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It's hard to check the writability of the currently running executable, so for now just check the writability of the dir which seems to improve this situation a little? Especially as the issue reported in https://phabricator.wikimedia.org/T293963 is actually to do with the /usr/bin/.mw.new file, which I guess is the result of the download?
Perhaps in the future we should just stop using this update library all together and write our own?