PowerDNS has moved to GitHub, the repository is at https://github.com/PowerDNS/pdns

Then:

$ ./bootstrap

you may need to do that twice. You also need libtool-1.4, 1.3 won't work.
Automake 1.6 is (almost) required.

Send any patches you may have to the mailinglist:
                        pdns-dev@mailman.powerdns.com

Thanks!