I'm afraid this has nothing to do with the program:

- if I understand correctly your CMS controls a site inside, let's say:

localhost/folder/

- someone else writes docs inside:

localhost/anotherfolder/docs/

- you link to them and paths are not relative: that's probably because your
CMS considers that folder an external page and thus you end with a full URL
(but instead of linking a web object, links a local object)

Maybe you should have all those "external" files somewhere inside your CMS
site: give a try cloning files with a tool like MS Synctoy or binding
directories in Linux

Hope this helps