create md version of paper

[rmflight]

I want to create a markdown version of the submitted paper, and host this on the gh-pages branch of the repo.

This will require a few things:

Rewriting the output so that we save the alignments for the mm and pm probes, and their overlapping exons from merged exons and base exons
Basically I want to be able to do the full paper generation from the output text files, or the RData file with all of the summary of results.

Saving the actual intensity difference matrix so we can refer back to it

Refactoring all of the big code chunks in the lapply into sub-functions so that we don't have to worry about deleting objects after we are done with them.

[rmflight]

Easiest way to refer back to figures and tables is to insert <a id="useRef"></a> directly before the code chunk that is going to create the object you want the link to appear at, and then using [link to useRef](#useRef) to provide an actual link.

[rmflight]

Implemented functions for working with tables and figure references. Have figure 1 inserted.