Modified citekey formatting to deal with cases where '\citekey' is already present

I also added new species names to italicise.
changed pandoc call so that it will work from any folder by adding complete paths to bib files
added code to create clickable urls in pdfs
added code to obtain document title from the first line rather than hard-coded
modified file names so that pdf name matches input file
fixed bug in citekey addition
Modified to work with preformatted bibliographies

I've finally given up on getting this to work with pandoc. For now at least, I'm
using the Papers reference formatting, which means there's only one pass needed here

I've kept in the citekey formatting and the pandoc command functions, but they are no longer
being used
changed boundaries around species names from \s to \b

this allows for names within {} tag delimiters to be italicised
removed space after species name since it's not needed when using \b instead of \s
Modified the formatting of links and added hyperlinks to email address