Using iThoughtsX links topics and notes with Marked
When using iThoughtsX with Marked 2, linking a topic (⌘K) will automatically generate a Markdown link for reading by Marked. In general, this just means you can take it easy and let the apps do the conversion work. However, if you want a link within the text of a topic or note, you need a workaround.
iThoughtsX automatically turns urls into hyperlinks, thus writing
Going [home](http://brettterpstra.com). will turn into
Going [home]([http://brettterpstra.com](http://brettterpstra.com)).. To make links work in this fashion, both in notes and in topic text, you'll need to use reference links and place the references in the notes of the main (central) topic. (you can also use notes on a new Floating Topic --- e.g. right click->New Floating, call it "References" --- though that leaves an extra headline in your preview document).
The trick is that if you put the references in the notes of a sub-topic, they're indented too far to be recognized as references by the Markdown processor. If you put them in a main topic, they're only indented 2 spaces (Markdown allows 3), so it works great.