fixed superpose bug in image
manual update

added sections to master document, added rough draft of preprocessing
flowchart
cleaned up files
restored preprocessingRoughDraft pdf and fixed IAnnotatedDataFrame varMetadata bug
fixed IAnnotatedDataFrame varMetadata init bug
cleaned up src
updated Cardinal-demo vignette
fixes to PCA and PLS and OPLS
First pass up to section 4
Demo edits

First pass from 3.5 through 6.1. pixelApply section example changed to
use the same dataset generated in section 1.
Demo updates

Added simulation section
Done with first pass on Demo vignette
added cvApply
updated plotting methods
updated plotting methods
added coregistration for SpatialKMeans and fixed plotting bugs
Added spaces after \R in demo
Demo: Italicized "m/z" and added space after
Demo: references section and bibtex file added
references and stuff once more