Changed function names, functions to indiv. files.

Changed function names to include underscores.  Fixed the help for
get_publications and divided the functions into separate files.
Changed get_download to return a better data object.

Updated get_download to return a matrix for the actual assemblage data,
and more concise matrix objects for the chronologies, sites, PIs and
other metadata.  Updated the help file with a better example of what can
be done now, and updated the list of parameters returned by the
function.
Removed "collate" in description

Collate wasn't letting the package compile properly because it was
calling a now non-existent file.  Fixed it by removing Collate in the
DESCRIPTION file.
Minor fixes & updated help files

Replaced some illegal characters and replaced the period with an
underscore in all the help files.  Made a change to the get_download
helpfile so that it indicates that only a single file can be downloaded
at a time.
Merged changes from Simon, resolved conflicts