Not sure if I understand your issue correctly

If I remove guides, the sidebar stops working for everything, I get a list of Example reference, Resources and my directory.

This is what an _index.md page looks like —by design (node_modules/@thulite/doks-core/layouts/_default/list.html):

This is what an index.md page looks like —by design (node_modules/@thulite/doks-core/layouts/_default/single.html):

If you'd like to have the sidebar on the _index.md pages, you'd have to copy node_modules/@thulite/doks-core/layouts/_default/list.html and paste as layouts/_default/list.html and make your changes in the latter (see node_modules/@thulite/doks-core/layouts/_default/single.html)

Thanks for looking into this!

I just created a sample project to test, here are exactly the steps I took:

npm create thulite@latest sidebar.com -- --template doks
cd sidebar.com
npm install
npm run dev

Here is a list of index.md files (there are no index.md files in docs):

find . -name index.md
./content/blog/example/index.md
./node_modules/@thulite/doks-core/archetypes/docs/lorem/ipsum/index.md

Docs has a sidebar:

Then I remove guides and change the url for the docs menu:

rm -Rf content/docs/guides/

# config/_default/menus/menus.en.toml

[[main]]
  name = "Docs"
  url = "/docs/" # I added this line
#  url = "/docs/guides/example-guide/" # this was the default
# url = "/docs/1.0/prologue/introduction/"
  weight = 10

Sidebar disappears

I can test creating an index.md file, but I don't understand how the sidebar worked out of the box without any index.md files or why the sidebar disappears when the guides directory is deleted?

I guess it needs an actual landing page, if I create a file called my_docs.md in /content/docs and update the config to url = "/docs/my-docs", sidebar works, thanks again!