diff --git a/t/lib-t6000.sh b/t/lib-t6000.sh
index 3f2d873fec9ed9e98b787cd708cd9e8e816e7573..b0ed4767e320e200c592e979dce0fa1e4cfd6ede 100644
--- a/t/lib-t6000.sh
+++ b/t/lib-t6000.sh
@@ -4,11 +4,11 @@ mkdir -p .git/refs/tags
 
 >sed.script
 
-# Answer the sha1 has associated with the tag. The tag must exist in .git/refs/tags
+# Answer the sha1 has associated with the tag. The tag must exist under refs/tags
 tag () {
 	_tag=$1
-	test -f ".git/refs/tags/$_tag" || error "tag: \"$_tag\" does not exist"
-	cat ".git/refs/tags/$_tag"
+	git rev-parse --verify "refs/tags/$_tag" ||
+	error "tag: \"$_tag\" does not exist"
 }
 
 # Generate a commit using the text specified to make it unique and the tree
diff --git a/t/t1401-symbolic-ref.sh b/t/t1401-symbolic-ref.sh
index 9e782a8122f84939156e2bb4e0f871d86399f938..a4ebb0b65fecfada915209cfbc994a1b8ddce439 100755
--- a/t/t1401-symbolic-ref.sh
+++ b/t/t1401-symbolic-ref.sh
@@ -65,7 +65,7 @@ reset_to_sane
 test_expect_success 'symbolic-ref fails to delete real ref' '
 	echo "fatal: Cannot delete refs/heads/foo, not a symbolic ref" >expect &&
 	test_must_fail git symbolic-ref -d refs/heads/foo >actual 2>&1 &&
-	test_path_is_file .git/refs/heads/foo &&
+	git rev-parse --verify refs/heads/foo &&
 	test_cmp expect actual
 '
 reset_to_sane
diff --git a/t/t3200-branch.sh b/t/t3200-branch.sh
index 6c0b7ea4addc8f1569b1b85f58dd3072fb863f33..1038c7e99bc002992a6972bc569c49f7c8883e7a 100755
--- a/t/t3200-branch.sh
+++ b/t/t3200-branch.sh
@@ -233,34 +233,34 @@ test_expect_success 'git branch -M master2 master2 should work when master is ch
 
 test_expect_success 'git branch -v -d t should work' '
 	git branch t &&
-	test_path_is_file .git/refs/heads/t &&
+	git rev-parse --verify refs/heads/t &&
 	git branch -v -d t &&
-	test_path_is_missing .git/refs/heads/t
+	test_must_fail git rev-parse --verify refs/heads/t
 '
 
 test_expect_success 'git branch -v -m t s should work' '
 	git branch t &&
-	test_path_is_file .git/refs/heads/t &&
+	git rev-parse --verify refs/heads/t &&
 	git branch -v -m t s &&
-	test_path_is_missing .git/refs/heads/t &&
-	test_path_is_file .git/refs/heads/s &&
+	test_must_fail git rev-parse --verify refs/heads/t &&
+	git rev-parse --verify refs/heads/s &&
 	git branch -d s
 '
 
 test_expect_success 'git branch -m -d t s should fail' '
 	git branch t &&
-	test_path_is_file .git/refs/heads/t &&
+	git rev-parse refs/heads/t &&
 	test_must_fail git branch -m -d t s &&
 	git branch -d t &&
-	test_path_is_missing .git/refs/heads/t
+	test_must_fail git rev-parse refs/heads/t
 '
 
 test_expect_success 'git branch --list -d t should fail' '
 	git branch t &&
-	test_path_is_file .git/refs/heads/t &&
+	git rev-parse refs/heads/t &&
 	test_must_fail git branch --list -d t &&
 	git branch -d t &&
-	test_path_is_missing .git/refs/heads/t
+	test_must_fail git rev-parse refs/heads/t
 '
 
 test_expect_success 'git branch --list -v with --abbrev' '
diff --git a/t/t3903-stash.sh b/t/t3903-stash.sh
index aefde7b1726bdc8d71d2b78e313e29daa2b31a24..1f871d3cca9aba4dcb32b5197b9b3d296fc5c1fa 100755
--- a/t/t3903-stash.sh
+++ b/t/t3903-stash.sh
@@ -726,7 +726,7 @@ test_expect_success 'store updates stash ref and reflog' '
 	git reset --hard &&
 	! grep quux bazzy &&
 	git stash store -m quuxery $STASH_ID &&
-	test $(cat .git/refs/stash) = $STASH_ID &&
+	test $(git rev-parse stash) = $STASH_ID &&
 	git reflog --format=%H stash| grep $STASH_ID &&
 	git stash pop &&
 	grep quux bazzy
diff --git a/t/t5500-fetch-pack.sh b/t/t5500-fetch-pack.sh
index 0680dec808574fb334612163ebd43d31418a37d5..d4f435155f5c9350f196904b910e2b5466c3ffd6 100755
--- a/t/t5500-fetch-pack.sh
+++ b/t/t5500-fetch-pack.sh
@@ -30,7 +30,7 @@ add () {
 	test_tick &&
 	commit=$(echo "$text" | git commit-tree $tree $parents) &&
 	eval "$name=$commit; export $name" &&
-	echo $commit > .git/refs/heads/$branch &&
+	git update-ref "refs/heads/$branch" "$commit" &&
 	eval ${branch}TIP=$commit
 }
 
@@ -45,10 +45,10 @@ pull_to_client () {
 
 			case "$heads" in
 			    *A*)
-				    echo $ATIP > .git/refs/heads/A;;
+				    git update-ref refs/heads/A "$ATIP";;
 			esac &&
 			case "$heads" in *B*)
-			    echo $BTIP > .git/refs/heads/B;;
+			    git update-ref refs/heads/B "$BTIP";;
 			esac &&
 			git symbolic-ref HEAD refs/heads/$(echo $heads \
 				| sed -e "s/^\(.\).*$/\1/") &&
@@ -92,8 +92,8 @@ test_expect_success 'setup' '
 		cur=$(($cur+1))
 	done &&
 	add B1 $A1 &&
-	echo $ATIP > .git/refs/heads/A &&
-	echo $BTIP > .git/refs/heads/B &&
+	git update-ref refs/heads/A "$ATIP" &&
+	git update-ref refs/heads/B "$BTIP" &&
 	git symbolic-ref HEAD refs/heads/B
 '
 
diff --git a/t/t5510-fetch.sh b/t/t5510-fetch.sh
index da9ac0055721237f177d3d475e56ddb38b25eff1..ea0f57354eb923757fb0965343c6532142d4c167 100755
--- a/t/t5510-fetch.sh
+++ b/t/t5510-fetch.sh
@@ -63,7 +63,7 @@ test_expect_success "fetch test" '
 	git commit -a -m "updated by origin" &&
 	cd two &&
 	git fetch &&
-	test -f .git/refs/heads/one &&
+	git rev-parse --verify refs/heads/one &&
 	mine=$(git rev-parse refs/heads/one) &&
 	his=$(cd ../one && git rev-parse refs/heads/master) &&
 	test "z$mine" = "z$his"
@@ -73,8 +73,8 @@ test_expect_success "fetch test for-merge" '
 	cd "$D" &&
 	cd three &&
 	git fetch &&
-	test -f .git/refs/heads/two &&
-	test -f .git/refs/heads/one &&
+	git rev-parse --verify refs/heads/two &&
+	git rev-parse --verify refs/heads/one &&
 	master_in_two=$(cd ../two && git rev-parse master) &&
 	one_in_two=$(cd ../two && git rev-parse one) &&
 	{
diff --git a/t/t6010-merge-base.sh b/t/t6010-merge-base.sh
index 31db7b5f9125ed346450d7bfe29d8bb5fac0460a..aa2d360ce35940a176a0ef04ca7ba8560adefb23 100755
--- a/t/t6010-merge-base.sh
+++ b/t/t6010-merge-base.sh
@@ -34,7 +34,7 @@ doit () {
 
 	commit=$(echo $NAME | git commit-tree $T $PARENTS) &&
 
-	echo $commit >.git/refs/tags/$NAME &&
+	git update-ref "refs/tags/$NAME" "$commit" &&
 	echo $commit
 }
 
diff --git a/t/t7201-co.sh b/t/t7201-co.sh
index 76c223c9675cd1531ac078fa9e0c1f8cc4e09781..ab9da61da391f1b6040076dda2454f602adef7d2 100755
--- a/t/t7201-co.sh
+++ b/t/t7201-co.sh
@@ -65,7 +65,7 @@ test_expect_success setup '
 test_expect_success "checkout from non-existing branch" '
 
 	git checkout -b delete-me master &&
-	rm .git/refs/heads/delete-me &&
+	git update-ref -d --no-deref refs/heads/delete-me &&
 	test refs/heads/delete-me = "$(git symbolic-ref HEAD)" &&
 	git checkout master &&
 	test refs/heads/master = "$(git symbolic-ref HEAD)"
diff --git a/t/t9104-git-svn-follow-parent.sh b/t/t9104-git-svn-follow-parent.sh
index cd480edf1606fda8d973ee3decb8e18e03356153..0c9c8f9f031f3e6561a3b962f77ef6041f1593c8 100755
--- a/t/t9104-git-svn-follow-parent.sh
+++ b/t/t9104-git-svn-follow-parent.sh
@@ -213,7 +213,8 @@ test_expect_success "multi-fetch continues to work" "
 	"
 
 test_expect_success "multi-fetch works off a 'clean' repository" '
-	rm -r "$GIT_DIR/svn" "$GIT_DIR/refs/remotes" "$GIT_DIR/logs" &&
+	rm -rf "$GIT_DIR/svn" "$GIT_DIR/refs/remotes" &&
+	git reflog expire --all --expire=all &&
 	mkdir "$GIT_DIR/svn" &&
 	git svn multi-fetch
 	'