Cleanup RTD build warnings

[nightlark]

There are a large number of warnings during read the docs builds.

• [ ] Fix doxygen /ref -> \ref
• [ ] Doxygen comments with characters that break formatting of generated C API reference page
• [ ] Undocumented functions and variables -- a lot of Doxygen errors here, maybe need a way to suppress some of them instead
• [ ] Doxygen no uniquely matching class member warnings
• [ ] Malformed table warnings
• [ ] toctree invalid option block warning
• [ ] toctree references to nonexisting document warnings
• [ ] document isn't included in any toctree warnings
• [ ] image file not readable warnings
• [ ] 'myst' reference target not found warnings
• [ ] undefined label warnings
• [ ] could not lex literal block as... warnings
• [ ] pygments lexer name is not known warning
• [ ] Multiple footnotes definitions found warnings
• [ ] Deprecated docs?

Also, look into why GitHub is making a few things red (invalid syntax?): https://github.com/GMLC-TDC/HELICS/blob/b87c7729e3fb9d2a5b534b23bb0cc440197b7670/docs/user-guide/examples/fundamental_examples/fundamental_endpoints.md?plain=1#L55