diff --git a/src/repoma/check_dev_files/commitlint.py b/src/repoma/check_dev_files/commitlint.py
index 78032884..057d9145 100644
--- a/src/repoma/check_dev_files/commitlint.py
+++ b/src/repoma/check_dev_files/commitlint.py
@@ -4,6 +4,7 @@
 """
 
 import os
+from textwrap import dedent
 
 from repoma.errors import PrecommitError
 
@@ -13,5 +14,8 @@ def main() -> None:
     if not os.path.exists(path):
         return
     os.remove(path)
-    msg = f"Remove outdated {path}"
+    msg = dedent(f"""
+    Remove outdated {path}. Commitlint is now configured through
+    https://github.com/ComPWA/commitlint-config.
+    """).strip().replace("\n", " ")
     raise PrecommitError(msg)
diff --git a/src/repoma/check_dev_files/ruff.py b/src/repoma/check_dev_files/ruff.py
index 41be2e29..c966ceaa 100644
--- a/src/repoma/check_dev_files/ruff.py
+++ b/src/repoma/check_dev_files/ruff.py
@@ -8,6 +8,7 @@
 from ruamel.yaml import YAML
 from ruamel.yaml.comments import CommentedMap
 from tomlkit.items import Array, Table
+from tomlkit.toml_document import TOMLDocument
 
 from repoma.check_dev_files.setup_cfg import (
     has_pyproject_build_system,
@@ -50,11 +51,9 @@ def main(has_notebooks: bool) -> None:
     executor(_check_setup_cfg)
     executor(_remove_flake8)
     executor(_remove_isort)
-    executor(_remove_nbqa)
     executor(_remove_pydocstyle)
     executor(_remove_pylint)
     executor(_update_ruff_settings, has_notebooks)
-    executor(_update_ruff_per_file_ignores, has_notebooks)
     executor(_update_ruff_pydocstyle_settings)
     executor(_update_precommit_hook, has_notebooks)
     executor(_update_pyproject)
@@ -289,6 +288,14 @@ def __remove_nbqa_settings() -> None:
 
 
 def _update_ruff_settings(has_notebooks: bool) -> None:
+    executor = Executor()
+    executor(__update_ruff_settings, has_notebooks)
+    executor(_update_ruff_per_file_ignores, has_notebooks)
+    executor(_remove_nbqa)
+    executor.finalize()
+
+
+def __update_ruff_settings(has_notebooks: bool) -> None:
     pyproject = load_pyproject()
     settings = get_sub_table(pyproject, "tool.ruff", create=True)
     extend_ignore = [
@@ -335,6 +342,37 @@ def _update_ruff_settings(has_notebooks: bool) -> None:
         raise PrecommitError(msg)
 
 
+def __get_ipynb_ignores(pyproject: TOMLDocument, per_file_settings: Table) -> Array:
+    notebook_ignores = {
+        "B018",  # useless-expression
+        "C90",  # complex-structure
+        "D",  # pydocstyle
+        "E703",  #  useless-semicolon
+        "N806",  # non-lowercase-variable-in-function
+        "N816",  # mixed-case-variable-in-global-scope
+        "PLR09",  # complicated logic
+        "PLR2004",  # magic-value-comparison
+        "PLW0602",  # global-variable-not-assigned
+        "PLW0603",  # global-statement
+        "TCH00",  # type-checking block
+    }
+    notebook_ignores.update(__get_existing_nbqa_ignores(pyproject))
+    notebook_ignores.update(per_file_settings.get("*.ipynb", []))
+    return to_toml_array(sorted(notebook_ignores))
+
+
+def __get_existing_nbqa_ignores(pyproject: TOMLDocument) -> Set[str]:
+    nbqa_table = get_sub_table(pyproject, "tool.nbqa.addopts", create=True)
+    if not nbqa_table:
+        return set()
+    ruff_rules: List[str] = nbqa_table.get("ruff", [])
+    return {
+        r.replace("--extend-ignore=", "")
+        for r in ruff_rules
+        if r.startswith("--extend-ignore=")
+    }
+
+
 def __get_selected_ruff_rules() -> Array:
     rules = {
         "A",
@@ -412,18 +450,7 @@ def _update_ruff_per_file_ignores(has_notebooks: bool) -> None:
     settings = get_sub_table(pyproject, "tool.ruff.per-file-ignores", create=True)
     minimal_settings = {}
     if has_notebooks:
-        notebook_ignores = [
-            "B018",
-            "C90",
-            "D",
-            "N806",
-            "N816",
-            "PLR09",
-            "PLR2004",
-            "PLW0602",
-            "PLW0603",
-        ]
-        minimal_settings["*.ipynb"] = to_toml_array(notebook_ignores)
+        minimal_settings["*.ipynb"] = __get_ipynb_ignores(pyproject, settings)
     docs_dir = "docs"
     if os.path.exists(docs_dir) and os.path.isdir(docs_dir):
         key = f"{docs_dir}/*"