diff --git a/checkpoint.json b/checkpoint.json
index 0778170bd..149dd966d 100644
--- a/checkpoint.json
+++ b/checkpoint.json
@@ -1,41 +1,54 @@
 {
-  "timestamp": "2026-03-16T12:07:15.564981Z",
-  "current_node": "solve",
+  "timestamp": "2026-03-16T12:07:22.826470Z",
+  "current_node": "extract_patch",
   "completed_nodes": [
     "start",
     "setup",
-    "solve"
+    "solve",
+    "extract_patch"
   ],
   "node_retries": {
     "solve": 1,
     "start": 1,
-    "setup": 1
+    "setup": 1,
+    "extract_patch": 1
   },
   "context_values": {
     "thread.setup.current_node": "solve",
     "last_stage": "solve",
     "internal.retry_count.solve": 1,
     "failure_class": "",
+    "internal.retry_count.extract_patch": 1,
     "command.stderr": "",
     "internal.node_visit_count": 1,
     "internal.retry_count.start": 1,
-    "internal.thread_id": "setup",
+    "internal.thread_id": "solve",
     "internal.run_id": "01KKV8D2S3VEG2V3PF00QMMRTP",
     "graph.rankdir": "LR",
-    "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\n## Completed stages\n- **setup**: fail\n  - Script: `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`\n  - Stdout:\n    ```\n    fatal: destination path '.' already exists and is not an empty directory.\n    ```\n  - Stderr: (empty)\n\n## Context\n- failure_class: deterministic\n- failure_signature: setup|deterministic|script failed with exit code: <n> ## stdout fatal: destination path '.' already exists and is not an empty directory.\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\n## Completed stages\n- **setup**: fail\n  - Script: `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`\n  - Stdout:\n    ```\n    fatal: destination path '.' already exists and is not an empty directory.\n    ```\n  - Stderr: (empty)\n- **solve**: success\n  - Model: claude-opus-4-6, 17.5k tokens in / 6.8k out\n  - Files: /home/daytona/workspace/astropy/modeling/separable.py, /tmp/astropy_fix/astropy/modeling/separable.py\n",
     "thread.start.current_node": "setup",
     "failure_signature": "",
     "outcome": "success",
     "internal.retry_count.setup": 1,
-    "command.output": "fatal: destination path '.' already exists and is not an empty directory.\n",
+    "command.output": "",
     "last_response": "The meaningful change is just the one line in `astropy/modeling/separable.py` line 245: changing `= 1` to `= right`.\n\n## Summary\n\nThe bug was in the `_cstack` function in `astropy/modeling/separable.p",
-    "current_node": "solve",
+    "current_node": "extract_patch",
+    "thread.solve.current_node": "extract_patch",
     "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",
     "internal.fidelity": "compact",
     "response.solve": "The meaningful change is just the one line in `astropy/modeling/separable.py` line 245: changing `= 1` to `= right`.\n\n## Summary\n\nThe bug was in the `_cstack` function in `astropy/modeling/separable.py`, which handles the `&` (concatenation) operator for compound models.\n\n**Root cause:** On line 245, when the `right` operand is an ndarray (which happens when it's the result of a nested CompoundModel that has already been processed into a separability matrix), the code was filling the bottom-right portion of the output matrix with `1` instead of copying the actual values from the `right` matrix:\n\n```python\n# Bug: fills with all 1s, destroying separability information\ncright[-right.shape[0]:, -right.shape[1]:] = 1\n```\n\n**Fix:** Copy the actual separability matrix values from `right`:\n\n```python\n# Fix: preserves the actual separability information\ncright[-right.shape[0]:, -right.shape[1]:] = right\n```\n\nThis is consistent with how the `left` operand is handled (line 240: `cleft[: left.shape[0], : left.shape[1]] = left`), where it correctly copies the actual matrix values. The `right` branch simply had a bug where it used `1` instead of `right`."
   },
   "logs": [],
   "node_outcomes": {
+    "extract_patch": {
+      "status": "success",
+      "context_updates": {
+        "command.stderr": "",
+        "command.output": ""
+      },
+      "notes": "Script completed: git diff",
+      "duration_ms": 53
+    },
     "setup": {
       "status": "fail",
       "context_updates": {
@@ -76,13 +89,14 @@
       "duration_ms": 288793
     }
   },
-  "next_node_id": "extract_patch",
+  "next_node_id": "exit",
   "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": {
+    "extract_patch": 1,
+    "solve": 1,
     "start": 1,
-    "setup": 1,
-    "solve": 1
+    "setup": 1
   }
 }
\ No newline at end of file
diff --git a/nodes/extract_patch/script_invocation.json b/nodes/extract_patch/script_invocation.json
new file mode 100644
index 000000000..6d29afc80
--- /dev/null
+++ b/nodes/extract_patch/script_invocation.json
@@ -0,0 +1,5 @@
+{
+  "command": "git diff",
+  "language": "shell",
+  "timeout_ms": null
+}
\ No newline at end of file
diff --git a/nodes/extract_patch/script_timing.json b/nodes/extract_patch/script_timing.json
new file mode 100644
index 000000000..dea71c338
--- /dev/null
+++ b/nodes/extract_patch/script_timing.json
@@ -0,0 +1,5 @@
+{
+  "duration_ms": 52,
+  "exit_code": 0,
+  "timed_out": false
+}
\ No newline at end of file
diff --git a/nodes/extract_patch/status.json b/nodes/extract_patch/status.json
new file mode 100644
index 000000000..17e1f5b07
--- /dev/null
+++ b/nodes/extract_patch/status.json
@@ -0,0 +1,6 @@
+{
+  "status": "success",
+  "notes": "Script completed: git diff",
+  "failure_reason": null,
+  "timestamp": "2026-03-16T12:07:22.826306+00:00"
+}
\ No newline at end of file