Move all capturing and wrapping to pre-knit processor

[noamross]

Moving all capture and wrapping to a pre-processor has some benefits. It will drop the need to use knit hooks, which reduces the interference with people building on top of the method. It also make it straightforward to explain to developers how to build on top of the approach.

It is also the appropriate place to capture additional components, such as raw LaTeX and HTML comments (and other raw HTML, specialized blocks, etc). This will allow HTML commends in worded or the \newpage` lua filter (#13).

Breaking from the legacy knitr parser would also allow things to be simpler, so easier to capture things like captions (#20).