diff --git a/checkpoint.json b/checkpoint.json
index 9b9ede5a7..ec8b02b1e 100644
--- a/checkpoint.json
+++ b/checkpoint.json
@@ -1,38 +1,42 @@
 {
-  "timestamp": "2026-03-16T12:05:37.721224Z",
-  "current_node": "solve",
+  "timestamp": "2026-03-16T12:05:40.375379Z",
+  "current_node": "extract_patch",
   "completed_nodes": [
     "start",
     "setup",
-    "solve"
+    "solve",
+    "extract_patch"
   ],
   "node_retries": {
-    "setup": 1,
+    "start": 1,
     "solve": 1,
-    "start": 1
+    "extract_patch": 1,
+    "setup": 1
   },
   "context_values": {
     "internal.retry_count.start": 1,
-    "internal.thread_id": "setup",
+    "internal.thread_id": "solve",
     "thread.start.current_node": "setup",
     "last_response": "Implemented the fix in the cloned Astropy checkout at `/home/daytona/workspace/astropy`.\n\nWhat changed:\n- `astropy/modeling/separable.py`\n  - Fixed `_cstack()` so that when the right-hand side is alre",
     "last_stage": "solve",
+    "thread.solve.current_node": "extract_patch",
     "internal.fidelity": "compact",
     "failure_class": "",
     "outcome": "success",
     "internal.retry_count.setup": 1,
-    "command.output": "fatal: destination path '.' already exists and is not an empty directory.\n",
+    "command.output": "diff --git a/astropy b/astropy\n--- a/astropy\n+++ b/astropy\n@@ -1 +1 @@\n-Subproject commit d16bfe05a744909de4b27f5875fe0d4ed41ce607\n+Subproject commit d16bfe05a744909de4b27f5875fe0d4ed41ce607-dirty\n",
     "thread.setup.current_node": "solve",
     "response.solve": "Implemented the fix in the cloned Astropy checkout at `/home/daytona/workspace/astropy`.\n\nWhat changed:\n- `astropy/modeling/separable.py`\n  - Fixed `_cstack()` so that when the right-hand side is already a computed separability matrix from a nested `CompoundModel`, it preserves that matrix instead of replacing it with all 1s.\n- `astropy/modeling/tests/test_separable.py`\n  - Added a regression test covering `models.Pix2Sky_TAN() & (models.Linear1D(10) & models.Linear1D(5))`.\n\nRoot cause:\n- Nested compound models reach `_cstack()` as ndarray separability matrices.\n- The right-hand ndarray branch incorrectly did:\n  - `cright[...] = 1`\n- That flattened all right-side dependencies into “non-separable”.\n- It now correctly does:\n  - `cright[...] = right`\n\nValidation:\n- Reproduced the original bug before the change.\n- Ran:\n  - `python -m pytest astropy/modeling/tests/test_separable.py -q`\n- Result:\n  - `12 passed`\n\nThe original example now returns the expected matrix:\n```python\n[[ True  True False False]\n [ True  True False False]\n [False False  True False]\n [False False False  True]]\n```",
     "internal.retry_count.solve": 1,
     "internal.run_id": "01KKV8D5GSGKS4B48NJAMDYHVF",
+    "internal.retry_count.extract_patch": 1,
     "command.stderr": "",
-    "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: gpt-5.4, 656.0k tokens in / 5.9k out\n",
     "internal.node_visit_count": 1,
     "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",
     "graph.rankdir": "LR",
     "failure_signature": "",
-    "current_node": "solve"
+    "current_node": "extract_patch"
   },
   "logs": [],
   "node_outcomes": {
@@ -54,10 +58,6 @@
       },
       "duration_ms": 187578
     },
-    "start": {
-      "status": "success",
-      "duration_ms": 0
-    },
     "setup": {
       "status": "fail",
       "context_updates": {
@@ -69,15 +69,29 @@
         "failure_class": "deterministic"
       },
       "duration_ms": 82
+    },
+    "extract_patch": {
+      "status": "success",
+      "context_updates": {
+        "command.stderr": "",
+        "command.output": "diff --git a/astropy b/astropy\n--- a/astropy\n+++ b/astropy\n@@ -1 +1 @@\n-Subproject commit d16bfe05a744909de4b27f5875fe0d4ed41ce607\n+Subproject commit d16bfe05a744909de4b27f5875fe0d4ed41ce607-dirty\n"
+      },
+      "notes": "Script completed: git diff",
+      "duration_ms": 54
+    },
+    "start": {
+      "status": "success",
+      "duration_ms": 0
     }
   },
-  "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": {
-    "start": 1,
     "solve": 1,
-    "setup": 1
+    "setup": 1,
+    "start": 1,
+    "extract_patch": 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..655fbf8d3
--- /dev/null
+++ b/nodes/extract_patch/script_timing.json
@@ -0,0 +1,5 @@
+{
+  "duration_ms": 51,
+  "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..7f19446f9
--- /dev/null
+++ b/nodes/extract_patch/status.json
@@ -0,0 +1,6 @@
+{
+  "status": "success",
+  "notes": "Script completed: git diff",
+  "failure_reason": null,
+  "timestamp": "2026-03-16T12:05:40.374268+00:00"
+}
\ No newline at end of file
diff --git a/nodes/solve/diff.patch b/nodes/solve/diff.patch
new file mode 100644
index 000000000..6a0437557
--- /dev/null
+++ b/nodes/solve/diff.patch
@@ -0,0 +1,7 @@
+diff --git a/astropy b/astropy
+new file mode 160000
+index 0000000..d16bfe0
+--- /dev/null
++++ b/astropy
+@@ -0,0 +1 @@
++Subproject commit d16bfe05a744909de4b27f5875fe0d4ed41ce607