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TOOLBOXEND appearing under navigation with extension-added links there instead of in toolbox
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Possibly a race condition on the wiki in question? Some other weird things also happening there:

CiteThisPage link is the one doing it there.

Event Timeline

I can't seem to reproduce this with CiteThisPage + Timeless; furthermore it doesn't appear that CiteThisPage is installed anymore on the aforementioned wiki, so maybe this indeed was a site-specific issue occurring under a very precise set of conditions?

As discussed yesterday, this is happening with extensions which use a combination of SkinTemplateBuildNavUrlsNav_urlsAfterPermalink and SkinTemplateToolboxEnd hook subscribers. CiteThisPage uses the newer, saner BaseTemplateToolbox hook and as such is not affected.

SkinTemplateToolboxEnd's manual page on notes that "BaseTemplateToolbox also does the same thing, is cleaner and more future proof than SkinTemplateToolboxEnd, but may not work in old skins that don't use BaseTemplate yet and hardcode the toolbox.". Looking at the page history, this notice was added to that page in July 2013. I'd say the future is now and it's time to work on deprecating and thus eventually removing SkinTemplateToolboxEnd.

Category:SkinTemplateToolboxEnd extensions lists 16 pages (extensions) allegedly using this extension, though it should be noted that Cite (actually CiteThisPage) no longer uses it, as per that extension's extension.json; this is just a classic case of T2001: [DO NOT USE] Documentation is out of date, incomplete (tracking) [superseded by #Documentation]. The other extensions there appear to be either unmaintained or unmaintained and not even hosted on WMF gerrit in the first place.

Isarra claimed this task.

@ashley evidently resolved this by removing the legacy hook in question entirely.