Add submodules for external libraries

Adds submodules for external libraries used in the paper and changes the source
code to use these local copies instead of installed versions.
Pull code out of noweb

Breaks up the monolithic noweb file, Documentation.nw, into many smaller source
code files, mostly in R.
Remove zip-archive target from Makefile

Archiving as a zip file will have to be done by hand now
Update ignore list