Some major changes to the coding, mostly adding echo, message and warning blocks to the Markdown R code sections.  Some revisions on the figures.  New table & text to accompany the CCA variance analysis.

Most importantly, I re-ran the MAT runs with fewer values.  It looks like the small intervals we use aren't really all that useful from 0 - 0.2, so I ditched them (hence the change to `bootstrap_mat.R`).  They're not useful for WAPLS or WA but I haven't implemented that yet.  That's why the Figure right before the Discussion has a weird dark/light pattern for WA and WAPLS.  New files come from knitting the paper fragments.