Adds categorize_wikipages.pl, README for protocol_pdf, misc. updates.

categorize_wikipages.pl connects to the wiki database to get more detailed
info about the wiki oldids and connects them to the page's most recent version.

Finished readme for the two perl scripts and fetch_pdf, with installation,
usage, and output file explanations.

Miscellaneous Updates :

renamed a couple files for consistency

Improved comments on SAMPLE.perl.conf and added categorize_wikipages section

Added some special cases in find_wikipage_references where the page names
were not being handled properly: celniker RNA pages that were referred to
only by their number, and links with a missing '&' in the
pagename&oldid= part.