The Autolink References feature is very useful, but only configurable at a repository level. Since there’s no org-level support, this makes it very difficult to use/keep up to date for multiple links (such as to support multiple projects in JIRA) across all of an org’s active repos.
There’s a suggestion for enabling it at the org level - but allowing us to update the list of links via the github apps API would solve the problem from a different angle, and would allow us to automatically keep the list up to date with all the links we may wish to support.