The links plugin is actually an extension of the content plugin.
At some point we will change the database handling, most of which will be moved to the library instead of plugins. At that point we will also look into merging the links and content plugins into one single plugin.
The links plugin handles connections between pages through two way links. Links are small structures composed of the name of the reference, whether the link is a single link or a multiple link (one to one, many to one, one to many, or many to many).
Links are specific to branches. So if create a new branch for a page, the links for that new branch can be different than the links in the previous branch. This makes it possible for a new branch to have a different type, theme, etc.