Improve hashed JS/CSS files creation.

The template.html, index-template.html and print-template.html now
all reference the same CSS files, allowing us to generate an hashed
app.css from it which in all three cases results in exactly the same
hash - so instead of three files we get just one CSS file.

Include prettify library also to concatenated CSS/JS.

Fix how JsDuck::TemplateDir copies over the files - ensuring that
it also copies the files containing MD5 hash in their names.