diff --git a/checkpoint.json b/checkpoint.json
index 886d8bf83..ad5b31784 100644
--- a/checkpoint.json
+++ b/checkpoint.json
@@ -1,15 +1,17 @@
 {
-  "timestamp": "2026-03-16T12:06:27.058706Z",
-  "current_node": "solve",
+  "timestamp": "2026-03-16T12:06:29.647532Z",
+  "current_node": "extract_patch",
   "completed_nodes": [
     "start",
     "setup",
-    "solve"
+    "solve",
+    "extract_patch"
   ],
   "node_retries": {
     "start": 1,
     "setup": 1,
-    "solve": 1
+    "solve": 1,
+    "extract_patch": 1
   },
   "context_values": {
     "thread.start.current_node": "setup",
@@ -18,24 +20,39 @@
     "response.solve": "Implemented the fix in the `astropy` checkout.\n\nWhat changed:\n- `astropy/io/ascii/qdp.py`\n  - Made QDP line parsing case-insensitive by compiling the line-type regex with `re.IGNORECASE`.\n  - Made `NO` masked-value handling case-insensitive too, so lowercase `no` is handled consistently once parsing is case-insensitive.\n- `astropy/io/ascii/tests/test_qdp.py`\n  - Added a regression test covering lowercase `read serr` and lowercase `no`.\n\nValidation:\n- Ran: `python -m pytest astropy/io/ascii/tests/test_qdp.py -q`\n- Result: `9 passed`\n\nAlso manually verified the reported repro now works:\n- `Table.read(..., format=\"ascii.qdp\", table_id=0, names=[\"a\", \"b\"])` successfully reads:\n  - `read serr 1 2`\n  - `1 0.5 1 0.5`\n\nFiles changed:\n- `astropy/io/ascii/qdp.py`\n- `astropy/io/ascii/tests/test_qdp.py`",
     "graph.goal": "ascii.qdp Table format assumes QDP commands are upper case\n### Description\n\nascii.qdp assumes that commands in a QDP file are upper case, for example, for errors they must be \"READ SERR 1 2\" whereas QDP itself is not case sensitive and case use \"read serr 1 2\". \r\n\r\nAs many QDP files are created by hand, the expectation that all commands be all-caps should be removed.\n\n### Expected behavior\n\nThe following qdp file should read into a `Table` with errors, rather than crashing.\r\n```\r\nread serr 1 2 \r\n1 0.5 1 0.5\r\n```\n\n### How to Reproduce\n\nCreate a QDP file:\r\n```\r\n> cat > test.qdp\r\nread serr 1 2 \r\n1 0.5 1 0.5\r\n<EOF>\r\n\r\n > python\r\nPython 3.10.9 (main, Dec  7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin\r\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\r\n>>> from astropy.table import Table\r\n>>> Table.read('test.qdp',format='ascii.qdp')\r\nWARNING: table_id not specified. Reading the first available table [astropy.io.ascii.qdp]\r\nTraceback (most recent call last):\r\n...\r\n    raise ValueError(f'Unrecognized QDP line: {line}')\r\nValueError: Unrecognized QDP line: read serr 1 2\r\n```\r\n\r\nRunning \"qdp test.qdp\" works just fine.\r\n\n\n### Versions\n\nPython 3.10.9 (main, Dec  7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)]\r\nastropy 5.1\r\nNumpy 1.24.1\r\npyerfa 2.0.0.1\r\nScipy 1.10.0\r\nMatplotlib 3.6.3\r\n\n\n\n\n## Additional Context\n\nWelcome to Astropy 👋 and thank you for your first issue!\n\nA project member will respond to you as soon as possible; in the meantime, please double-check the [guidelines for submitting issues](https://github.com/astropy/astropy/blob/main/CONTRIBUTING.md#reporting-issues) and make sure you've provided the requested details.\n\nGitHub issues in the Astropy repository are used to track bug reports and feature requests; If your issue poses a question about how to use Astropy, please instead raise your question in the [Astropy Discourse user forum](https://community.openastronomy.org/c/astropy/8) and close this issue.\n\nIf you feel that this issue has not been responded to in a timely manner, please send a message directly to the [development mailing list](http://groups.google.com/group/astropy-dev).  If the issue is urgent or sensitive in nature (e.g., a security vulnerability) please send an e-mail directly to the private e-mail feedback@astropy.org.\nHuh, so we do have this format... https://docs.astropy.org/en/stable/io/ascii/index.html\r\n\r\n@taldcroft , you know anything about this?\nThis is the format I'm using, which has the issue: https://docs.astropy.org/en/stable/api/astropy.io.ascii.QDP.html\r\n\nThe issue is that the regex that searches for QDP commands is not case insensitive. \r\n\r\nThis attached patch fixes the issue, but I'm sure there's a better way of doing it.\r\n\r\n[qdp.patch](https://github.com/astropy/astropy/files/10667923/qdp.patch)\r\n\n@jak574 - the fix is probably as simple as that. Would you like to put in a bugfix PR?",
     "internal.retry_count.start": 1,
-    "current.preamble": "Goal: ascii.qdp Table format assumes QDP commands are upper case\n### Description\n\nascii.qdp assumes that commands in a QDP file are upper case, for example, for errors they must be \"READ SERR 1 2\" whereas QDP itself is not case sensitive and case use \"read serr 1 2\". \r\n\r\nAs many QDP files are created by hand, the expectation that all commands be all-caps should be removed.\n\n### Expected behavior\n\nThe following qdp file should read into a `Table` with errors, rather than crashing.\r\n```\r\nread serr 1 2 \r\n1 0.5 1 0.5\r\n```\n\n### How to Reproduce\n\nCreate a QDP file:\r\n```\r\n> cat > test.qdp\r\nread serr 1 2 \r\n1 0.5 1 0.5\r\n<EOF>\r\n\r\n > python\r\nPython 3.10.9 (main, Dec  7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin\r\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\r\n>>> from astropy.table import Table\r\n>>> Table.read('test.qdp',format='ascii.qdp')\r\nWARNING: table_id not specified. Reading the first available table [astropy.io.ascii.qdp]\r\nTraceback (most recent call last):\r\n...\r\n    raise ValueError(f'Unrecognized QDP line: {line}')\r\nValueError: Unrecognized QDP line: read serr 1 2\r\n```\r\n\r\nRunning \"qdp test.qdp\" works just fine.\r\n\n\n### Versions\n\nPython 3.10.9 (main, Dec  7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)]\r\nastropy 5.1\r\nNumpy 1.24.1\r\npyerfa 2.0.0.1\r\nScipy 1.10.0\r\nMatplotlib 3.6.3\r\n\n\n\n\n## Additional Context\n\nWelcome to Astropy 👋 and thank you for your first issue!\n\nA project member will respond to you as soon as possible; in the meantime, please double-check the [guidelines for submitting issues](https://github.com/astropy/astropy/blob/main/CONTRIBUTING.md#reporting-issues) and make sure you've provided the requested details.\n\nGitHub issues in the Astropy repository are used to track bug reports and feature requests; If your issue poses a question about how to use Astropy, please instead raise your question in the [Astropy Discourse user forum](https://community.openastronomy.org/c/astropy/8) and close this issue.\n\nIf you feel that this issue has not been responded to in a timely manner, please send a message directly to the [development mailing list](http://groups.google.com/group/astropy-dev).  If the issue is urgent or sensitive in nature (e.g., a security vulnerability) please send an e-mail directly to the private e-mail feedback@astropy.org.\nHuh, so we do have this format... https://docs.astropy.org/en/stable/io/ascii/index.html\r\n\r\n@taldcroft , you know anything about this?\nThis is the format I'm using, which has the issue: https://docs.astropy.org/en/stable/api/astropy.io.ascii.QDP.html\r\n\nThe issue is that the regex that searches for QDP commands is not case insensitive. \r\n\r\nThis attached patch fixes the issue, but I'm sure there's a better way of doing it.\r\n\r\n[qdp.patch](https://github.com/astropy/astropy/files/10667923/qdp.patch)\r\n\n@jak574 - the fix is probably as simple as that. Would you like to put in a bugfix PR?\n\n## Completed stages\n- **setup**: fail\n  - Script: `git clone https://github.com/astropy/astropy.git . && git checkout 7269fa3e33e8d02485a647da91a5a2a60a06af61 && 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: ascii.qdp Table format assumes QDP commands are upper case\n### Description\n\nascii.qdp assumes that commands in a QDP file are upper case, for example, for errors they must be \"READ SERR 1 2\" whereas QDP itself is not case sensitive and case use \"read serr 1 2\". \r\n\r\nAs many QDP files are created by hand, the expectation that all commands be all-caps should be removed.\n\n### Expected behavior\n\nThe following qdp file should read into a `Table` with errors, rather than crashing.\r\n```\r\nread serr 1 2 \r\n1 0.5 1 0.5\r\n```\n\n### How to Reproduce\n\nCreate a QDP file:\r\n```\r\n> cat > test.qdp\r\nread serr 1 2 \r\n1 0.5 1 0.5\r\n<EOF>\r\n\r\n > python\r\nPython 3.10.9 (main, Dec  7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin\r\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\r\n>>> from astropy.table import Table\r\n>>> Table.read('test.qdp',format='ascii.qdp')\r\nWARNING: table_id not specified. Reading the first available table [astropy.io.ascii.qdp]\r\nTraceback (most recent call last):\r\n...\r\n    raise ValueError(f'Unrecognized QDP line: {line}')\r\nValueError: Unrecognized QDP line: read serr 1 2\r\n```\r\n\r\nRunning \"qdp test.qdp\" works just fine.\r\n\n\n### Versions\n\nPython 3.10.9 (main, Dec  7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)]\r\nastropy 5.1\r\nNumpy 1.24.1\r\npyerfa 2.0.0.1\r\nScipy 1.10.0\r\nMatplotlib 3.6.3\r\n\n\n\n\n## Additional Context\n\nWelcome to Astropy 👋 and thank you for your first issue!\n\nA project member will respond to you as soon as possible; in the meantime, please double-check the [guidelines for submitting issues](https://github.com/astropy/astropy/blob/main/CONTRIBUTING.md#reporting-issues) and make sure you've provided the requested details.\n\nGitHub issues in the Astropy repository are used to track bug reports and feature requests; If your issue poses a question about how to use Astropy, please instead raise your question in the [Astropy Discourse user forum](https://community.openastronomy.org/c/astropy/8) and close this issue.\n\nIf you feel that this issue has not been responded to in a timely manner, please send a message directly to the [development mailing list](http://groups.google.com/group/astropy-dev).  If the issue is urgent or sensitive in nature (e.g., a security vulnerability) please send an e-mail directly to the private e-mail feedback@astropy.org.\nHuh, so we do have this format... https://docs.astropy.org/en/stable/io/ascii/index.html\r\n\r\n@taldcroft , you know anything about this?\nThis is the format I'm using, which has the issue: https://docs.astropy.org/en/stable/api/astropy.io.ascii.QDP.html\r\n\nThe issue is that the regex that searches for QDP commands is not case insensitive. \r\n\r\nThis attached patch fixes the issue, but I'm sure there's a better way of doing it.\r\n\r\n[qdp.patch](https://github.com/astropy/astropy/files/10667923/qdp.patch)\r\n\n@jak574 - the fix is probably as simple as that. Would you like to put in a bugfix PR?\n\n## Completed stages\n- **setup**: fail\n  - Script: `git clone https://github.com/astropy/astropy.git . && git checkout 7269fa3e33e8d02485a647da91a5a2a60a06af61 && 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, 958.3k tokens in / 8.8k out\n",
     "outcome": "success",
     "last_response": "Implemented the fix in the `astropy` checkout.\n\nWhat changed:\n- `astropy/io/ascii/qdp.py`\n  - Made QDP line parsing case-insensitive by compiling the line-type regex with `re.IGNORECASE`.\n  - Made `NO",
-    "internal.thread_id": "setup",
+    "internal.thread_id": "solve",
+    "internal.retry_count.extract_patch": 1,
     "internal.fidelity": "compact",
     "thread.setup.current_node": "solve",
     "internal.retry_count.solve": 1,
     "last_stage": "solve",
     "internal.run_id": "01KKV8D5GS2X8B3R6MJ7BEP47B",
     "graph.rankdir": "LR",
-    "current_node": "solve",
-    "command.output": "fatal: destination path '.' already exists and is not an empty directory.\n",
+    "current_node": "extract_patch",
+    "command.output": "diff --git a/astropy b/astropy\n--- a/astropy\n+++ b/astropy\n@@ -1 +1 @@\n-Subproject commit 7269fa3e33e8d02485a647da91a5a2a60a06af61\n+Subproject commit 7269fa3e33e8d02485a647da91a5a2a60a06af61-dirty\n",
     "command.stderr": "",
     "failure_class": "",
+    "thread.solve.current_node": "extract_patch",
     "failure_signature": ""
   },
   "logs": [],
   "node_outcomes": {
+    "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 7269fa3e33e8d02485a647da91a5a2a60a06af61\n+Subproject commit 7269fa3e33e8d02485a647da91a5a2a60a06af61-dirty\n"
+      },
+      "notes": "Script completed: git diff",
+      "duration_ms": 54
+    },
+    "start": {
+      "status": "success",
+      "duration_ms": 0
+    },
     "setup": {
       "status": "fail",
       "context_updates": {
@@ -48,10 +65,6 @@
       },
       "duration_ms": 50
     },
-    "start": {
-      "status": "success",
-      "duration_ms": 0
-    },
     "solve": {
       "status": "success",
       "context_updates": {
@@ -71,13 +84,14 @@
       "duration_ms": 236883
     }
   },
-  "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,
+    "extract_patch": 1,
+    "setup": 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..3ec21f9cf
--- /dev/null
+++ b/nodes/extract_patch/script_timing.json
@@ -0,0 +1,5 @@
+{
+  "duration_ms": 54,
+  "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..f6d0e9e3d
--- /dev/null
+++ b/nodes/extract_patch/status.json
@@ -0,0 +1,6 @@
+{
+  "status": "success",
+  "notes": "Script completed: git diff",
+  "failure_reason": null,
+  "timestamp": "2026-03-16T12:06:29.647337+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..53a7f7ef8
--- /dev/null
+++ b/nodes/solve/diff.patch
@@ -0,0 +1,7 @@
+diff --git a/astropy b/astropy
+new file mode 160000
+index 0000000..7269fa3
+--- /dev/null
++++ b/astropy
+@@ -0,0 +1 @@
++Subproject commit 7269fa3e33e8d02485a647da91a5a2a60a06af61