_expect_success 'git branch -M baz bam should succeed when baz is checked ou
 	test $(git rev-parse --abbrev-ref HEAD) = bam
 '
 
-test_expect_success 'git branch -M baz bam should add entries to .git/logs/HEAD' '
-	msg="Branch: renamed refs/heads/baz to refs/heads/bam" &&
-	grep " $ZERO_OID.*$msg$" .git/logs/HEAD &&
-	grep "^$ZERO_OID.*$msg$" .git/logs/HEAD
+test_expect_success 'git branch -M baz bam should add entries to HEAD reflog' '
+	git reflog show HEAD >actual &&
+	grep "HEAD@{0}: Branch: renamed refs/heads/baz to refs/heads/bam" actual
 '
 
 test_expect_success 'git branch -M should leave orphaned HEAD alone' '
@@ -215,17 +214,20 @@ test_expect_success 'git branch -M should leave orphaned HEAD alone' '
 		cd orphan &&
 		test_commit initial &&
 		git checkout --orphan lonely &&
-		grep lonely .git/HEAD &&
+		git symbolic-ref HEAD >expect &&
+		echo refs/heads/lonely >actual &&
+		test_cmp expect actual &&
 		test_ref_missing refs/head/lonely &&
 		git branch -M main mistress &&
-		grep lonely .git/HEAD
+		git symbolic-ref HEAD >expect &&
+		test_cmp expect actual
 	)
 '
 
 test_expect_success 'resulting reflog can be shown by log -g' '
 	oid=$(git rev-parse HEAD) &&
 	cat >expect <<-EOF &&
-	HEAD@{0} $oid $msg
+	HEAD@{0} $oid Branch: renamed refs/heads/baz to refs/heads/bam
 	HEAD@{2} $oid checkout: moving from foo to baz
 	EOF
 	git log -g --format="%gd %H %gs" -2 HEAD >actual &&
@@ -243,7 +245,7 @@ test_expect_success 'git branch -M baz bam should succeed when baz is checked ou
 	git worktree prune
 '
 
-test_expect_success 'git branch -M fails if updating any linked working tree fails' '
+test_expect_success REFFILES 'git branch -M fails if updating any linked working tree fails' '
 	git worktree add -b baz bazdir1 &&
 	git worktree add -f bazdir2 baz &&
 	touch .git/worktrees/bazdir1/HEAD.lock &&
@@ -699,7 +701,8 @@ test_expect_success 'git branch -C c1 c2 should succeed when c1 is checked out'
 
 test_expect_success 'git branch -C c1 c2 should never touch HEAD' '
 	msg="Branch: copied refs/heads/c1 to refs/heads/c2" &&
-	! grep "$msg$" .git/logs/HEAD
+	git reflog HEAD >actual &&
+	! grep "$msg$" actual
 '
 
 test_expect_success 'git branch -C main should work when main is checked out' '
@@ -809,7 +812,7 @@ test_expect_success 'deleting a symref' '
 
 test_expect_success 'deleting a dangling symref' '
 	git symbolic-ref refs/heads/dangling-symref nowhere &&
-	test_path_is_file .git/refs/heads/dangling-symref &&
+	git symbolic-ref --no-recurse refs/heads/dangling-symref &&
 	echo "Deleted branch dangling-symref (was nowhere)." >expect &&
 	git branch -d dangling-symref >actual &&
 	test_ref_missing refs/heads/dangling-symref &&
@@ -833,14 +836,14 @@ test_expect_success 'renaming a symref is not allowed' '
 	test_ref_missing refs/heads/new-topic
 '
 
-test_expect_success SYMLINKS 'git branch -m u v should fail when the reflog for u is a symlink' '
+test_expect_success SYMLINKS,REFFILES 'git branch -m u v should fail when the reflog for u is a symlink' '
 	git branch --create-reflog u &&
 	mv .git/logs/refs/heads/u real-u &&
 	ln -s real-u .git/logs/refs/heads/u &&
 	test_must_fail git branch -m u v
 '
 
-test_expect_success SYMLINKS 'git branch -m with symlinked .git/refs' '
+test_expect_success SYMLINKS,REFFILES 'git branch -m with symlinked .git/refs' '
 	test_when_finished "rm -rf subdir" &&
 	git init --bare subdir &&
 
@@ -1140,14 +1143,14 @@ test_expect_success '--set-upstream-to notices an error to set branch as own ups
 
 # Keep this test last, as it changes the current branch
 cat >expect <<EOF
-$ZERO_OID $HEAD $GIT_COMMITTER_NAME <$GIT_COMMITTER_EMAIL> 1117150200 +0000	branch: Created from main
+$HEAD refs/heads/g/h/i@{0}: branch: Created from main
 EOF
 test_expect_success 'git checkout -b g/h/i -l should create a branch and a log' '
 	GIT_COMMITTER_DATE="2005-05-26 23:30" \
 	git checkout -b g/h/i -l main &&
 	test_ref_exists refs/heads/g/h/i &&
-	test_path_is_file .git/logs/refs/heads/g/h/i &&
-	test_cmp expect .git/logs/refs/heads/g/h/i
+	git reflog show --no-abbrev-commit refs/heads/g/h/i >actual &&
+	test_cmp expect actual
 '
 
 test_expect_success 'checkout -b makes reflog by default' '
diff --git a/t/t3400-rebase.sh b/t/t3400-rebase.sh
index 24a539c662..57f1392926 100755
--- a/t/t3400-rebase.sh
+++ b/t/t3400-rebase.sh
@@ -424,7 +424,7 @@ test_expect_success 'refuse to switch to branch checked out elsewhere' '
 	test_grep "already used by worktree at" err
 '
 
-test_expect_success MINGW,SYMLINKS_WINDOWS 'rebase when .git/logs is a symlink' '
+test_expect_success REFFILES,MINGW,SYMLINKS_WINDOWS 'rebase when .git/logs is a symlink' '
 	git checkout main &&
 	mv .git/logs actual_logs &&
 	cmd //c "mklink /D .git\logs ..\actual_logs" &&
diff --git a/t/t3404-rebase-interactive.sh b/t/t3404-rebase-interactive.sh
index c5f30554c6..64b641002e 100755
--- a/t/t3404-rebase-interactive.sh
+++ b/t/t3404-rebase-interactive.sh
@@ -2160,7 +2160,7 @@ test_expect_success '--update-refs: check failed ref update' '
 	# recorded in the update-refs file. We will force-update the
 	# "second" ref, but "git branch -f" will not work because of
 	# the lock in the update-refs file.
-	git rev-parse third >.git/refs/heads/second &&
+	git update-ref refs/heads/second third &&
 
 	test_must_fail git rebase --continue 2>err &&
 	grep "update_ref failed for ref '\''refs/heads/second'\''" err &&
diff --git a/t/t4013-diff-various.sh b/t/t4013-diff-various.sh
index 5cc17c2e0d..c4d508e00a 100755
--- a/t/t4013-diff-various.sh
+++ b/t/t4013-diff-various.sh
@@ -522,7 +522,7 @@ test_expect_success 'log -S requires an argument' '
 '
 
 test_expect_success 'diff --cached on unborn branch' '
-	echo ref: refs/heads/unborn >.git/HEAD &&
+	git symbolic-ref HEAD refs/heads/unborn &&
 	git diff --cached >result &&
 	process_diffs result >actual &&
 	process_diffs "$TEST_DIRECTORY/t4013/diff.diff_--cached" >expected &&
diff --git a/t/t4202-log.sh b/t/t4202-log.sh
index 708636671a..ddd205f98a 100755
--- a/t/t4202-log.sh
+++ b/t/t4202-log.sh
@@ -2265,7 +2265,7 @@ test_expect_success REFFILES 'log diagnoses bogus HEAD hash' '
 
 test_expect_success REFFILES 'log diagnoses bogus HEAD symref' '
 	git init empty &&
-	echo "ref: refs/heads/invalid.lock" > empty/.git/HEAD &&
+	test-tool -C empty ref-store main create-symref HEAD refs/heads/invalid.lock &&
 	test_must_fail git -C empty log 2>stderr &&
 	test_grep broken stderr &&
 	test_must_fail git -C empty log --default totally-bogus 2>stderr &&
diff --git a/t/t4207-log-decoration-colors.sh b/t/t4207-log-decoration-colors.sh
index 21986a866d..73ea9e5155 100755
--- a/t/t4207-log-decoration-colors.sh
+++ b/t/t4207-log-decoration-colors.sh
@@ -70,8 +70,14 @@ ${c_tag}tag: ${c_reset}${c_tag}A${c_reset}${c_commit})${c_reset} A
 	cmp_filtered_decorations
 '
 
+remove_replace_refs () {
+	git for-each-ref 'refs/replace*/**' --format='delete %(refname)' >in &&
+	git update-ref --stdin <in &&
+	rm in
+}
+
 test_expect_success 'test coloring with replace-objects' '
-	test_when_finished rm -rf .git/refs/replace* &&
+	test_when_finished remove_replace_refs &&
 	test_commit C &&
 	test_commit D &&
 
@@ -99,7 +105,7 @@ EOF
 '
 
 test_expect_success 'test coloring with grafted commit' '
-	test_when_finished rm -rf .git/refs/replace* &&
+	test_when_finished remove_replace_refs &&
 
 	git replace --graft HEAD HEAD~2 &&
 
diff --git a/t/t5526-fetch-submodules.sh b/t/t5526-fetch-submodules.sh
index 26e933f93a..7ab220fa31 100755
--- a/t/t5526-fetch-submodules.sh
+++ b/t/t5526-fetch-submodules.sh
@@ -771,7 +771,7 @@ test_expect_success 'fetching submodule into a broken repository' '
 	git -C dst fetch --recurse-submodules &&
 
 	# Break the receiving submodule
-	rm -f dst/sub/.git/HEAD &&
+	test-tool -C dst/sub ref-store main delete-refs REF_NO_DEREF msg HEAD &&
 
 	# NOTE: without the fix the following tests will recurse forever!
 	# They should terminate with an error.
diff --git a/t/t5605-clone-local.sh b/t/t5605-clone-local.sh
index 946c575188..a3055869bc 100755
--- a/t/t5605-clone-local.sh
+++ b/t/t5605-clone-local.sh
@@ -65,7 +65,7 @@ test_expect_success 'Even without -l, local will make a hardlink' '
 '
 
 test_expect_success 'local clone of repo with nonexistent ref in HEAD' '
-	echo "ref: refs/heads/nonexistent" > a.git/HEAD &&
+	git -C a.git symbolic-ref HEAD refs/heads/nonexistent &&
 	git clone a d &&
 	(cd d &&
 	git fetch &&
@@ -157,7 +157,7 @@ test_expect_success 'cloning locally respects "-u" for fetching refs' '
 	test_must_fail git clone --bare -u false a should_not_work.git
 '
 
-test_expect_success 'local clone from repo with corrupt refs fails gracefully' '
+test_expect_success REFFILES 'local clone from repo with corrupt refs fails gracefully' '
 	git init corrupt &&
 	test_commit -C corrupt one &&
 	echo a >corrupt/.git/refs/heads/topic &&
diff --git a/t/t5702-protocol-v2.sh b/t/t5702-protocol-v2.sh
index 3c0c6047d5..6ef4971845 100755
--- a/t/t5702-protocol-v2.sh
+++ b/t/t5702-protocol-v2.sh
@@ -221,7 +221,9 @@ test_expect_success 'clone of empty repo propagates name of default branch' '
 	GIT_TEST_DEFAULT_INITIAL_BRANCH_NAME= \
 	git -c init.defaultBranch=main -c protocol.version=2 \
 		clone "file://$(pwd)/file_empty_parent" file_empty_child &&
-	grep "refs/heads/mydefaultbranch" file_empty_child/.git/HEAD
+	echo refs/heads/mydefaultbranch >expect &&
+	git -C file_empty_child symbolic-ref HEAD >actual &&
+	test_cmp expect actual
 '
 
 test_expect_success '...but not if explicitly forbidden by config' '
@@ -234,7 +236,9 @@ test_expect_success '...but not if explicitly forbidden by config' '
 	GIT_TEST_DEFAULT_INITIAL_BRANCH_NAME= \
 	git -c init.defaultBranch=main -c protocol.version=2 \
 		clone "file://$(pwd)/file_empty_parent" file_empty_child &&
-	! grep "refs/heads/mydefaultbranch" file_empty_child/.git/HEAD
+	echo refs/heads/main >expect &&
+	git -C file_empty_child symbolic-ref HEAD >actual &&
+	test_cmp expect actual
 '
 
 test_expect_success 'bare clone propagates empty default branch' '
@@ -247,7 +251,9 @@ test_expect_success 'bare clone propagates empty default branch' '
 	git -c init.defaultBranch=main -c protocol.version=2 \
 		clone --bare \
 		"file://$(pwd)/file_empty_parent" file_empty_child.git &&
-	grep "refs/heads/mydefaultbranch" file_empty_child.git/HEAD
+	echo "refs/heads/mydefaultbranch" >expect &&
+	git -C file_empty_child.git symbolic-ref HEAD >actual &&
+	test_cmp expect actual
 '
 
 test_expect_success 'clone propagates unborn HEAD from non-empty repo' '
@@ -265,7 +271,9 @@ test_expect_success 'clone propagates unborn HEAD from non-empty repo' '
 	git -c init.defaultBranch=main -c protocol.version=2 \
 		clone "file://$(pwd)/file_unborn_parent" \
 		file_unborn_child 2>stderr &&
-	grep "refs/heads/mydefaultbranch" file_unborn_child/.git/HEAD &&
+	echo "refs/heads/mydefaultbranch" >expect &&
+	git -C file_unborn_child symbolic-ref HEAD >actual &&
+	test_cmp expect actual &&
 	grep "warning: remote HEAD refers to nonexistent ref" stderr
 '
 
@@ -295,7 +303,9 @@ test_expect_success 'bare clone propagates unborn HEAD from non-empty repo' '
 	git -c init.defaultBranch=main -c protocol.version=2 \
 		clone --bare "file://$(pwd)/file_unborn_parent" \
 		file_unborn_child.git 2>stderr &&
-	grep "refs/heads/mydefaultbranch" file_unborn_child.git/HEAD &&
+	echo "refs/heads/mydefaultbranch" >expect &&
+	git -C file_unborn_child.git symbolic-ref HEAD >actual &&
+	test_cmp expect actual &&
 	! grep "warning:" stderr
 '
 
@@ -315,7 +325,9 @@ test_expect_success 'defaulted HEAD uses remote branch if available' '
 	git -c init.defaultBranch=branchwithstuff -c protocol.version=2 \
 		clone "file://$(pwd)/file_unborn_parent" \
 		file_unborn_child 2>stderr &&
-	grep "refs/heads/branchwithstuff" file_unborn_child/.git/HEAD &&
+	echo "refs/heads/branchwithstuff" >expect &&
+	git -C file_unborn_child symbolic-ref HEAD >actual &&
+	test_cmp expect actual &&
 	test_path_is_file file_unborn_child/stuff.t &&
 	! grep "warning:" stderr
 '
diff --git a/t/t7300-clean.sh b/t/t7300-clean.sh
index 1a310a45fd..611b3dd3ae 100755
--- a/t/t7300-clean.sh
+++ b/t/t7300-clean.sh
@@ -517,8 +517,12 @@ test_expect_success 'nested (empty) git should be kept' '
 	git init empty_repo &&
 	mkdir to_clean &&
 	>to_clean/should_clean.this &&
+	# Note that we put the expect file in the .git directory so that it
+	# does not get cleaned.
+	find empty_repo | sort >.git/expect &&
 	git clean -f -d &&
-	test_path_is_file empty_repo/.git/HEAD &&
+	find empty_repo | sort >actual &&
+	test_cmp .git/expect actual &&
 	test_path_is_missing to_clean
 '
 
@@ -559,10 +563,10 @@ test_expect_success 'giving path in nested git work tree will NOT remove it' '
 		mkdir -p bar/baz &&
 		test_commit msg bar/baz/hello.world
 	) &&
+	find repo | sort >expect &&
 	git clean -f -d repo/bar/baz &&
-	test_path_is_file repo/.git/HEAD &&
-	test_path_is_dir repo/bar/ &&
-	test_path_is_file repo/bar/baz/hello.world
+	find repo | sort >actual &&
+	test_cmp expect actual
 '
 
 test_expect_success 'giving path to nested .git will not remove it' '
@@ -573,10 +577,10 @@ test_expect_success 'giving path to nested .git will not remove it' '
 		git init &&
 		test_commit msg hello.world
 	) &&
+	find repo | sort >expect &&
 	git clean -f -d repo/.git &&
-	test_path_is_file repo/.git/HEAD &&
-	test_path_is_dir repo/.git/refs &&
-	test_path_is_dir repo/.git/objects &&
+	find repo | sort >actual &&
+	test_cmp expect actual &&
 	test_path_is_dir untracked/
 '
 
@@ -588,9 +592,10 @@ test_expect_success 'giving path to nested .git/ will NOT remove contents' '
 		git init &&
 		test_commit msg hello.world
 	) &&
+	find repo | sort >expect &&
 	git clean -f -d repo/.git/ &&
-	test_path_is_dir repo/.git &&
-	test_path_is_file repo/.git/HEAD &&
+	find repo | sort >actual &&
+	test_cmp expect actual &&
 	test_path_is_dir untracked/
 '
 
diff --git a/t/t7900-maintenance.sh b/t/t7900-maintenance.sh
index 935df6a1db..00d29871e6 100755
--- a/t/t7900-maintenance.sh
+++ b/t/t7900-maintenance.sh
@@ -157,7 +157,8 @@ test_expect_success 'prefetch multiple remotes' '
 	fetchargs="--prefetch --prune --no-tags --no-write-fetch-head --recurse-submodules=no --quiet" &&
 	test_subcommand git fetch remote1 $fetchargs <run-prefetch.txt &&
 	test_subcommand git fetch remote2 $fetchargs <run-prefetch.txt &&
-	test_path_is_missing .git/refs/remotes &&
+	git for-each-ref refs/remotes >actual &&
+	test_must_be_empty actual &&
 	git log prefetch/remotes/remote1/one &&
 	git log prefetch/remotes/remote2/two &&
 	git fetch --all &&
diff --git a/t/t9133-git-svn-nested-git-repo.sh b/t/t9133-git-svn-nested-git-repo.sh
index d8d536269c..8ca24670ac 100755
--- a/t/t9133-git-svn-nested-git-repo.sh
+++ b/t/t9133-git-svn-nested-git-repo.sh
@@ -11,7 +11,7 @@ test_expect_success 'setup repo with a git repo inside it' '
 	(
 		cd s &&
 		git init &&
-		test -f .git/HEAD &&
+		git symbolic-ref HEAD &&
 		> .git/a &&
 		echo a > a &&
 		svn_cmd add .git a &&