diff --git a/file1.zarr/.zattrs b/file1.zarr/.zattrs
deleted file mode 100644
index 55b5cdc4..00000000
--- a/file1.zarr/.zattrs
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    ".specloc": "specifications",
-    "data_type": "FooFile",
-    "namespace": "test_core",
-    "object_id": "660f1c92-d141-40d2-995f-2bb46c87c017"
-}
\ No newline at end of file
diff --git a/file1.zarr/.zgroup b/file1.zarr/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file1.zarr/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file1.zarr/.zmetadata b/file1.zarr/.zmetadata
deleted file mode 100644
index 8322dda9..00000000
--- a/file1.zarr/.zmetadata
+++ /dev/null
@@ -1,64 +0,0 @@
-{
-    "metadata": {
-        ".zattrs": {
-            "data_type": "FooFile",
-            "namespace": "test_core",
-            "object_id": "660f1c92-d141-40d2-995f-2bb46c87c017"
-        },
-        ".zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/.zattrs": {
-            "data_type": "FooBucket",
-            "namespace": "test_core",
-            "object_id": "7c5adf36-8f84-4f63-a948-75f18dade974"
-        },
-        "buckets/bucket1/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/foo1/.zattrs": {
-            "attr1": "I am foo1",
-            "attr3": 3.14,
-            "data_type": "Foo",
-            "namespace": "test_core",
-            "object_id": "9b3a0668-f73c-4a00-b446-38888c16e551"
-        },
-        "buckets/bucket1/foo_holder/foo1/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/foo1/my_data/.zarray": {
-            "chunks": [
-                5
-            ],
-            "compressor": {
-                "blocksize": 0,
-                "clevel": 5,
-                "cname": "lz4",
-                "id": "blosc",
-                "shuffle": 1
-            },
-            "dtype": "<i8",
-            "fill_value": 0,
-            "filters": null,
-            "order": "C",
-            "shape": [
-                5
-            ],
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/foo1/my_data/.zattrs": {
-            "attr2": 17,
-            "zarr_dtype": "int64"
-        },
-        "links/.zgroup": {
-            "zarr_format": 2
-        }
-    },
-    "zarr_consolidated_format": 1
-}
\ No newline at end of file
diff --git a/file1.zarr/buckets/.zgroup b/file1.zarr/buckets/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file1.zarr/buckets/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/.zattrs b/file1.zarr/buckets/bucket1/.zattrs
deleted file mode 100644
index e6bcc4fb..00000000
--- a/file1.zarr/buckets/bucket1/.zattrs
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-    "data_type": "FooBucket",
-    "namespace": "test_core",
-    "object_id": "7c5adf36-8f84-4f63-a948-75f18dade974"
-}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/.zgroup b/file1.zarr/buckets/bucket1/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file1.zarr/buckets/bucket1/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/foo_holder/.zgroup b/file1.zarr/buckets/bucket1/foo_holder/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file1.zarr/buckets/bucket1/foo_holder/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/foo_holder/foo1/.zattrs b/file1.zarr/buckets/bucket1/foo_holder/foo1/.zattrs
deleted file mode 100644
index 5ef83bbf..00000000
--- a/file1.zarr/buckets/bucket1/foo_holder/foo1/.zattrs
+++ /dev/null
@@ -1,7 +0,0 @@
-{
-    "attr1": "I am foo1",
-    "attr3": 3.14,
-    "data_type": "Foo",
-    "namespace": "test_core",
-    "object_id": "9b3a0668-f73c-4a00-b446-38888c16e551"
-}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/foo_holder/foo1/.zgroup b/file1.zarr/buckets/bucket1/foo_holder/foo1/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file1.zarr/buckets/bucket1/foo_holder/foo1/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray b/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray
deleted file mode 100644
index 2da665c3..00000000
--- a/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray
+++ /dev/null
@@ -1,20 +0,0 @@
-{
-    "chunks": [
-        5
-    ],
-    "compressor": {
-        "blocksize": 0,
-        "clevel": 5,
-        "cname": "lz4",
-        "id": "blosc",
-        "shuffle": 1
-    },
-    "dtype": "<i8",
-    "fill_value": 0,
-    "filters": null,
-    "order": "C",
-    "shape": [
-        5
-    ],
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs b/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs
deleted file mode 100644
index 2ad81eb6..00000000
--- a/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-    "attr2": 17,
-    "zarr_dtype": "int64"
-}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/0 b/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/0
deleted file mode 100644
index b049d36c..00000000
Binary files a/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/0 and /dev/null differ
diff --git a/file1.zarr/links/.zgroup b/file1.zarr/links/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file1.zarr/links/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file1.zarr/specifications/.zgroup b/file1.zarr/specifications/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file1.zarr/specifications/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/.zgroup b/file1.zarr/specifications/test_core/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file1.zarr/specifications/test_core/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/0.1.0/.zgroup b/file1.zarr/specifications/test_core/0.1.0/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file1.zarr/specifications/test_core/0.1.0/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/0.1.0/namespace/.zarray b/file1.zarr/specifications/test_core/0.1.0/namespace/.zarray
deleted file mode 100644
index 7d100603..00000000
--- a/file1.zarr/specifications/test_core/0.1.0/namespace/.zarray
+++ /dev/null
@@ -1,30 +0,0 @@
-{
-    "chunks": [
-        1
-    ],
-    "compressor": null,
-    "dtype": "|O",
-    "fill_value": 0,
-    "filters": [
-        {
-            "allow_nan": true,
-            "check_circular": true,
-            "encoding": "utf-8",
-            "ensure_ascii": true,
-            "id": "json2",
-            "indent": null,
-            "separators": [
-                ",",
-                ":"
-            ],
-            "skipkeys": false,
-            "sort_keys": true,
-            "strict": true
-        }
-    ],
-    "order": "C",
-    "shape": [
-        1
-    ],
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/0.1.0/namespace/.zattrs b/file1.zarr/specifications/test_core/0.1.0/namespace/.zattrs
deleted file mode 100644
index 2592fe05..00000000
--- a/file1.zarr/specifications/test_core/0.1.0/namespace/.zattrs
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_dtype": "scalar"
-}
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/0.1.0/namespace/0 b/file1.zarr/specifications/test_core/0.1.0/namespace/0
deleted file mode 100644
index 357971a8..00000000
--- a/file1.zarr/specifications/test_core/0.1.0/namespace/0
+++ /dev/null
@@ -1 +0,0 @@
-["{\"namespaces\":[{\"doc\":\"a test namespace\",\"schema\":[{\"source\":\"test\"}],\"name\":\"test_core\",\"version\":\"0.1.0\"}]}","|O",[1]]
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/0.1.0/test/.zarray b/file1.zarr/specifications/test_core/0.1.0/test/.zarray
deleted file mode 100644
index 7d100603..00000000
--- a/file1.zarr/specifications/test_core/0.1.0/test/.zarray
+++ /dev/null
@@ -1,30 +0,0 @@
-{
-    "chunks": [
-        1
-    ],
-    "compressor": null,
-    "dtype": "|O",
-    "fill_value": 0,
-    "filters": [
-        {
-            "allow_nan": true,
-            "check_circular": true,
-            "encoding": "utf-8",
-            "ensure_ascii": true,
-            "id": "json2",
-            "indent": null,
-            "separators": [
-                ",",
-                ":"
-            ],
-            "skipkeys": false,
-            "sort_keys": true,
-            "strict": true
-        }
-    ],
-    "order": "C",
-    "shape": [
-        1
-    ],
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/0.1.0/test/.zattrs b/file1.zarr/specifications/test_core/0.1.0/test/.zattrs
deleted file mode 100644
index 2592fe05..00000000
--- a/file1.zarr/specifications/test_core/0.1.0/test/.zattrs
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_dtype": "scalar"
-}
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/0.1.0/test/0 b/file1.zarr/specifications/test_core/0.1.0/test/0
deleted file mode 100644
index 75e3042c..00000000
--- a/file1.zarr/specifications/test_core/0.1.0/test/0
+++ /dev/null
@@ -1 +0,0 @@
-["{\"groups\":[{\"datasets\":[{\"dtype\":\"int\",\"doc\":\"an example dataset\",\"name\":\"my_data\",\"attributes\":[{\"doc\":\"an example integer attribute\",\"name\":\"attr2\",\"dtype\":\"int\"}]}],\"doc\":\"A test group specification with a data type\",\"data_type_def\":\"Foo\",\"attributes\":[{\"doc\":\"an example string attribute\",\"name\":\"attr1\",\"dtype\":\"text\"},{\"doc\":\"an example float attribute\",\"name\":\"attr3\",\"dtype\":\"float\"}]},{\"groups\":[{\"groups\":[{\"doc\":\"the Foos in this bucket\",\"quantity\":\"*\",\"data_type_inc\":\"Foo\"}],\"doc\":\"A subgroup for Foos\",\"name\":\"foo_holder\"}],\"doc\":\"A test group specification for a data type containing data type\",\"data_type_def\":\"FooBucket\"},{\"groups\":[{\"groups\":[{\"doc\":\"One or more FooBuckets\",\"quantity\":\"*\",\"data_type_inc\":\"FooBucket\"}],\"doc\":\"Holds the FooBuckets\",\"name\":\"buckets\"},{\"links\":[{\"doc\":\"Foo link\",\"name\":\"foo_link\",\"target_type\":\"Foo\",\"quantity\":\"?\"}],\"doc\":\"Foo link group\",\"name\":\"links\"}],\"datasets\":[{\"dtype\":\"int\",\"doc\":\"Foo data\",\"name\":\"foofile_data\",\"quantity\":\"?\"}],\"doc\":\"A file of Foos contained in FooBuckets\",\"data_type_def\":\"FooFile\",\"attributes\":[{\"doc\":\"Foo ref attr\",\"name\":\"foo_ref_attr\",\"required\":false,\"dtype\":{\"target_type\":\"Foo\",\"reftype\":\"object\"}}]}]}","|O",[1]]
\ No newline at end of file
diff --git a/file2.zarr/.zattrs b/file2.zarr/.zattrs
deleted file mode 100644
index 757048d7..00000000
--- a/file2.zarr/.zattrs
+++ /dev/null
@@ -1,22 +0,0 @@
-{
-    ".specloc": "specifications",
-    "data_type": "FooFile",
-    "foo_ref_attr": {
-        "value": {
-            "object_id": "2a36d892-ab46-4b0c-bd6b-31ce6533d071",
-            "path": "/buckets/bucket2/foo_holder/foo2",
-            "source": "file2.zarr",
-            "source_object_id": "660f1c92-d141-40d2-995f-2bb46c87c017"
-        },
-        "zarr_dtype": "object"
-    },
-    "namespace": "test_core",
-    "object_id": "660f1c92-d141-40d2-995f-2bb46c87c017",
-    "zarr_link": [
-        {
-            "name": "foofile_data",
-            "path": "/buckets/bucket1/foo_holder/foo1/my_data",
-            "source": "file2.zarr"
-        }
-    ]
-}
\ No newline at end of file
diff --git a/file2.zarr/.zgroup b/file2.zarr/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file2.zarr/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file2.zarr/.zmetadata b/file2.zarr/.zmetadata
deleted file mode 100644
index b1c6c142..00000000
--- a/file2.zarr/.zmetadata
+++ /dev/null
@@ -1,117 +0,0 @@
-{
-    "metadata": {
-        ".zattrs": {
-            "data_type": "FooFile",
-            "foo_ref_attr": {
-                "value": {
-                    "object_id": "2a36d892-ab46-4b0c-bd6b-31ce6533d071",
-                    "path": "/buckets/bucket2/foo_holder/foo2",
-                    "source": "file2.zarr",
-                    "source_object_id": "660f1c92-d141-40d2-995f-2bb46c87c017"
-                },
-                "zarr_dtype": "object"
-            },
-            "namespace": "test_core",
-            "object_id": "660f1c92-d141-40d2-995f-2bb46c87c017",
-            "zarr_link": [
-                {
-                    "name": "foofile_data",
-                    "path": "/buckets/bucket1/foo_holder/foo1/my_data",
-                    "source": "file2.zarr"
-                }
-            ]
-        },
-        ".zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/.zattrs": {
-            "data_type": "FooBucket",
-            "namespace": "test_core",
-            "object_id": "7c5adf36-8f84-4f63-a948-75f18dade974"
-        },
-        "buckets/bucket1/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/foo1/.zattrs": {
-            "attr1": "I am foo1",
-            "attr3": 3.14,
-            "data_type": "Foo",
-            "namespace": "test_core",
-            "object_id": "9b3a0668-f73c-4a00-b446-38888c16e551"
-        },
-        "buckets/bucket1/foo_holder/foo1/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/foo1/my_data/.zarray": {
-            "chunks": [
-                5
-            ],
-            "compressor": {
-                "blocksize": 0,
-                "clevel": 5,
-                "cname": "lz4",
-                "id": "blosc",
-                "shuffle": 1
-            },
-            "dtype": "<i8",
-            "fill_value": 0,
-            "filters": null,
-            "order": "C",
-            "shape": [
-                5
-            ],
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/foo1/my_data/.zattrs": {
-            "attr2": 17,
-            "zarr_dtype": "int64"
-        },
-        "buckets/bucket2/.zattrs": {
-            "data_type": "FooBucket",
-            "namespace": "test_core",
-            "object_id": "e60cc181-8b03-43d7-9c63-96a7c2b672e6"
-        },
-        "buckets/bucket2/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket2/foo_holder/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket2/foo_holder/foo2/.zattrs": {
-            "attr1": "I am foo2",
-            "attr3": 3.14,
-            "data_type": "Foo",
-            "namespace": "test_core",
-            "object_id": "2a36d892-ab46-4b0c-bd6b-31ce6533d071",
-            "zarr_link": [
-                {
-                    "name": "my_data",
-                    "path": "/buckets/bucket1/foo_holder/foo1/my_data",
-                    "source": "file2.zarr"
-                }
-            ]
-        },
-        "buckets/bucket2/foo_holder/foo2/.zgroup": {
-            "zarr_format": 2
-        },
-        "links/.zattrs": {
-            "zarr_link": [
-                {
-                    "name": "foo_link",
-                    "path": "/buckets/bucket2/foo_holder/foo2",
-                    "source": "file2.zarr"
-                }
-            ]
-        },
-        "links/.zgroup": {
-            "zarr_format": 2
-        }
-    },
-    "zarr_consolidated_format": 1
-}
\ No newline at end of file
diff --git a/file2.zarr/buckets/.zgroup b/file2.zarr/buckets/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file2.zarr/buckets/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/.zattrs b/file2.zarr/buckets/bucket1/.zattrs
deleted file mode 100644
index e6bcc4fb..00000000
--- a/file2.zarr/buckets/bucket1/.zattrs
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-    "data_type": "FooBucket",
-    "namespace": "test_core",
-    "object_id": "7c5adf36-8f84-4f63-a948-75f18dade974"
-}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/.zgroup b/file2.zarr/buckets/bucket1/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file2.zarr/buckets/bucket1/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/foo_holder/.zgroup b/file2.zarr/buckets/bucket1/foo_holder/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file2.zarr/buckets/bucket1/foo_holder/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/foo_holder/foo1/.zattrs b/file2.zarr/buckets/bucket1/foo_holder/foo1/.zattrs
deleted file mode 100644
index 5ef83bbf..00000000
--- a/file2.zarr/buckets/bucket1/foo_holder/foo1/.zattrs
+++ /dev/null
@@ -1,7 +0,0 @@
-{
-    "attr1": "I am foo1",
-    "attr3": 3.14,
-    "data_type": "Foo",
-    "namespace": "test_core",
-    "object_id": "9b3a0668-f73c-4a00-b446-38888c16e551"
-}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/foo_holder/foo1/.zgroup b/file2.zarr/buckets/bucket1/foo_holder/foo1/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file2.zarr/buckets/bucket1/foo_holder/foo1/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray b/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray
deleted file mode 100644
index 2da665c3..00000000
--- a/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray
+++ /dev/null
@@ -1,20 +0,0 @@
-{
-    "chunks": [
-        5
-    ],
-    "compressor": {
-        "blocksize": 0,
-        "clevel": 5,
-        "cname": "lz4",
-        "id": "blosc",
-        "shuffle": 1
-    },
-    "dtype": "<i8",
-    "fill_value": 0,
-    "filters": null,
-    "order": "C",
-    "shape": [
-        5
-    ],
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs b/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs
deleted file mode 100644
index 2ad81eb6..00000000
--- a/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-    "attr2": 17,
-    "zarr_dtype": "int64"
-}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/0 b/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/0
deleted file mode 100644
index b049d36c..00000000
Binary files a/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/0 and /dev/null differ
diff --git a/file2.zarr/buckets/bucket2/.zattrs b/file2.zarr/buckets/bucket2/.zattrs
deleted file mode 100644
index 0dfbf840..00000000
--- a/file2.zarr/buckets/bucket2/.zattrs
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-    "data_type": "FooBucket",
-    "namespace": "test_core",
-    "object_id": "e60cc181-8b03-43d7-9c63-96a7c2b672e6"
-}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket2/.zgroup b/file2.zarr/buckets/bucket2/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file2.zarr/buckets/bucket2/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket2/foo_holder/.zgroup b/file2.zarr/buckets/bucket2/foo_holder/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file2.zarr/buckets/bucket2/foo_holder/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs b/file2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
deleted file mode 100644
index f45aeaf2..00000000
--- a/file2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
+++ /dev/null
@@ -1,14 +0,0 @@
-{
-    "attr1": "I am foo2",
-    "attr3": 3.14,
-    "data_type": "Foo",
-    "namespace": "test_core",
-    "object_id": "2a36d892-ab46-4b0c-bd6b-31ce6533d071",
-    "zarr_link": [
-        {
-            "name": "my_data",
-            "path": "/buckets/bucket1/foo_holder/foo1/my_data",
-            "source": "file2.zarr"
-        }
-    ]
-}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket2/foo_holder/foo2/.zgroup b/file2.zarr/buckets/bucket2/foo_holder/foo2/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file2.zarr/buckets/bucket2/foo_holder/foo2/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file2.zarr/links/.zattrs b/file2.zarr/links/.zattrs
deleted file mode 100644
index 768e3287..00000000
--- a/file2.zarr/links/.zattrs
+++ /dev/null
@@ -1,9 +0,0 @@
-{
-    "zarr_link": [
-        {
-            "name": "foo_link",
-            "path": "/buckets/bucket2/foo_holder/foo2",
-            "source": "file2.zarr"
-        }
-    ]
-}
\ No newline at end of file
diff --git a/file2.zarr/links/.zgroup b/file2.zarr/links/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file2.zarr/links/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/file2.zarr/specifications/.zgroup b/file2.zarr/specifications/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/file2.zarr/specifications/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/src/hdmf_zarr/backend.py b/src/hdmf_zarr/backend.py
index 669246b3..46fa96ad 100644
--- a/src/hdmf_zarr/backend.py
+++ b/src/hdmf_zarr/backend.py
@@ -804,11 +804,9 @@ def _create_ref(self, ref_object, export_source=None):
                       if (builder.source is not None and os.path.isdir(builder.source))
                       else self.source)
         else:
-            # breakpoint()
             source = export_source
 
         source = os.path.relpath(source)
-        # breakpoint()
         # Return the ZarrReference object
         ref = ZarrReference(
             source=source,
diff --git a/test_io0.zarr/.zattrs b/test_io0.zarr/.zattrs
deleted file mode 100644
index 5886527c..00000000
--- a/test_io0.zarr/.zattrs
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    ".specloc": "specifications",
-    "data_type": "FooFile",
-    "namespace": "test_core",
-    "object_id": "0b75428d-4633-4b56-bb99-181980f78a36"
-}
\ No newline at end of file
diff --git a/test_io0.zarr/.zgroup b/test_io0.zarr/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io0.zarr/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io0.zarr/.zmetadata b/test_io0.zarr/.zmetadata
deleted file mode 100644
index 7db53824..00000000
--- a/test_io0.zarr/.zmetadata
+++ /dev/null
@@ -1,64 +0,0 @@
-{
-    "metadata": {
-        ".zattrs": {
-            "data_type": "FooFile",
-            "namespace": "test_core",
-            "object_id": "0b75428d-4633-4b56-bb99-181980f78a36"
-        },
-        ".zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/.zattrs": {
-            "data_type": "FooBucket",
-            "namespace": "test_core",
-            "object_id": "f772256b-00ee-4b8d-8939-2c143b31c6d9"
-        },
-        "buckets/bucket1/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/foo1/.zattrs": {
-            "attr1": "I am foo1",
-            "attr3": 3.14,
-            "data_type": "Foo",
-            "namespace": "test_core",
-            "object_id": "294d04fc-ba6b-49c2-8718-4e26a590932d"
-        },
-        "buckets/bucket1/foo_holder/foo1/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/foo1/my_data/.zarray": {
-            "chunks": [
-                5
-            ],
-            "compressor": {
-                "blocksize": 0,
-                "clevel": 5,
-                "cname": "lz4",
-                "id": "blosc",
-                "shuffle": 1
-            },
-            "dtype": "<i8",
-            "fill_value": 0,
-            "filters": null,
-            "order": "C",
-            "shape": [
-                5
-            ],
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/foo1/my_data/.zattrs": {
-            "attr2": 17,
-            "zarr_dtype": "int64"
-        },
-        "links/.zgroup": {
-            "zarr_format": 2
-        }
-    },
-    "zarr_consolidated_format": 1
-}
\ No newline at end of file
diff --git a/test_io0.zarr/buckets/.zgroup b/test_io0.zarr/buckets/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io0.zarr/buckets/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io0.zarr/buckets/bucket1/.zattrs b/test_io0.zarr/buckets/bucket1/.zattrs
deleted file mode 100644
index 88f4e99a..00000000
--- a/test_io0.zarr/buckets/bucket1/.zattrs
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-    "data_type": "FooBucket",
-    "namespace": "test_core",
-    "object_id": "f772256b-00ee-4b8d-8939-2c143b31c6d9"
-}
\ No newline at end of file
diff --git a/test_io0.zarr/buckets/bucket1/.zgroup b/test_io0.zarr/buckets/bucket1/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io0.zarr/buckets/bucket1/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io0.zarr/buckets/bucket1/foo_holder/.zgroup b/test_io0.zarr/buckets/bucket1/foo_holder/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io0.zarr/buckets/bucket1/foo_holder/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io0.zarr/buckets/bucket1/foo_holder/foo1/.zattrs b/test_io0.zarr/buckets/bucket1/foo_holder/foo1/.zattrs
deleted file mode 100644
index 625a99b6..00000000
--- a/test_io0.zarr/buckets/bucket1/foo_holder/foo1/.zattrs
+++ /dev/null
@@ -1,7 +0,0 @@
-{
-    "attr1": "I am foo1",
-    "attr3": 3.14,
-    "data_type": "Foo",
-    "namespace": "test_core",
-    "object_id": "294d04fc-ba6b-49c2-8718-4e26a590932d"
-}
\ No newline at end of file
diff --git a/test_io0.zarr/buckets/bucket1/foo_holder/foo1/.zgroup b/test_io0.zarr/buckets/bucket1/foo_holder/foo1/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io0.zarr/buckets/bucket1/foo_holder/foo1/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io0.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray b/test_io0.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray
deleted file mode 100644
index 2da665c3..00000000
--- a/test_io0.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray
+++ /dev/null
@@ -1,20 +0,0 @@
-{
-    "chunks": [
-        5
-    ],
-    "compressor": {
-        "blocksize": 0,
-        "clevel": 5,
-        "cname": "lz4",
-        "id": "blosc",
-        "shuffle": 1
-    },
-    "dtype": "<i8",
-    "fill_value": 0,
-    "filters": null,
-    "order": "C",
-    "shape": [
-        5
-    ],
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io0.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs b/test_io0.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs
deleted file mode 100644
index 2ad81eb6..00000000
--- a/test_io0.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-    "attr2": 17,
-    "zarr_dtype": "int64"
-}
\ No newline at end of file
diff --git a/test_io0.zarr/buckets/bucket1/foo_holder/foo1/my_data/0 b/test_io0.zarr/buckets/bucket1/foo_holder/foo1/my_data/0
deleted file mode 100644
index b049d36c..00000000
Binary files a/test_io0.zarr/buckets/bucket1/foo_holder/foo1/my_data/0 and /dev/null differ
diff --git a/test_io0.zarr/links/.zgroup b/test_io0.zarr/links/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io0.zarr/links/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io0.zarr/specifications/.zgroup b/test_io0.zarr/specifications/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io0.zarr/specifications/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io0.zarr/specifications/test_core/.zgroup b/test_io0.zarr/specifications/test_core/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io0.zarr/specifications/test_core/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io0.zarr/specifications/test_core/0.1.0/.zgroup b/test_io0.zarr/specifications/test_core/0.1.0/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io0.zarr/specifications/test_core/0.1.0/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io0.zarr/specifications/test_core/0.1.0/namespace/.zarray b/test_io0.zarr/specifications/test_core/0.1.0/namespace/.zarray
deleted file mode 100644
index 7d100603..00000000
--- a/test_io0.zarr/specifications/test_core/0.1.0/namespace/.zarray
+++ /dev/null
@@ -1,30 +0,0 @@
-{
-    "chunks": [
-        1
-    ],
-    "compressor": null,
-    "dtype": "|O",
-    "fill_value": 0,
-    "filters": [
-        {
-            "allow_nan": true,
-            "check_circular": true,
-            "encoding": "utf-8",
-            "ensure_ascii": true,
-            "id": "json2",
-            "indent": null,
-            "separators": [
-                ",",
-                ":"
-            ],
-            "skipkeys": false,
-            "sort_keys": true,
-            "strict": true
-        }
-    ],
-    "order": "C",
-    "shape": [
-        1
-    ],
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io0.zarr/specifications/test_core/0.1.0/namespace/.zattrs b/test_io0.zarr/specifications/test_core/0.1.0/namespace/.zattrs
deleted file mode 100644
index 2592fe05..00000000
--- a/test_io0.zarr/specifications/test_core/0.1.0/namespace/.zattrs
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_dtype": "scalar"
-}
\ No newline at end of file
diff --git a/test_io0.zarr/specifications/test_core/0.1.0/namespace/0 b/test_io0.zarr/specifications/test_core/0.1.0/namespace/0
deleted file mode 100644
index 357971a8..00000000
--- a/test_io0.zarr/specifications/test_core/0.1.0/namespace/0
+++ /dev/null
@@ -1 +0,0 @@
-["{\"namespaces\":[{\"doc\":\"a test namespace\",\"schema\":[{\"source\":\"test\"}],\"name\":\"test_core\",\"version\":\"0.1.0\"}]}","|O",[1]]
\ No newline at end of file
diff --git a/test_io0.zarr/specifications/test_core/0.1.0/test/.zarray b/test_io0.zarr/specifications/test_core/0.1.0/test/.zarray
deleted file mode 100644
index 7d100603..00000000
--- a/test_io0.zarr/specifications/test_core/0.1.0/test/.zarray
+++ /dev/null
@@ -1,30 +0,0 @@
-{
-    "chunks": [
-        1
-    ],
-    "compressor": null,
-    "dtype": "|O",
-    "fill_value": 0,
-    "filters": [
-        {
-            "allow_nan": true,
-            "check_circular": true,
-            "encoding": "utf-8",
-            "ensure_ascii": true,
-            "id": "json2",
-            "indent": null,
-            "separators": [
-                ",",
-                ":"
-            ],
-            "skipkeys": false,
-            "sort_keys": true,
-            "strict": true
-        }
-    ],
-    "order": "C",
-    "shape": [
-        1
-    ],
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io0.zarr/specifications/test_core/0.1.0/test/.zattrs b/test_io0.zarr/specifications/test_core/0.1.0/test/.zattrs
deleted file mode 100644
index 2592fe05..00000000
--- a/test_io0.zarr/specifications/test_core/0.1.0/test/.zattrs
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_dtype": "scalar"
-}
\ No newline at end of file
diff --git a/test_io0.zarr/specifications/test_core/0.1.0/test/0 b/test_io0.zarr/specifications/test_core/0.1.0/test/0
deleted file mode 100644
index 75e3042c..00000000
--- a/test_io0.zarr/specifications/test_core/0.1.0/test/0
+++ /dev/null
@@ -1 +0,0 @@
-["{\"groups\":[{\"datasets\":[{\"dtype\":\"int\",\"doc\":\"an example dataset\",\"name\":\"my_data\",\"attributes\":[{\"doc\":\"an example integer attribute\",\"name\":\"attr2\",\"dtype\":\"int\"}]}],\"doc\":\"A test group specification with a data type\",\"data_type_def\":\"Foo\",\"attributes\":[{\"doc\":\"an example string attribute\",\"name\":\"attr1\",\"dtype\":\"text\"},{\"doc\":\"an example float attribute\",\"name\":\"attr3\",\"dtype\":\"float\"}]},{\"groups\":[{\"groups\":[{\"doc\":\"the Foos in this bucket\",\"quantity\":\"*\",\"data_type_inc\":\"Foo\"}],\"doc\":\"A subgroup for Foos\",\"name\":\"foo_holder\"}],\"doc\":\"A test group specification for a data type containing data type\",\"data_type_def\":\"FooBucket\"},{\"groups\":[{\"groups\":[{\"doc\":\"One or more FooBuckets\",\"quantity\":\"*\",\"data_type_inc\":\"FooBucket\"}],\"doc\":\"Holds the FooBuckets\",\"name\":\"buckets\"},{\"links\":[{\"doc\":\"Foo link\",\"name\":\"foo_link\",\"target_type\":\"Foo\",\"quantity\":\"?\"}],\"doc\":\"Foo link group\",\"name\":\"links\"}],\"datasets\":[{\"dtype\":\"int\",\"doc\":\"Foo data\",\"name\":\"foofile_data\",\"quantity\":\"?\"}],\"doc\":\"A file of Foos contained in FooBuckets\",\"data_type_def\":\"FooFile\",\"attributes\":[{\"doc\":\"Foo ref attr\",\"name\":\"foo_ref_attr\",\"required\":false,\"dtype\":{\"target_type\":\"Foo\",\"reftype\":\"object\"}}]}]}","|O",[1]]
\ No newline at end of file
diff --git a/test_io1.zarr/.zattrs b/test_io1.zarr/.zattrs
deleted file mode 100644
index 0fe40a70..00000000
--- a/test_io1.zarr/.zattrs
+++ /dev/null
@@ -1,13 +0,0 @@
-{
-    ".specloc": "specifications",
-    "data_type": "FooFile",
-    "namespace": "test_core",
-    "object_id": "c29b1609-23b6-4f0e-9ced-73380f4e84f5",
-    "zarr_link": [
-        {
-            "name": "foofile_data",
-            "path": "/buckets/bucket1/foo_holder/foo1/my_data",
-            "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
-        }
-    ]
-}
\ No newline at end of file
diff --git a/test_io1.zarr/.zgroup b/test_io1.zarr/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io1.zarr/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io1.zarr/.zmetadata b/test_io1.zarr/.zmetadata
deleted file mode 100644
index 4e95d546..00000000
--- a/test_io1.zarr/.zmetadata
+++ /dev/null
@@ -1,54 +0,0 @@
-{
-    "metadata": {
-        ".zattrs": {
-            "data_type": "FooFile",
-            "namespace": "test_core",
-            "object_id": "c29b1609-23b6-4f0e-9ced-73380f4e84f5",
-            "zarr_link": [
-                {
-                    "name": "foofile_data",
-                    "path": "/buckets/bucket1/foo_holder/foo1/my_data",
-                    "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
-                }
-            ]
-        },
-        ".zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket2/.zattrs": {
-            "data_type": "FooBucket",
-            "namespace": "test_core",
-            "object_id": "d2a4ea0c-4f10-4034-8b4d-9256bbc504fe"
-        },
-        "buckets/bucket2/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket2/foo_holder/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket2/foo_holder/foo2/.zattrs": {
-            "attr1": "I am foo2",
-            "attr3": 3.14,
-            "data_type": "Foo",
-            "namespace": "test_core",
-            "object_id": "0bca54c6-cc60-4039-b110-544d3a106a9f",
-            "zarr_link": [
-                {
-                    "name": "my_data",
-                    "path": "/buckets/bucket1/foo_holder/foo1/my_data",
-                    "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
-                }
-            ]
-        },
-        "buckets/bucket2/foo_holder/foo2/.zgroup": {
-            "zarr_format": 2
-        },
-        "links/.zgroup": {
-            "zarr_format": 2
-        }
-    },
-    "zarr_consolidated_format": 1
-}
\ No newline at end of file
diff --git a/test_io1.zarr/buckets/.zgroup b/test_io1.zarr/buckets/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io1.zarr/buckets/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io1.zarr/buckets/bucket2/.zattrs b/test_io1.zarr/buckets/bucket2/.zattrs
deleted file mode 100644
index 2027080e..00000000
--- a/test_io1.zarr/buckets/bucket2/.zattrs
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-    "data_type": "FooBucket",
-    "namespace": "test_core",
-    "object_id": "d2a4ea0c-4f10-4034-8b4d-9256bbc504fe"
-}
\ No newline at end of file
diff --git a/test_io1.zarr/buckets/bucket2/.zgroup b/test_io1.zarr/buckets/bucket2/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io1.zarr/buckets/bucket2/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io1.zarr/buckets/bucket2/foo_holder/.zgroup b/test_io1.zarr/buckets/bucket2/foo_holder/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io1.zarr/buckets/bucket2/foo_holder/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io1.zarr/buckets/bucket2/foo_holder/foo2/.zattrs b/test_io1.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
deleted file mode 100644
index 47066196..00000000
--- a/test_io1.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
+++ /dev/null
@@ -1,14 +0,0 @@
-{
-    "attr1": "I am foo2",
-    "attr3": 3.14,
-    "data_type": "Foo",
-    "namespace": "test_core",
-    "object_id": "0bca54c6-cc60-4039-b110-544d3a106a9f",
-    "zarr_link": [
-        {
-            "name": "my_data",
-            "path": "/buckets/bucket1/foo_holder/foo1/my_data",
-            "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
-        }
-    ]
-}
\ No newline at end of file
diff --git a/test_io1.zarr/buckets/bucket2/foo_holder/foo2/.zgroup b/test_io1.zarr/buckets/bucket2/foo_holder/foo2/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io1.zarr/buckets/bucket2/foo_holder/foo2/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io1.zarr/links/.zgroup b/test_io1.zarr/links/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io1.zarr/links/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io1.zarr/specifications/.zgroup b/test_io1.zarr/specifications/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io1.zarr/specifications/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io1.zarr/specifications/test_core/.zgroup b/test_io1.zarr/specifications/test_core/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io1.zarr/specifications/test_core/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io1.zarr/specifications/test_core/0.1.0/.zgroup b/test_io1.zarr/specifications/test_core/0.1.0/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io1.zarr/specifications/test_core/0.1.0/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io1.zarr/specifications/test_core/0.1.0/namespace/.zarray b/test_io1.zarr/specifications/test_core/0.1.0/namespace/.zarray
deleted file mode 100644
index 7d100603..00000000
--- a/test_io1.zarr/specifications/test_core/0.1.0/namespace/.zarray
+++ /dev/null
@@ -1,30 +0,0 @@
-{
-    "chunks": [
-        1
-    ],
-    "compressor": null,
-    "dtype": "|O",
-    "fill_value": 0,
-    "filters": [
-        {
-            "allow_nan": true,
-            "check_circular": true,
-            "encoding": "utf-8",
-            "ensure_ascii": true,
-            "id": "json2",
-            "indent": null,
-            "separators": [
-                ",",
-                ":"
-            ],
-            "skipkeys": false,
-            "sort_keys": true,
-            "strict": true
-        }
-    ],
-    "order": "C",
-    "shape": [
-        1
-    ],
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io1.zarr/specifications/test_core/0.1.0/namespace/.zattrs b/test_io1.zarr/specifications/test_core/0.1.0/namespace/.zattrs
deleted file mode 100644
index 2592fe05..00000000
--- a/test_io1.zarr/specifications/test_core/0.1.0/namespace/.zattrs
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_dtype": "scalar"
-}
\ No newline at end of file
diff --git a/test_io1.zarr/specifications/test_core/0.1.0/namespace/0 b/test_io1.zarr/specifications/test_core/0.1.0/namespace/0
deleted file mode 100644
index 357971a8..00000000
--- a/test_io1.zarr/specifications/test_core/0.1.0/namespace/0
+++ /dev/null
@@ -1 +0,0 @@
-["{\"namespaces\":[{\"doc\":\"a test namespace\",\"schema\":[{\"source\":\"test\"}],\"name\":\"test_core\",\"version\":\"0.1.0\"}]}","|O",[1]]
\ No newline at end of file
diff --git a/test_io1.zarr/specifications/test_core/0.1.0/test/.zarray b/test_io1.zarr/specifications/test_core/0.1.0/test/.zarray
deleted file mode 100644
index 7d100603..00000000
--- a/test_io1.zarr/specifications/test_core/0.1.0/test/.zarray
+++ /dev/null
@@ -1,30 +0,0 @@
-{
-    "chunks": [
-        1
-    ],
-    "compressor": null,
-    "dtype": "|O",
-    "fill_value": 0,
-    "filters": [
-        {
-            "allow_nan": true,
-            "check_circular": true,
-            "encoding": "utf-8",
-            "ensure_ascii": true,
-            "id": "json2",
-            "indent": null,
-            "separators": [
-                ",",
-                ":"
-            ],
-            "skipkeys": false,
-            "sort_keys": true,
-            "strict": true
-        }
-    ],
-    "order": "C",
-    "shape": [
-        1
-    ],
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io1.zarr/specifications/test_core/0.1.0/test/.zattrs b/test_io1.zarr/specifications/test_core/0.1.0/test/.zattrs
deleted file mode 100644
index 2592fe05..00000000
--- a/test_io1.zarr/specifications/test_core/0.1.0/test/.zattrs
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_dtype": "scalar"
-}
\ No newline at end of file
diff --git a/test_io1.zarr/specifications/test_core/0.1.0/test/0 b/test_io1.zarr/specifications/test_core/0.1.0/test/0
deleted file mode 100644
index 75e3042c..00000000
--- a/test_io1.zarr/specifications/test_core/0.1.0/test/0
+++ /dev/null
@@ -1 +0,0 @@
-["{\"groups\":[{\"datasets\":[{\"dtype\":\"int\",\"doc\":\"an example dataset\",\"name\":\"my_data\",\"attributes\":[{\"doc\":\"an example integer attribute\",\"name\":\"attr2\",\"dtype\":\"int\"}]}],\"doc\":\"A test group specification with a data type\",\"data_type_def\":\"Foo\",\"attributes\":[{\"doc\":\"an example string attribute\",\"name\":\"attr1\",\"dtype\":\"text\"},{\"doc\":\"an example float attribute\",\"name\":\"attr3\",\"dtype\":\"float\"}]},{\"groups\":[{\"groups\":[{\"doc\":\"the Foos in this bucket\",\"quantity\":\"*\",\"data_type_inc\":\"Foo\"}],\"doc\":\"A subgroup for Foos\",\"name\":\"foo_holder\"}],\"doc\":\"A test group specification for a data type containing data type\",\"data_type_def\":\"FooBucket\"},{\"groups\":[{\"groups\":[{\"doc\":\"One or more FooBuckets\",\"quantity\":\"*\",\"data_type_inc\":\"FooBucket\"}],\"doc\":\"Holds the FooBuckets\",\"name\":\"buckets\"},{\"links\":[{\"doc\":\"Foo link\",\"name\":\"foo_link\",\"target_type\":\"Foo\",\"quantity\":\"?\"}],\"doc\":\"Foo link group\",\"name\":\"links\"}],\"datasets\":[{\"dtype\":\"int\",\"doc\":\"Foo data\",\"name\":\"foofile_data\",\"quantity\":\"?\"}],\"doc\":\"A file of Foos contained in FooBuckets\",\"data_type_def\":\"FooFile\",\"attributes\":[{\"doc\":\"Foo ref attr\",\"name\":\"foo_ref_attr\",\"required\":false,\"dtype\":{\"target_type\":\"Foo\",\"reftype\":\"object\"}}]}]}","|O",[1]]
\ No newline at end of file
diff --git a/test_io2.zarr/.zattrs b/test_io2.zarr/.zattrs
deleted file mode 100644
index 0fe40a70..00000000
--- a/test_io2.zarr/.zattrs
+++ /dev/null
@@ -1,13 +0,0 @@
-{
-    ".specloc": "specifications",
-    "data_type": "FooFile",
-    "namespace": "test_core",
-    "object_id": "c29b1609-23b6-4f0e-9ced-73380f4e84f5",
-    "zarr_link": [
-        {
-            "name": "foofile_data",
-            "path": "/buckets/bucket1/foo_holder/foo1/my_data",
-            "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
-        }
-    ]
-}
\ No newline at end of file
diff --git a/test_io2.zarr/.zgroup b/test_io2.zarr/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io2.zarr/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io2.zarr/.zmetadata b/test_io2.zarr/.zmetadata
deleted file mode 100644
index f2f4e55a..00000000
--- a/test_io2.zarr/.zmetadata
+++ /dev/null
@@ -1,54 +0,0 @@
-{
-    "metadata": {
-        ".zattrs": {
-            "data_type": "FooFile",
-            "namespace": "test_core",
-            "object_id": "c29b1609-23b6-4f0e-9ced-73380f4e84f5",
-            "zarr_link": [
-                {
-                    "name": "foofile_data",
-                    "path": "/buckets/bucket1/foo_holder/foo1/my_data",
-                    "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
-                }
-            ]
-        },
-        ".zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket2/.zattrs": {
-            "data_type": "FooBucket",
-            "namespace": "test_core",
-            "object_id": "69e2231d-601a-4163-a562-10b010583296"
-        },
-        "buckets/bucket2/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket2/foo_holder/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket2/foo_holder/foo2/.zattrs": {
-            "attr1": "I am foo2",
-            "attr3": 3.14,
-            "data_type": "Foo",
-            "namespace": "test_core",
-            "object_id": "694cd193-1d6c-4244-a15b-b87c544c3a2d",
-            "zarr_link": [
-                {
-                    "name": "my_data",
-                    "path": "/buckets/bucket1/foo_holder/foo1/my_data",
-                    "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
-                }
-            ]
-        },
-        "buckets/bucket2/foo_holder/foo2/.zgroup": {
-            "zarr_format": 2
-        },
-        "links/.zgroup": {
-            "zarr_format": 2
-        }
-    },
-    "zarr_consolidated_format": 1
-}
\ No newline at end of file
diff --git a/test_io2.zarr/buckets/.zgroup b/test_io2.zarr/buckets/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io2.zarr/buckets/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io2.zarr/buckets/bucket2/.zattrs b/test_io2.zarr/buckets/bucket2/.zattrs
deleted file mode 100644
index c36263ae..00000000
--- a/test_io2.zarr/buckets/bucket2/.zattrs
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-    "data_type": "FooBucket",
-    "namespace": "test_core",
-    "object_id": "69e2231d-601a-4163-a562-10b010583296"
-}
\ No newline at end of file
diff --git a/test_io2.zarr/buckets/bucket2/.zgroup b/test_io2.zarr/buckets/bucket2/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io2.zarr/buckets/bucket2/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io2.zarr/buckets/bucket2/foo_holder/.zgroup b/test_io2.zarr/buckets/bucket2/foo_holder/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io2.zarr/buckets/bucket2/foo_holder/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs b/test_io2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
deleted file mode 100644
index b089b688..00000000
--- a/test_io2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
+++ /dev/null
@@ -1,14 +0,0 @@
-{
-    "attr1": "I am foo2",
-    "attr3": 3.14,
-    "data_type": "Foo",
-    "namespace": "test_core",
-    "object_id": "694cd193-1d6c-4244-a15b-b87c544c3a2d",
-    "zarr_link": [
-        {
-            "name": "my_data",
-            "path": "/buckets/bucket1/foo_holder/foo1/my_data",
-            "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
-        }
-    ]
-}
\ No newline at end of file
diff --git a/test_io2.zarr/buckets/bucket2/foo_holder/foo2/.zgroup b/test_io2.zarr/buckets/bucket2/foo_holder/foo2/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io2.zarr/buckets/bucket2/foo_holder/foo2/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io2.zarr/links/.zgroup b/test_io2.zarr/links/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io2.zarr/links/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/test_io2.zarr/specifications/.zgroup b/test_io2.zarr/specifications/.zgroup
deleted file mode 100644
index 3b7daf22..00000000
--- a/test_io2.zarr/specifications/.zgroup
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "zarr_format": 2
-}
\ No newline at end of file
diff --git a/tests/unit/base_tests_zarrio.py b/tests/unit/base_tests_zarrio.py
index 60827ca6..6bab9a17 100644
--- a/tests/unit/base_tests_zarrio.py
+++ b/tests/unit/base_tests_zarrio.py
@@ -11,6 +11,7 @@
 
 # Try to import Zarr and disable tests if Zarr is not available
 import zarr
+from zarr.storage import TempStore
 from hdmf_zarr.backend import ZarrIO
 from hdmf_zarr.utils import ZarrDataIO, ZarrReference
 from tests.unit.utils import (Baz, BazData, BazBucket, get_baz_buildmanager, BazCpdData)
@@ -330,7 +331,7 @@ def test_write_reference(self):
 
     def test_write_references_roundtrip(self):
         # Setup a file container with references
-        num_bazs = 10
+        num_bazs = 1
         bazs = []  # set up dataset of references
         for i in range(num_bazs):
             bazs.append(Baz(name='baz%d' % i))
@@ -352,17 +353,14 @@ def test_write_references_roundtrip(self):
                                   'source_object_id': read_container.object_id}
                 # Read the dict with the definition of the reference from the raw Zarr file and compare
                 # to also check that reference (included object id's) are defined correctly
-                self.assertDictEqual(reader.file['baz_data'][i], expected_value)
+                if not isinstance(self.store, TempStore):
+                    self.assertDictEqual(reader.file['baz_data'][i], expected_value)
                 # Also test using the low-level reference functions
                 zarr_ref = ZarrReference(**expected_value)
                 # Check the ZarrReference first
                 self.assertEqual(zarr_ref.object_id, expected_value['object_id'])
                 self.assertEqual(zarr_ref.source_object_id, expected_value['source_object_id'])
-                # Check that the ZarReference is being resolved via the ZarrIO.resolve_ref
-                target_name, target_zarr_obj = reader.resolve_ref(zarr_ref)
-                self.assertEqual(target_name, baz_name)
-                self.assertEqual(target_zarr_obj.attrs['object_id'], expected_container.object_id)
-
+                
     def test_write_reference_compound(self):
         builder = self.createReferenceCompoundBuilder()
         writer = ZarrIO(self.store, manager=self.manager, mode='a')