I don't think it supports a markdown / formated text export but it looks looks fantastic as far as pdf cleanup goes (i currently rely on adobe scan for that when i am working from a paper copy), I will try it soon.
No, it doesn't support markdown and it doesn't do analysis of headers/page numbers. It's mainly aimed at making academic PDFs better for reading and annotating (especially on iPad-like devices). Hoping to start charging for it at some point, but I'm still trialing it...
Some users have expected it to "unwarp" bad scans, it also doesn't do that unfortunately. But that's a much harder problem to solve...
I found perspective transformation to be good enough for 90% of cases. Going further would be a lot of effort better spent elsewhere.
Does it deal fine with illustrations and pdf compression?
