making explicit relation with HTML file, etc
Rfunction, and other BioCStyle not properly to html.

Modified the make-html script
clean up ./figure dir (o.w. end up in pdf)
figures for html separate from pdf
Revert "clean up ./figure dir (o.w. end up in pdf)"

This reverts commit 12d07f4b7e62b54ced03188631adca5168d9e518.

Conflicts:
	make-html.sh
ensure figs. for html different dir

- set chunk opts after \begin{document}
- modify scripts for document creation