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Deleting an interwiki prefix should be undoable
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As I understand it, removing a row from Special:Interwiki is not reversible on-wiki. It can be re-entered anew (hopefully we wrote down the flag values or can guess them from local policy), but the links themselves won't work again until a maintenance script is run (!) or a null edit done to each page (but which pages?).

This seems too technical for the average admin, in addition to being non-scalable drudgery. Even if the admin tries to do the right thing and "orphan" the prefix before deleting, there is no human-readable list of links; a dump scan or API query is needed.

Revisions and files can be undeleted, and those tables are much bigger, so I'm assuming there's no performance issue. T113034 is arguably a blocker, in case there are major schema changes.

Adding core tag because iwlinks is in core. (Does the same situation result from deleting a prefix from the shell, without the extension?)

Disclaimer: Like most third-party projects, my home wiki lacks a sandbox environment, and the sysadmin doesn't want tests that could cause permanent data loss. Imagine that. So I'm probably missing obvious details, and when we did see this in the wild, it was for a now-EOLed version of MediaWiki. Sorry. If subsequent upgrades have made the issue INVALID, so be it.

Event Timeline

Which exact versions of MediaWiki and the Interwiki extension is this about?

I don't remember. It happened right after an upgrade and we didn't document everything because we were fighting fires. It might have been MediaWiki 1.24.

Absence of a link search for an active prefix (second paragraph) is still true today at least, in MediaWiki 1.27.4 and Interwiki extension v3.1. The standard core search box isn't a workaround because the brackets are ignored. If this functionality existed, it would take the edge off the situation IMO; perhaps we would then restrict the interwiki userright to people who had been trained. :>

Believe me, I would have tested this again before reporting, but I myself only have said userright on one wiki, whose ops staff have vetoed the idea using much harsher language than yours.