toctree is wrong for python modules named "md" #10914
Description
Describe the bug
When constructing the toctree suffixes are stripped in
sphinx/sphinx/directives/other.py
Line 116 in d924acf
However, if the toctree is for a python package that includes a subpackage which is named md, in our production case wfl.generate.md, the final package name is stripped off, because it happens to match a valid suffix (.md for markdown), and the toctree is broken. Instead of wfl.generate toc including the items from wfl.generate.md, it tries to include itself (because the .md was removed while adding nodes for sub-packages), and so there is no link to the wfl.generate.md docs, and there are lots of warnings about circular references.
How to Reproduce
tar xzf sphinx_suffix_bug.tar.gz
cd sphinx_suffix_bug
source README
Expected behavior
Both "working" and "broken" versions of the package should get documentation generated identically and correctly, except for the subpackage name of md vs. mda.
Instead, I get the output in sphinx_suffix_bug.output.txt
and the resulting docs are different - the working one shows mda as a subpackage of pkg, while the other puts another copy of the contents of pkg inside pkg, and nothing from md (see screenshots below).
Your project
The real thing is at https://libatoms.github.io/workflow/modules.html, but a small example has been attached to the "how to reproduce" section
Screenshots
images of top level index.html, showing subpackage mda ("working"), but nothing for subpackage md ("broken")
OS
Rocky Linux 8
Python version
3.9.7
Sphinx version
4.5.0
Sphinx extensions
many, most relevantly autodoc and napoleon
Extra tools
No response
Additional context
No response