diff --git a/checkpoint.json b/checkpoint.json
index afce0fa5f..652b91bc6 100644
--- a/checkpoint.json
+++ b/checkpoint.json
@@ -1,21 +1,24 @@
 {
-  "timestamp": "2026-03-16T12:01:41.355870Z",
-  "current_node": "solve",
+  "timestamp": "2026-03-16T12:01:43.727004Z",
+  "current_node": "extract_patch",
   "completed_nodes": [
     "start",
     "setup",
-    "solve"
+    "solve",
+    "extract_patch"
   ],
   "node_retries": {
-    "setup": 1,
     "solve": 1,
+    "setup": 1,
+    "extract_patch": 1,
     "start": 1
   },
   "context_values": {
     "failure_class": "",
+    "thread.solve.current_node": "extract_patch",
     "internal.node_visit_count": 1,
-    "current.preamble": "Goal: Please support header rows in RestructuredText output\n### Description\r\n\r\nIt would be great if the following would work:\r\n\r\n```Python\r\n>>> from astropy.table import QTable\r\n>>> import astropy.units as u\r\n>>> import sys\r\n>>> tbl = QTable({'wave': [350,950]*u.nm, 'response': [0.7, 1.2]*u.count})\r\n>>> tbl.write(sys.stdout,  format=\"ascii.rst\")\r\n===== ========\r\n wave response\r\n===== ========\r\n350.0      0.7\r\n950.0      1.2\r\n===== ========\r\n>>> tbl.write(sys.stdout,  format=\"ascii.fixed_width\", header_rows=[\"name\", \"unit\"])\r\n|  wave | response |\r\n|    nm |       ct |\r\n| 350.0 |      0.7 |\r\n| 950.0 |      1.2 |\r\n>>> tbl.write(sys.stdout,  format=\"ascii.rst\", header_rows=[\"name\", \"unit\"])\r\nTraceback (most recent call last):\r\n  File \"<stdin>\", line 1, in <module>\r\n  File \"/usr/lib/python3/dist-packages/astropy/table/connect.py\", line 129, in __call__\r\n    self.registry.write(instance, *args, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/registry/core.py\", line 369, in write\r\n    return writer(data, *args, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/ascii/connect.py\", line 26, in io_write\r\n    return write(table, filename, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/ascii/ui.py\", line 856, in write\r\n    writer = get_writer(Writer=Writer, fast_writer=fast_writer, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/ascii/ui.py\", line 800, in get_writer\r\n    writer = core._get_writer(Writer, fast_writer, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/ascii/core.py\", line 1719, in _get_writer\r\n    writer = Writer(**writer_kwargs)\r\nTypeError: RST.__init__() got an unexpected keyword argument 'header_rows'\r\n```\r\n\r\n\r\n### Additional context\r\n\r\nRestructuredText output is a great way to fill autogenerated documentation with content, so having this flexible makes the life easier `:-)`\r\n\r\n\n\n\n## Completed stages\n- **setup**: fail\n  - Script: `git clone https://github.com/astropy/astropy.git . && git checkout a5917978be39d13cd90b517e1de4e7a539ffaa48 && 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",
-    "command.output": "fatal: destination path '.' already exists and is not an empty directory.\n",
+    "current.preamble": "Goal: Please support header rows in RestructuredText output\n### Description\r\n\r\nIt would be great if the following would work:\r\n\r\n```Python\r\n>>> from astropy.table import QTable\r\n>>> import astropy.units as u\r\n>>> import sys\r\n>>> tbl = QTable({'wave': [350,950]*u.nm, 'response': [0.7, 1.2]*u.count})\r\n>>> tbl.write(sys.stdout,  format=\"ascii.rst\")\r\n===== ========\r\n wave response\r\n===== ========\r\n350.0      0.7\r\n950.0      1.2\r\n===== ========\r\n>>> tbl.write(sys.stdout,  format=\"ascii.fixed_width\", header_rows=[\"name\", \"unit\"])\r\n|  wave | response |\r\n|    nm |       ct |\r\n| 350.0 |      0.7 |\r\n| 950.0 |      1.2 |\r\n>>> tbl.write(sys.stdout,  format=\"ascii.rst\", header_rows=[\"name\", \"unit\"])\r\nTraceback (most recent call last):\r\n  File \"<stdin>\", line 1, in <module>\r\n  File \"/usr/lib/python3/dist-packages/astropy/table/connect.py\", line 129, in __call__\r\n    self.registry.write(instance, *args, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/registry/core.py\", line 369, in write\r\n    return writer(data, *args, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/ascii/connect.py\", line 26, in io_write\r\n    return write(table, filename, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/ascii/ui.py\", line 856, in write\r\n    writer = get_writer(Writer=Writer, fast_writer=fast_writer, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/ascii/ui.py\", line 800, in get_writer\r\n    writer = core._get_writer(Writer, fast_writer, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/ascii/core.py\", line 1719, in _get_writer\r\n    writer = Writer(**writer_kwargs)\r\nTypeError: RST.__init__() got an unexpected keyword argument 'header_rows'\r\n```\r\n\r\n\r\n### Additional context\r\n\r\nRestructuredText output is a great way to fill autogenerated documentation with content, so having this flexible makes the life easier `:-)`\r\n\r\n\n\n\n## Completed stages\n- **setup**: fail\n  - Script: `git clone https://github.com/astropy/astropy.git . && git checkout a5917978be39d13cd90b517e1de4e7a539ffaa48 && 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, 22.0k tokens in / 5.5k out\n  - Files: /tmp/astropy/astropy/io/ascii/rst.py\n",
+    "command.output": "",
     "thread.setup.current_node": "solve",
     "response.solve": "The fix works perfectly. Here's a summary of the minimal change made:\n\n## Changes Made\n\n**File: `astropy/io/ascii/rst.py`** (2 changes in the `RST` class)\n\n1. **`__init__` method**: Added `header_rows=None` parameter and passed it through to the parent `FixedWidth.__init__()`:\n   - Before: `def __init__(self):` → `super().__init__(delimiter_pad=None, bookend=False)`\n   - After: `def __init__(self, header_rows=None):` → `super().__init__(delimiter_pad=None, bookend=False, header_rows=header_rows)`\n\n2. **`write` method**: Made the position line index dynamic instead of hardcoded to `1`:\n   - Before: `lines = [lines[1]] + lines + [lines[1]]`\n   - After: `idx = len(self.header.header_rows)` then `lines = [lines[idx]] + lines + [lines[idx]]`\n\nThe hardcoded `lines[1]` only worked when there was exactly 1 header row (the \"name\" row), because the position/separator line (`=====`) was always at index 1. With multiple header rows (e.g., `[\"name\", \"unit\"]`), the separator line moves to a later index — specifically `len(header_rows)`.",
     "last_stage": "solve",
@@ -23,19 +26,45 @@
     "internal.retry_count.solve": 1,
     "internal.retry_count.setup": 1,
     "internal.fidelity": "compact",
+    "internal.retry_count.extract_patch": 1,
     "graph.rankdir": "LR",
     "thread.start.current_node": "setup",
     "last_response": "The fix works perfectly. Here's a summary of the minimal change made:\n\n## Changes Made\n\n**File: `astropy/io/ascii/rst.py`** (2 changes in the `RST` class)\n\n1. **`__init__` method**: Added `header_rows",
     "command.stderr": "",
     "internal.run_id": "01KKV857HVVYX8Z5MRDPYTFTA4",
-    "internal.thread_id": "setup",
+    "internal.thread_id": "solve",
     "failure_signature": "",
     "graph.goal": "Please support header rows in RestructuredText output\n### Description\r\n\r\nIt would be great if the following would work:\r\n\r\n```Python\r\n>>> from astropy.table import QTable\r\n>>> import astropy.units as u\r\n>>> import sys\r\n>>> tbl = QTable({'wave': [350,950]*u.nm, 'response': [0.7, 1.2]*u.count})\r\n>>> tbl.write(sys.stdout,  format=\"ascii.rst\")\r\n===== ========\r\n wave response\r\n===== ========\r\n350.0      0.7\r\n950.0      1.2\r\n===== ========\r\n>>> tbl.write(sys.stdout,  format=\"ascii.fixed_width\", header_rows=[\"name\", \"unit\"])\r\n|  wave | response |\r\n|    nm |       ct |\r\n| 350.0 |      0.7 |\r\n| 950.0 |      1.2 |\r\n>>> tbl.write(sys.stdout,  format=\"ascii.rst\", header_rows=[\"name\", \"unit\"])\r\nTraceback (most recent call last):\r\n  File \"<stdin>\", line 1, in <module>\r\n  File \"/usr/lib/python3/dist-packages/astropy/table/connect.py\", line 129, in __call__\r\n    self.registry.write(instance, *args, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/registry/core.py\", line 369, in write\r\n    return writer(data, *args, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/ascii/connect.py\", line 26, in io_write\r\n    return write(table, filename, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/ascii/ui.py\", line 856, in write\r\n    writer = get_writer(Writer=Writer, fast_writer=fast_writer, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/ascii/ui.py\", line 800, in get_writer\r\n    writer = core._get_writer(Writer, fast_writer, **kwargs)\r\n  File \"/usr/lib/python3/dist-packages/astropy/io/ascii/core.py\", line 1719, in _get_writer\r\n    writer = Writer(**writer_kwargs)\r\nTypeError: RST.__init__() got an unexpected keyword argument 'header_rows'\r\n```\r\n\r\n\r\n### Additional context\r\n\r\nRestructuredText output is a great way to fill autogenerated documentation with content, so having this flexible makes the life easier `:-)`\r\n\r\n\n",
-    "current_node": "solve",
+    "current_node": "extract_patch",
     "outcome": "success"
   },
   "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": 137
+    },
+    "start": {
+      "status": "success",
+      "duration_ms": 0
+    },
+    "extract_patch": {
+      "status": "success",
+      "context_updates": {
+        "command.output": "",
+        "command.stderr": ""
+      },
+      "notes": "Script completed: git diff",
+      "duration_ms": 57
+    },
     "solve": {
       "status": "success",
       "context_updates": {
@@ -57,31 +86,16 @@
         "/tmp/astropy/astropy/io/ascii/rst.py"
       ],
       "duration_ms": 210600
-    },
-    "start": {
-      "status": "success",
-      "duration_ms": 0
-    },
-    "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": 137
     }
   },
-  "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": {
-    "solve": 1,
+    "setup": 1,
+    "extract_patch": 1,
     "start": 1,
-    "setup": 1
+    "solve": 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..7f2f377e0
--- /dev/null
+++ b/nodes/extract_patch/script_timing.json
@@ -0,0 +1,5 @@
+{
+  "duration_ms": 53,
+  "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..4b9275aa1
--- /dev/null
+++ b/nodes/extract_patch/status.json
@@ -0,0 +1,6 @@
+{
+  "status": "success",
+  "notes": "Script completed: git diff",
+  "failure_reason": null,
+  "timestamp": "2026-03-16T12:01:43.724806+00:00"
+}
\ No newline at end of file