Issue: All areas link to main page.

Okay I see at some point, you had XenForo rewritten URLs disabled, at the same time that VaultWiki rewritten URLs were enabled. While this makes for an interesting combination, changing the XenForo setting does not trigger a URL re-base (and it can't under the current design, until https://www.vaultwiki.org/issues/3811/ is resolved).

So any URLs that were cached one way will not work properly until URLs are re-based again. I have tried to re-base your URLs manually but there is a fatal error that must be resolved first. In vault/core/controller/dm/redirect/vw.php, find:
Replace with:
I'm not sure if re-basing the URLs will resolve the situation completely, but it should be a step in the right direction.

When both types of rewritten URLs are active (as your case now), I need to look into why index.php?wiki/Page doesn't redirect to the canonical /wiki/Page when they should point to the same resource, but instead falls back to /wiki/ as if /wiki/Page doesn't exist and can't be created. It seems this behavior is limited to XenForo installations, as I can duplicate the behavior on our XenForo demo but not the vBulletin demo.

btw: i rebased it before. The new build is uploaded now.

Fixed the canonical redirect under XenForo. It had to do with the routes for XenForo's standard URLs ending in a slash. You may notice that most wiki pages don't end in a slash. After rebasing our demo, canonical redirects work as expected, rather than forwarding to the wiki index.

Unfortunately I cannot mark this issue as fixed until the case of toggling XenForo's friendly URLs setting properly triggers a rebase.

Its still not working on my site. Is this what you mean or should it work now?

It is only fixed in our demo. I cannot try the changes on your site until my IP finishes whitelisting. But I will try it later tonight; if not, the morning.

Confirmed fixed on your site.

Fixed the URL re-base tool in Integrity > Counters, which was not using a clean slate to generate URLs for children of areas. That method can be used to more easily re-base URLs as of the next release.

Marked as fixed in the next release.