In versions of Confluence prior to Confluence 3.5, a version of Atlassian Application Links was included that featured the ability to automatically turn textual references to entities in other applications into hyperlinks (for example, you could type "PROJECT-123" into a Confluence page and, if you had an entity link configured to a matching JIRA project, the issue key would be transformed into a hyperlink to "http://my-jira/browse/PROJECT-123" when the page was viewed).

This feature was removed from Atlassian Application Links 3.0, which is the version of Application Links that was shipped with Confluence 3.5.

Any customer that upgrades to Confluence 3.5 from an earlier version will find that any application links such as this that were visible on their Confluence pages have now reverted back to plain, unlinked text.

A new, separate plugin was written for JIRA to restore this functionality (https://plugins.atlassian.com/plugin/details/559566), but it doesn't work in Confluence.