diff --git a/Makefile b/Makefile
index c47cb750a..d5d709fca 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-.PHONY: clean clean-gallery
+.PHONY: clean clean-gallery clean-prep clean-full
 
 SPHINXOPTS =
 
@@ -18,10 +18,17 @@ clean:
 	rm -rf $(docs_dir)/_build/
 	rm -rf $(docs_dir)/api/napari*.rst
 
+clean-prep: clean
+	rm -rf $(docs_dir)/guides/preferences.md
+	rm -rf $(docs_dir)/developers/architecture/ui_sections/*ui.md
+	rm -rf $(doc_dir)/plugins/_npe2*.md
+
 clean-gallery:
 	rm -rf $(docs_dir)/gallery/*
 	rm -rf $(docs_dir)/_tags
 
+clean-full: clean-prep clean-gallery
+
 prep-docs:
 	python $(docs_dir)/_scripts/prep_docs.py
 
diff --git a/docs/_scripts/prep_docs.py b/docs/_scripts/prep_docs.py
index 0924c4dbf..8af6a9ccc 100644
--- a/docs/_scripts/prep_docs.py
+++ b/docs/_scripts/prep_docs.py
@@ -30,20 +30,21 @@ def prep_npe2():
 
 def main(stubs=False):
     if stubs:
+        #prep_npe2()
         # Generate stub files for plugin docs
-        plugin_docs = [
-            "plugins/_npe2_sample_data_guide.md",
-            "plugins/_npe2_readers_guide.md",
-            "plugins/_npe2_widgets_guide.md",
-            "plugins/_npe2_manifest.md",
-            "plugins/_npe2_writers_guide.md",
-            "plugins/_npe2_contributions.md",
-        ]
-        for doc in plugin_docs:
+        plugin_docs = {
+            "plugins/_npe2_sample_data_guide.md": "(sample-data-contribution-guide)=\n",
+            "plugins/_npe2_readers_guide.md": "(readers-contribution-guide)=\n",
+            "plugins/_npe2_widgets_guide.md": "(widgets-contribution-guide)=\n",
+            "plugins/_npe2_manifest.md": "# Manifest Reference\n",
+            "plugins/_npe2_writers_guide.md": "(writers-contribution-guide)=\n",
+            "plugins/_npe2_contributions.md": "# Contributions Reference\n(contributions-themes)=\n(contributions-commands)=\n(contributions-widgets)=\n(contributions-readers)=\n(contributions-writers)=\n(contributions-sample-data)=\n(layer-type-constraints)=\n",
+        }
+        for doc, target in plugin_docs.items():
             file_path = DOCS / doc
-            if not file_path.exists():  # Avoid overwriting existing files
+            if file_path.exists():  # Avoid overwriting existing files
                 file_path.write_text(
-                    "This is a stub. The real file is autogenerated in a full build.",
+                    f"{target}This is a stub. The real file is autogenerated in a full build.",
                     encoding="utf-8",
                 )
         # Generate stub files from the other scripts
diff --git a/docs/_scripts/update_preference_docs.py b/docs/_scripts/update_preference_docs.py
index d8db8d15f..85a9fb944 100644
--- a/docs/_scripts/update_preference_docs.py
+++ b/docs/_scripts/update_preference_docs.py
@@ -182,7 +182,7 @@ def main(stubs=False):
         file_path = GUIDES_PATH / "preferences.md"
         if not file_path.exists():  # Avoid overwriting existing files
             file_path.write_text(
-                "This is a stub. The real file is autogenerated in a full build.",
+                "(napari-preferences)=\n# Preferences\nThis is a stub. The real file is autogenerated in a full build.",
                 encoding="utf-8",
             )
     else:
diff --git a/docs/_scripts/update_ui_sections_docs.py b/docs/_scripts/update_ui_sections_docs.py
index 792139f2d..0fd2a1e3a 100644
--- a/docs/_scripts/update_ui_sections_docs.py
+++ b/docs/_scripts/update_ui_sections_docs.py
@@ -707,7 +707,7 @@ def main(stubs=False):
             if not output_page.exists():  # Avoid overwriting existing files
                 output_page.parent.mkdir(exist_ok=True, parents=True)
                 output_page.write_text(
-                    "This is a stub. The real file is autogenerated in a full build.",
+                    f"## {section_name}\nThis is a stub. The real file is autogenerated in a full build.",
                     encoding="utf-8",
                 )
         else: