I am trying to use tel-links (http://www.marketingtechblog.com/hyperlink-phone-number/) in the FCKEditor.
Magnolia interprets them as internal links and mangles them up.
It make maintaining a mobile-site a bit of a pain.

The problem is that tel-links is not detected in the LinkUtil.EXTERNAL_LINK_PATTERN and thus is categorized as an internal link and treated as such.
Since the problem is occurring in the Loader for the FCKEditor you can still create the link and have it work if you refrain from editing the text afterwards. If you do edit the text however, the link will be corrupted.

Fix:

info.magnolia.link.LinkUtil.EXTERNAL_LINK_PATTERN should be changed from:
Pattern.compile("^(\\w*://|mailto:|javascript:).*");

to this:

Pattern.compile("^(\\w*://|mailto:|javascript:|tel:).*");