diff --git a/.amazonq/rules/memory-bank/guidelines.md b/.amazonq/rules/memory-bank/guidelines.md
index 0bac9cc3c..9e2ac2f4d 100644
--- a/.amazonq/rules/memory-bank/guidelines.md
+++ b/.amazonq/rules/memory-bank/guidelines.md
@@ -366,12 +366,12 @@
       coverage_root: Path | None = None,
   ) -> tuple[list[str], list[str]]:
       """Normalize filenames within a Cobertura XML report.
-      
+
       Args:
           report_path: Path to the Cobertura XML.
           repo_root: Root of the repository.
           coverage_root: Directory gcovr treated as root.
-      
+
       Returns:
           A tuple containing missing files and external files.
       """
diff --git a/.github/actions/README.md b/.github/actions/README.md
index 8f4537f8e..137687865 100644
--- a/.github/actions/README.md
+++ b/.github/actions/README.md
@@ -92,24 +92,24 @@ jobs:
     runs-on: ubuntu-24.04
     container:
       image: ghcr.io/framework-r-d/phlex-ci:latest
-    
+
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
       with:
         path: phlex-src
-    
+
     - name: Setup build environment
       uses: ./phlex-src/.github/actions/setup-build-env
-    
+
     - name: Configure CMake
       uses: ./phlex-src/.github/actions/configure-cmake
       with:
         build-type: Release
-    
+
     - name: Build
       uses: ./phlex-src/.github/actions/build-cmake
-    
+
     - name: Run tests
       run: |
         . /entrypoint.sh
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 70d85b24d..e3d6073ff 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -39,3 +39,8 @@ repos:
     hooks:
       - id: prettier
         types_or: [yaml]
+  - repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.21.0
+    hooks:
+      - id: markdownlint-cli2
+        args: [--fix]
diff --git a/.prettierignore b/.prettierignore
new file mode 100644
index 000000000..cc9fad3bd
--- /dev/null
+++ b/.prettierignore
@@ -0,0 +1,2 @@
+.clang-format
+.clang-tidy
diff --git a/DEVELOPING.md b/DEVELOPING.md
index f915e6252..6e8ee3e81 100644
--- a/DEVELOPING.md
+++ b/DEVELOPING.md
@@ -131,7 +131,7 @@ To set up this tool locally, first install `pre-commit` (or `prek`, a faster re-
 
 So set up the hooks in the Phlex repository, run the `pre-commit install` command once in the repository. The hooks now should run automatically prior to each commit.
 
-To skip a check temporarily, run `SKIP=ruff-format git commit -m "...". To skip all hooks, you can use the `--no-verify` flag to `git commit`.
+To skip a check temporarily, run `SKIP=ruff-format git commit -m "..."`. To skip all hooks, you can use the `--no-verify` flag to `git commit`.
 
 To manually run hooks over all files, run `pre-commit run --all-files`.
 
diff --git a/Modules/CMakeLists.txt b/Modules/CMakeLists.txt
deleted file mode 100644
index 8b1378917..000000000
--- a/Modules/CMakeLists.txt
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/plugins/python/python/phlex/_typing.py b/plugins/python/python/phlex/_typing.py
index dede90608..34018a205 100644
--- a/plugins/python/python/phlex/_typing.py
+++ b/plugins/python/python/phlex/_typing.py
@@ -78,7 +78,7 @@ def _build_ctypes_map() -> dict[type, str]:
     for tp in _CTYPES_INTEGER:
         bits = ctypes.sizeof(tp) * 8
         # _type_ uses struct format chars: lowercase = signed, uppercase = unsigned
-        signed = tp._type_.islower() # type: ignore # somehow mypy is confused
+        signed = tp._type_.islower()  # type: ignore # somehow mypy is confused
         result[tp] = f"{'int' if signed else 'uint'}{bits}_t"
     return result
 
diff --git a/test/demo-giantdata/waveform_generator.cpp b/test/demo-giantdata/waveform_generator.cpp
index 101b89a29..069cf30cf 100644
--- a/test/demo-giantdata/waveform_generator.cpp
+++ b/test/demo-giantdata/waveform_generator.cpp
@@ -25,4 +25,4 @@ std::pair<std::size_t, demo::Waveforms> demo::WaveformGenerator::op(std::size_t
   auto result =
     std::make_pair(made_so_far + newsize, Waveforms{newsize, 1.0 * made_so_far, -1, -1, -1, -1});
   return result;
-}
\ No newline at end of file
+}
diff --git a/test/python/test_typing.py b/test/python/test_typing.py
index 12cf1898e..69ce1afba 100644
--- a/test/python/test_typing.py
+++ b/test/python/test_typing.py
@@ -66,7 +66,7 @@ def test_numpy_array_normalization(self):
             (np.float32, "float"),
             (np.float64, "double"),
         ):
-            assert normalize_type(npt.NDArray[t]) == "ndarray["+s+"]"
+            assert normalize_type(npt.NDArray[t]) == "ndarray[" + s + "]"
 
     def test_special_cases(self):
         """Special cases."""
@@ -74,8 +74,8 @@ def test_special_cases(self):
         assert normalize_type(None) == "None"
 
         # use of namespaces for evaluation
-        assert("foo") == "foo"
-        global foo # lgtm[py/unused-global-variable]
+        assert ("foo") == "foo"
+        global foo  # lgtm[py/unused-global-variable]
         foo = np.int64
         assert normalize_type("foo", globals()) == "int64_t"
         bar = np.int32