The easiest way to avoid this is to move the special page outside of the main content namespace, e.g. like https://de.wikipedia.org/wiki/Wikipedia:Hauptseite (and update MediaWiki:Mainpage to point there).

I don't think it makes sense to exclude the main page from Special:Lonelypages any more than from Special:AncientPages, Special:LongPages, Special:UncategorizedPages (oh hey it actually appears here), or any other similar report page.

My point is that I don't think it does qualify under the criteria as it is linked to via the navigation that is present on every page.

The whole point of this special page is to find pages that are inaccessible, and the main page is the exact opposite of that, as you can always get to it in one click.

Having given it some thought, I'd go one stage further and say that any pages in the site navigation should also be excluded from this list.

I don't think it makes sense to exclude the main page from Special:Lonelypages any more than from Special:AncientPages, Special:LongPages, Special:UncategorizedPages (oh hey it actually appears here), or any other similar report page.

For the reasons given above, I disagree with that statement. The main page may fit one of the other categories (being too long, for example) but it is definitely not 'orphaned'.

The easiest way to avoid this is to move the special page outside of the main content namespace, e.g. like https://de.wikipedia.org/wiki/Wikipedia:Hauptseite (and update MediaWiki:Mainpage to point there).

If best-practice is for this page to be outside the main namespace, then moving it may be the answer. In that case, we should also log a ticket to change the default location for new installations, e.g. so the main page is located at "Project:Main Page"?

If this is not best practice, then I don't think moving it in order to work round a software limitation is a sensible solution.

Do you think then that https://en.wikipedia.org/wiki/Special:WhatLinksHere/Main_Page should contain a list of all pages on the wiki (and similarly for other pages linked in the navigation)? I think it would be contradictory if it didn't.

In T272308#6756383, @HappyDog wrote:

If best-practice is for this page to be outside the main namespace, then moving it may be the answer. In that case, we should also log a ticket to change the default location for new installations, e.g. so the main page is located at "Project:Main Page"?

If this is not best practice, then I don't think moving it in order to work round a software limitation is a sensible solution.

I'm not sure if it's considered a "best practice" yet, but it's definitely a common practice. Six of the ten top wikis on https://www.wikipedia.org/ have the main page in the project namespace.

Do you think then that https://en.wikipedia.org/wiki/Special:WhatLinksHere/Main_Page should contain a list of all pages on the wiki (and similarly for other pages linked in the navigation)? I think it would be contradictory if it didn't.

No - again, you need to look at the purpose of the page, not the underlying technical implementation. The purpose of this page is to tell you what pages on the wiki have a link to the current page, primarily for the purposes of maintenance, e.g. fixing redirects, understanding the impact of moving the page, etc. Once you look at this way, you can see that it would be extremely unhelpful to include every page on the wiki in this list.

However, what would be helpful would be to include MediaWiki:Mainpage in the list, so that there is some visibility on this. And, similarly, include MediaWiki:Sidebar for all pages linked to from the navigation. These are the pages that actually contain the links and it therefore makes sense to include them in the list of links.

A page is orphaned when it is not linked from anothers page content (or from within other pages). Links from navigations typically not treated as "used" or "linked" as that is a implemantation detail of the software, while an actual link from another page is a detail by the user of the wiki.

Just link the main page from your user page or from a help page and it would be gone from the special page, because currently the page does not check from where a page is "linked" (T10516)

A page is orphaned when it is not linked from anothers page content (or from within other pages). Links from navigations typically not treated as "used" or "linked" as that is a implemantation detail of the software, while an actual link from another page is a detail by the user of the wiki.

This sounds like you are describing current behaviour, rather than describing desired behaviour, i.e. the behaviour that is most useful to users.

Also, given that the navigation and main page are controlled by users of the wiki, via pages on the wiki, this is not simply a software implementation detail. It is a user-generated link.

Just link the main page from your user page or from a help page and it would be gone from the special page, because currently the page does not check from where a page is "linked" (T10516)

Aside from being somewhat of a hack, this also sounds like it might break in a future software update (if that task is fixed), so I'm not sure it's a great solution.