linked markdown documents are not linked in html output ... or not even found

[TinkerSteve]

Describe the bug

context
include a markdown document which is outside the sphinx root tree an which links to another markdown document in the same folder.

I am using the method described here:

https://myst-parser.readthedocs.io/en/latest/faq/index.html

this is my directory structure:

|-- level2
|   |-- img
|   |   `-- Clipboard02.png
|   |-- level21.md
|   `-- level22.md
`-- root
    |-- conf.py
    |-- index.rst
    |-- level1.md
    `-- level1_wrapper.rst

this is the content of the files:

index.rst:

test_toc
========

.. toctree::
  :hidden:

  level1_wrapper

level1_wrapper.rst

.. include:: level1.md
  :parser: myst_parser.sphinx_

level21.md:

# level2

here we include an image

![image](./img/Clipboard02.png)


here we try to link to another file, which fails

[level22](level22.md)

level22.md:

# level2

here we include an image

![image](./img/Clipboard02.png)


here we try to link to another file, which fails

[level22](level22.md)

expectation
I would expect level22.md be correctly linked after building the doc

bug
But instead I receive the following errors on the console:

preparing documents... done
writing output... [100%] level1_wrapper                                                                                                                                                            
/home/builder/myst_test/level2/level21.md:11: WARNING: 'myst' reference target not found: level22.md
/home/builder/myst_test/level2/level21.md:11: WARNING: 'myst' reference target not found: level22.md
generating indices... genindex done
writing additional pages... search done
copying images... [100%] ../level2/img/Clipboard02.png    

and links to the file do not get resolved in final document ... actually the file is not even getting converted

problem
This is a problem for people building distributed projects because they cannot build integrated docs out of it.

Reproduce the bug

1. extract the attached archive

2. run

   cd myst_test
   python -m venv .venv
   source .venv/bin/activate
   sphinx-build root docs
   

3. look at the result

myst_test.zip

List your environment

python --version
Python 3.9.15

uname -a
Linux ISCN5CG2375QXY 5.10.102.1-microsoft-standard-WSL2 #1 SMP Wed Mar 2 00:30:59 UTC 2022 x86_64 GNU/Linux

alabaster==0.7.12
Babel==2.11.0
certifi==2022.12.7
charset-normalizer==2.1.1
docutils==0.19
idna==3.4
imagesize==1.4.1
importlib-metadata==5.1.0
Jinja2==3.1.2
Markdown==3.4.1
markdown-it-py==2.1.0
MarkupSafe==2.1.1
mdit-py-plugins==0.3.3
mdurl==0.1.2
myst-parser==0.18.1
packaging==22.0
Pygments==2.13.0
pytz==2022.6
PyYAML==6.0
requests==2.28.1
snowballstemmer==2.2.0
Sphinx==5.3.0
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
typing_extensions==4.4.0
urllib3==1.26.13
zipp==3.11.0

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[chrisjsewell]

Heya,
This is the formal behaviour of sphinx: sphinx-doc/sphinx#6805 (comment)

include directive considers the file is a part of the current document

It's an upstream issue, that is not something that myst-parser can change

[chrisjsewell]

As mentioned in https://myst-parser.readthedocs.io/en/latest/faq/index.html#include-a-file-from-outside-the-docs-folder-like-readme-md

For including Markdown files ONLY within other Markdown files, then there are the relative-doc, relative-img options,
but for including from an rst file, thats reliant on sphinx