I'm torn over this decision.
I'm building an app similar to Evernote:
... but it's mostly focused on flashcard creation, incremental reading, and managing your reading and annotations as notes.
I think Evernote could clone it in a few months if they really wanted to.
If I were to ship Evernote support it could act as a good distribution channel.
However, Evernote could just cut me off and then clone my feature set assuming it did REALLY well.
It's a tough decision.
If I had some unassailable feature set it would be a safe bet but I don't think we're at that point yet.
The other alternative is they buy your tech if you own a market niche. And if it's a niche that they won't be focusing on. Looks like you might be focusing on academia, given you have a research paper in the example on the homepage. ( Only thing is academia doesn't spend money! )