Update the create_website.sh script that builds the publications webpage.

@benkirk I've hard-coded your header and footer in my script, which
seems wrong.  Are you autogenerating those somehow?
Removing the old publications.php file from the html docs.
build infrastructure for new doc target
replacing old content
moving doxygen input snippets
move doxygen work into doc/html Makefile
make all web pages use both doxygen & styles css pages, to avoid display discrepancies
updates for in-tree builds
updated examples
fix for make dist
fix for make upload
do not have make doc overwirte the examples documentation, manually run make examples_doc for that
Paste header/footer into publications.html file.
upload, clean fixes