Before using Portfolio, we created a "hierarchy" for our issues across multiple projects using Issue Links.  We mistakenly assumed that Porfolio would understand these links based on the hierarchy we set up in the Portfolio settings, but it does not.  Portfolio uses its own linking mechanism (via the Parent Link field, for example) and doesn't respect any of the existing issue links.  As a user I do not want to re-link several hundred issues in Portfolio by hand.  

Please make Portfolio understand JIRA Issue Links, with respect to the hierarchy defined in the Portfolio admin settings, so the Issue Links can also be visible on the Plan.