When rendered, all custom URL schemes used in <a> tags are erased. For example, the docs-for-xcode scheme below:

<p>Click to 
<a href="docs-for-xcode://http%3A%2F%2Fcocoadocs.org%2Fdocsets%2FAFNetworking%2Fxcode-docset.atom">add to Xcode</a> 
(via <a href="http://documancer.com/xcode/">Docs for Xcode</a>)</p>

It would be useful to allow them to ease some tool interactions. This support could be controlled with a checkbox in the security settings.