You can clone with
Hyperlinked index is important for a PDF as well. make sure there is a usable index in the PDF, as the first release of the book lacks one.
This is included in the PDF produced by the Makefile. I'll make sure to make some stopgap way of getting the artifacts out there.
Recent build will end up here for now: http://www.33bits.eu/crypto-handbook (including hyperref index).