diff --git a/checkpoint.json b/checkpoint.json
index e85f7d783..9c725bfae 100644
--- a/checkpoint.json
+++ b/checkpoint.json
@@ -1,30 +1,37 @@
 {
-  "timestamp": "2026-03-16T11:58:07.402704Z",
-  "current_node": "setup",
+  "timestamp": "2026-03-16T12:00:34.997886Z",
+  "current_node": "solve",
   "completed_nodes": [
     "start",
-    "setup"
+    "setup",
+    "solve"
   ],
   "node_retries": {
     "start": 1,
+    "solve": 1,
     "setup": 1
   },
   "context_values": {
     "graph.rankdir": "LR",
-    "current_node": "setup",
+    "current_node": "solve",
     "internal.node_visit_count": 1,
     "internal.retry_count.start": 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",
-    "failure_signature": "setup|deterministic|script failed with exit code: <n> ## stdout fatal: destination path '.' already exists and is not an empty directory.",
+    "failure_signature": "",
     "command.stderr": "",
-    "outcome": "fail",
+    "response.solve": "The fix is applied. Here's a summary:\n\n## Root Cause\n\nIn `astropy/modeling/separable.py`, the `_cstack` function handles the `&` (concatenation) operator for computing separability matrices. When the right operand is already an ndarray (which happens when it's a nested CompoundModel that has already been recursively evaluated by `_separable`), line 245 was:\n\n```python\ncright[-right.shape[0]:, -right.shape[1]:] = 1\n```\n\nThis set the entire bottom-right block to `1`, **discarding** the actual separability information that was computed for the nested compound model. This made all outputs appear to depend on all inputs for that sub-model.\n\n## Fix\n\nChanged line 245 from `= 1` to `= right`:\n\n```python\ncright[-right.shape[0]:, -right.shape[1]:] = right\n```\n\nThis preserves the actual separability matrix computed for the nested compound model, just like the `left` branch already correctly does on line 240 (`= left`).\n\nThis is a one-line fix that makes the `right` branch consistent with the `left` branch — both now properly copy the pre-computed separability matrix instead of replacing it with all ones.",
+    "outcome": "success",
+    "last_stage": "solve",
     "thread.start.current_node": "setup",
     "internal.fidelity": "compact",
-    "internal.thread_id": "start",
-    "failure_class": "deterministic",
+    "internal.retry_count.solve": 1,
+    "thread.setup.current_node": "solve",
+    "internal.thread_id": "setup",
+    "failure_class": "",
     "internal.run_id": "01KKV857H2RFAYPQBG0N9873NR",
-    "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.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",
     "internal.retry_count.setup": 1,
+    "last_response": "The fix is applied. Here's a summary:\n\n## Root Cause\n\nIn `astropy/modeling/separable.py`, the `_cstack` function handles the `&` (concatenation) operator for computing separability matrices. When the ",
     "command.output": "fatal: destination path '.' already exists and is not an empty directory.\n"
   },
   "logs": [],
@@ -44,14 +51,37 @@
     "start": {
       "status": "success",
       "duration_ms": 0
+    },
+    "solve": {
+      "status": "success",
+      "context_updates": {
+        "last_stage": "solve",
+        "last_response": "The fix is applied. Here's a summary:\n\n## Root Cause\n\nIn `astropy/modeling/separable.py`, the `_cstack` function handles the `&` (concatenation) operator for computing separability matrices. When the ",
+        "response.solve": "The fix is applied. Here's a summary:\n\n## Root Cause\n\nIn `astropy/modeling/separable.py`, the `_cstack` function handles the `&` (concatenation) operator for computing separability matrices. When the right operand is already an ndarray (which happens when it's a nested CompoundModel that has already been recursively evaluated by `_separable`), line 245 was:\n\n```python\ncright[-right.shape[0]:, -right.shape[1]:] = 1\n```\n\nThis set the entire bottom-right block to `1`, **discarding** the actual separability information that was computed for the nested compound model. This made all outputs appear to depend on all inputs for that sub-model.\n\n## Fix\n\nChanged line 245 from `= 1` to `= right`:\n\n```python\ncright[-right.shape[0]:, -right.shape[1]:] = right\n```\n\nThis preserves the actual separability matrix computed for the nested compound model, just like the `left` branch already correctly does on line 240 (`= left`).\n\nThis is a one-line fix that makes the `right` branch consistent with the `left` branch — both now properly copy the pre-computed separability matrix instead of replacing it with all ones."
+      },
+      "notes": "Stage completed: solve",
+      "usage": {
+        "model": "claude-opus-4-6",
+        "input_tokens": 11383,
+        "output_tokens": 3256,
+        "cache_read_tokens": 173779,
+        "cache_write_tokens": 16637,
+        "reasoning_tokens": 63,
+        "cost": 0.414945
+      },
+      "files_touched": [
+        "/home/daytona/workspace/astropy_repo/astropy/modeling/separable.py"
+      ],
+      "duration_ms": 144779
     }
   },
-  "next_node_id": "solve",
+  "next_node_id": "extract_patch",
   "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,
-    "setup": 1
+    "setup": 1,
+    "solve": 1
   }
 }
\ No newline at end of file
diff --git a/nodes/solve/prompt.md b/nodes/solve/prompt.md
new file mode 100644
index 000000000..111e037eb
--- /dev/null
+++ b/nodes/solve/prompt.md
@@ -0,0 +1,57 @@
+Goal: Modeling's `separability_matrix` does not compute separability correctly for nested CompoundModels
+Consider the following model:
+
+```python
+from astropy.modeling import models as m
+from astropy.modeling.separable import separability_matrix
+
+cm = m.Linear1D(10) & m.Linear1D(5)
+```
+
+It's separability matrix as you might expect is a diagonal:
+
+```python
+>>> separability_matrix(cm)
+array([[ True, False],
+       [False,  True]])
+```
+
+If I make the model more complex:
+```python
+>>> separability_matrix(m.Pix2Sky_TAN() & m.Linear1D(10) & m.Linear1D(5))
+array([[ True,  True, False, False],
+       [ True,  True, False, False],
+       [False, False,  True, False],
+       [False, False, False,  True]])
+```
+
+The output matrix is again, as expected, the outputs and inputs to the linear models are separable and independent of each other.
+
+If however, I nest these compound models:
+```python
+>>> separability_matrix(m.Pix2Sky_TAN() & cm)
+array([[ True,  True, False, False],
+       [ True,  True, False, False],
+       [False, False,  True,  True],
+       [False, False,  True,  True]])
+```
+Suddenly the inputs and outputs are no longer separable?
+
+This feels like a bug to me, but I might be missing something?
+
+
+## Completed stages
+- **setup**: fail
+  - 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`
+  - Stdout:
+    ```
+    fatal: destination path '.' already exists and is not an empty directory.
+    ```
+  - Stderr: (empty)
+
+## Context
+- failure_class: deterministic
+- failure_signature: setup|deterministic|script failed with exit code: <n> ## stdout fatal: destination path '.' already exists and is not an empty directory.
+
+
+Fix this GitHub issue in the repository. Make the minimal code change needed.
\ No newline at end of file
diff --git a/nodes/solve/provider_used.json b/nodes/solve/provider_used.json
new file mode 100644
index 000000000..c1905ff10
--- /dev/null
+++ b/nodes/solve/provider_used.json
@@ -0,0 +1,5 @@
+{
+  "mode": "agent",
+  "provider": "anthropic",
+  "model": "claude-opus-4-6"
+}
\ No newline at end of file
diff --git a/nodes/solve/response.md b/nodes/solve/response.md
new file mode 100644
index 000000000..7d094e1ef
--- /dev/null
+++ b/nodes/solve/response.md
@@ -0,0 +1,23 @@
+The fix is applied. Here's a summary:
+
+## Root Cause
+
+In `astropy/modeling/separable.py`, the `_cstack` function handles the `&` (concatenation) operator for computing separability matrices. When the right operand is already an ndarray (which happens when it's a nested CompoundModel that has already been recursively evaluated by `_separable`), line 245 was:
+
+```python
+cright[-right.shape[0]:, -right.shape[1]:] = 1
+```
+
+This set the entire bottom-right block to `1`, **discarding** the actual separability information that was computed for the nested compound model. This made all outputs appear to depend on all inputs for that sub-model.
+
+## Fix
+
+Changed line 245 from `= 1` to `= right`:
+
+```python
+cright[-right.shape[0]:, -right.shape[1]:] = right
+```
+
+This preserves the actual separability matrix computed for the nested compound model, just like the `left` branch already correctly does on line 240 (`= left`).
+
+This is a one-line fix that makes the `right` branch consistent with the `left` branch — both now properly copy the pre-computed separability matrix instead of replacing it with all ones.
\ No newline at end of file
diff --git a/nodes/solve/status.json b/nodes/solve/status.json
new file mode 100644
index 000000000..a5185d51d
--- /dev/null
+++ b/nodes/solve/status.json
@@ -0,0 +1,6 @@
+{
+  "status": "success",
+  "notes": "Stage completed: solve",
+  "failure_reason": null,
+  "timestamp": "2026-03-16T12:00:34.997519+00:00"
+}
\ No newline at end of file