diff --git a/checkpoint.json b/checkpoint.json
new file mode 100644
index 000000000..78d9e73d1
--- /dev/null
+++ b/checkpoint.json
@@ -0,0 +1,57 @@
+{
+  "timestamp": "2026-03-16T11:58:06.870498Z",
+  "current_node": "setup",
+  "completed_nodes": [
+    "start",
+    "setup"
+  ],
+  "node_retries": {
+    "setup": 1,
+    "start": 1
+  },
+  "context_values": {
+    "failure_class": "deterministic",
+    "internal.fidelity": "compact",
+    "internal.run_id": "01KKV856P1H91WW3YFKZSFGBS6",
+    "internal.node_visit_count": 1,
+    "internal.retry_count.setup": 1,
+    "internal.thread_id": "start",
+    "thread.start.current_node": "setup",
+    "failure_signature": "setup|deterministic|script failed with exit code: <n> ## stdout fatal: destination path '.' already exists and is not an empty directory.",
+    "command.stderr": "",
+    "graph.goal": "Modeling's `separability_matrix` does not compute separability correctly for nested CompoundModels\nConsider the following model:\r\n\r\n```python\r\nfrom astropy.modeling import models as m\r\nfrom astropy.modeling.separable import separability_matrix\r\n\r\ncm = m.Linear1D(10) & m.Linear1D(5)\r\n```\r\n\r\nIt's separability matrix as you might expect is a diagonal:\r\n\r\n```python\r\n>>> separability_matrix(cm)\r\narray([[ True, False],\r\n       [False,  True]])\r\n```\r\n\r\nIf I make the model more complex:\r\n```python\r\n>>> separability_matrix(m.Pix2Sky_TAN() & m.Linear1D(10) & m.Linear1D(5))\r\narray([[ True,  True, False, False],\r\n       [ True,  True, False, False],\r\n       [False, False,  True, False],\r\n       [False, False, False,  True]])\r\n```\r\n\r\nThe output matrix is again, as expected, the outputs and inputs to the linear models are separable and independent of each other.\r\n\r\nIf however, I nest these compound models:\r\n```python\r\n>>> separability_matrix(m.Pix2Sky_TAN() & cm)\r\narray([[ True,  True, False, False],\r\n       [ True,  True, False, False],\r\n       [False, False,  True,  True],\r\n       [False, False,  True,  True]])\r\n```\r\nSuddenly the inputs and outputs are no longer separable?\r\n\r\nThis feels like a bug to me, but I might be missing something?\n",
+    "current.preamble": "Goal: Modeling's `separability_matrix` does not compute separability correctly for nested CompoundModels\nConsider the following model:\r\n\r\n```python\r\nfrom astropy.modeling import models as m\r\nfrom astropy.modeling.separable import separability_matrix\r\n\r\ncm = m.Linear1D(10) & m.Linear1D(5)\r\n```\r\n\r\nIt's separability matrix as you might expect is a diagonal:\r\n\r\n```python\r\n>>> separability_matrix(cm)\r\narray([[ True, False],\r\n       [False,  True]])\r\n```\r\n\r\nIf I make the model more complex:\r\n```python\r\n>>> separability_matrix(m.Pix2Sky_TAN() & m.Linear1D(10) & m.Linear1D(5))\r\narray([[ True,  True, False, False],\r\n       [ True,  True, False, False],\r\n       [False, False,  True, False],\r\n       [False, False, False,  True]])\r\n```\r\n\r\nThe output matrix is again, as expected, the outputs and inputs to the linear models are separable and independent of each other.\r\n\r\nIf however, I nest these compound models:\r\n```python\r\n>>> separability_matrix(m.Pix2Sky_TAN() & cm)\r\narray([[ True,  True, False, False],\r\n       [ True,  True, False, False],\r\n       [False, False,  True,  True],\r\n       [False, False,  True,  True]])\r\n```\r\nSuddenly the inputs and outputs are no longer separable?\r\n\r\nThis feels like a bug to me, but I might be missing something?\n\n",
+    "current_node": "setup",
+    "internal.retry_count.start": 1,
+    "outcome": "fail",
+    "command.output": "fatal: destination path '.' already exists and is not an empty directory.\n",
+    "graph.rankdir": "LR"
+  },
+  "logs": [],
+  "node_outcomes": {
+    "setup": {
+      "status": "fail",
+      "context_updates": {
+        "command.stderr": "",
+        "command.output": "fatal: destination path '.' already exists and is not an empty directory.\n"
+      },
+      "failure": {
+        "message": "Script failed with exit code: 128\n\n## stdout\nfatal: destination path '.' already exists and is not an empty directory.\n",
+        "failure_class": "deterministic"
+      },
+      "duration_ms": 107
+    },
+    "start": {
+      "status": "success",
+      "duration_ms": 0
+    }
+  },
+  "next_node_id": "solve",
+  "loop_failure_signatures": {
+    "setup|deterministic|script failed with exit code: <n> ## stdout fatal: destination path '.' already exists and is not an empty directory.": 1
+  },
+  "node_visits": {
+    "setup": 1,
+    "start": 1
+  }
+}
\ No newline at end of file
diff --git a/nodes/setup/script_invocation.json b/nodes/setup/script_invocation.json
new file mode 100644
index 000000000..c76e11c55
--- /dev/null
+++ b/nodes/setup/script_invocation.json
@@ -0,0 +1,5 @@
+{
+  "command": "git clone https://github.com/astropy/astropy.git . && git checkout d16bfe05a744909de4b27f5875fe0d4ed41ce607 && sed -i 's/requires = \\[\"setuptools\",/requires = \\[\"setuptools==68.0.0\",/' pyproject.toml && python -m pip install -e .[test] --verbose",
+  "language": "shell",
+  "timeout_ms": null
+}
\ No newline at end of file
diff --git a/nodes/setup/script_timing.json b/nodes/setup/script_timing.json
new file mode 100644
index 000000000..c89db25a6
--- /dev/null
+++ b/nodes/setup/script_timing.json
@@ -0,0 +1,5 @@
+{
+  "duration_ms": 106,
+  "exit_code": 128,
+  "timed_out": false
+}
\ No newline at end of file
diff --git a/nodes/setup/status.json b/nodes/setup/status.json
new file mode 100644
index 000000000..05198edf9
--- /dev/null
+++ b/nodes/setup/status.json
@@ -0,0 +1,6 @@
+{
+  "status": "fail",
+  "notes": null,
+  "failure_reason": "Script failed with exit code: 128\n\n## stdout\nfatal: destination path '.' already exists and is not an empty directory.\n",
+  "timestamp": "2026-03-16T11:58:06.870292+00:00"
+}
\ No newline at end of file
diff --git a/nodes/start/status.json b/nodes/start/status.json
new file mode 100644
index 000000000..fefdcd53a
--- /dev/null
+++ b/nodes/start/status.json
@@ -0,0 +1,6 @@
+{
+  "status": "success",
+  "notes": null,
+  "failure_reason": null,
+  "timestamp": "2026-03-16T11:58:06.761919+00:00"
+}
\ No newline at end of file