jupyter book WARNING: document isn't included in any toctree

• after processing (jupyter-book build) the TOC-navigation does not appear.
• My _toc.yml is - at least I think so - according to the Jupyter Book tutorial.
• The processing information tells: "WARNING: toctree contains reference to nonexisting document". But the source files I provide are processed. In the HTML-view I can find them by using the local search (a Jupyter Book function).
• Beside the source files that are registered in the TOC, there are images that are not registered that are ready to be inserted in the HTML view. into the source files. They are inserted correctly after processing, as can be seen.

I am grateful for some debugging ideas! Tx!

update

• here is the website without TOC-navigation in GitHub Pages: https://smartoncology.github.io/Manuals-v0.1
• in SEARCH enter: "numpy", and all the "nonexisting documents" will appear
• here is the repository with all sources: https://github.com/SmartOncology/Manuals-v0.1

jupyter_book provides support for .md & .rst file by default.

You can use following command to consider specific extension files for toc.

jb toc from-project path/to/book/ --extension .ipynb -e .md

you can use either jb or jupyter_book.

Reference link: customize/toc