diff --git a/.markdown-link-config.json b/.markdown-link-config.json
new file mode 100644
index 00000000..de14e9ec
--- /dev/null
+++ b/.markdown-link-config.json
@@ -0,0 +1,7 @@
+{
+  "ignorePatterns": [
+    {
+      "pattern": "@ref"
+    }
+  ]
+}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 084d359d..49f1c39c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -28,7 +28,7 @@ repos:
   - repo: https://github.com/igorshubovych/markdownlint-cli
     rev: v0.37.0
     hooks:
-      - id: markdownlint
+      - id: markdownlint-fix
   - repo: https://github.com/citation-file-format/cffconvert
     rev: 054bda51dbe278b3e86f27c890e3f3ac877d616c
     hooks:
@@ -51,3 +51,5 @@ repos:
     rev: v3.11.2
     hooks:
       - id: markdown-link-check
+        args:
+          - --config=.markdown-link-config.json
diff --git a/copier.yml b/copier.yml
index 73dd09c7..9118e426 100644
--- a/copier.yml
+++ b/copier.yml
@@ -62,6 +62,6 @@ _skip_if_exists:
   - "**/*.jl"
   - "!docs/make.jl"
   - "**/*.md"
-  - "**/*.toml"
+  - "**/Project.toml"
   - CITATION.cff
   - LICENSE