Install pdftk from here first:

http://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/

It's in most linux repos too.

mkdir HoAC_tmp && cd $_ && wget -r -np -l 1 -A pdf http://cacr.uwaterloo.ca/hac/ -nd && pdftk toc3.pdf chap1.pdf chap2.pdf chap3.pdf chap4.pdf chap5.pdf chap6.pdf chap7.pdf chap8.pdf chap9.pdf chap10.pdf chap11.pdf chap12.pdf chap13.pdf chap14.pdf chap15.pdf appendix.pdf references.pdf index.pdf cat output "../Handbook of Applied Crytopgraphy.pdf" && cd .. && rm -r HoAC_tmp

This might be too much ... :)

Stapler is an alternative to pdftk with much lighter dependencies.

https://github.com/hellerbarde/stapler