Shell-escape and compression by default

Many tt theses need source code listings and minted works pretty good with those. Sadly it does require shell-escape in order to work properly, which I have manually added to every student writing thesis.

These changes enable shell-escape by default for pdflatex and xelatex and they should also work in Overleaf/sharelatex.

This pr also adds more aggressive compression to limit file sizes for compiled PDFs. Some PDFs get ridiculously big if using 0 level compression. Ideally these would be separate PRs though, but I'm lazy. We can modify the pr if necessary.