If your not a fan of the code floating, that can be disabled. We are working on getting some better code styles as well that should fix the contrast issue.
Wow, we even looked around when naming Daux to make sure there wouldn't be any conflicts. I took a look at the dox project and I think we are going to be ok. It looks to be a significantly different approach.
This is completely true, and I started a Github issue to create an optional build script to generate a static set of files that could be deployed to S3, Github Pages or something similar. https://github.com/justinwalsh/daux.io/issues/6
I agree I should have used a template engine. I wrote most of this with the idea that it would be a proof of concept but ended up turning into something I felt others would still benefit from. It's still simple enough to get around the code without a template engine, but I would love to refactor one in.
The forced .md and underscores was mostly for speed of development on the first version of Daux. I agree it is a bit arbitrary and I plan on making the requirements a bit less strict in the future.