Some clients prefer to unset the configuration setting 'repositoryallowexternallinks'. One of the reasons could be to make sure that their moodle works in intranet without external Internet connection (and to enable data consistency, etc.)
They might want to prevent teachers from creating references to the external repositories as well.
But we cannot make it a global setting because we don't know if this repository is actually external for institution intranet or not.
Repositories that can be external (Equella, FileSystem?, WebDav, etc.) need to have per-repository setting whether to allow file references or not.
We assume that for local repositories (local,user,coursefiles,recent) references are always allowed.
Also we need to add to the description of 'repositoryallowexternallinks' setting that it does not affect references and admin also needs to check settings of particular repositories.
By the way, it is decided to translate internal term 'reference' as 'alias/shortcut' in UI