Switching from 'glossary' package to 'glossaries', from '\include' to '\input' and correcting the README file

I made three commits, each fixing one of the following:

- I changed all the \include commands in favour of \input, as it allows nesting two levels of files. Therefore it is possible to \input tables or other files inside each chapter.
- I switched from the 'glossary' package to the newer 'glossaries'
- I fixed a small problem with the README file and the 'prelim/tothejury' options of the class