Removing \include commands in favour of \input

Input is a little more favourable as it allows nested files to be
included. For example, it allows inserting a table from an external file
in a chapter, that is included in the main thesis.tex file
Updating from obsolete 'glossary' package to the newer 'glossaries'
Correcting the README and the documentclass to correspond to each other

The 'prelim' option was renamed to 'tothejury', to correspond to the
option available in the adsphd documentclass. The 'framefalse' option was
added to the 'tothejury' option, to correspond to the description in the
README file