Temporary repo to debug stuff here: squidfunk/mkdocs-material#2592

git clone https://github.com/meleu/docs-debug
cd docs-debug/
docker container run --rm -v ${PWD}:/docs squidfunk/mkdocs-material build

Now, inside the site/ dir, every index.html file that is inside a subdirectory, when they have a link to another pages, they are not linked to ../Another-Page. Instead, they are linked to Current-Page/Another-Page.

A detailed example is described below.

In the mkdocs.yml file, we have a nav like this:

nav:
  - General:
    - index.md
    - RetroAchievements Manifesto: RetroAchievements-Manifesto.md
  - Portugues:
    - Introdução: Home-pt_BR.md
    - Geral:
      - Manifesto RetroAchievements: RetroAchievements-Manifesto-pt_BR.md

In docs.wiki/Home-pt_BR.md there's a line with this link:

[Manifesto RetroAchievements](RetroAchievements-Manifesto-pt_BR)

I've built the site with this command:

docker container run --rm -v ${PWD}:/docs squidfunk/mkdocs-material build

In the generated Home-pt_BR/index.html the generated link is:

<a href="RetroAchievements-Manifesto-pt_BR">Manifesto RetroAchievements</a>

As you can see, the href points to RetroAchievements-Manifesto-pt_BR, and as we're in the Home-pt_BR dir, the link actually goes to Home-pt_BR/RetroAchievements-Manifesto-pt_BR

In an old installation of mkdocs-material, it converted that same link in that .md file like this:

<a href="../RetroAchievements-Manifesto-pt_BR">Manifesto RetroAchievements</a>

(the file can be seen here: https://github.com/RetroAchievements/docs/blob/gh-pages/Home-pt_BR/index.html#L2348)

As you can see, the link automatically came prefixed with the ../.