The short answer is that if you get it from CCP4, it does. If you get it from me it doesn't, becuase autoconf is unreasonably complex and I have better things to fill my head with.

The long answer is that when Paul (who is an autoconf guru) and I set up autoconf for clipper it took us a week, and required sufficient specialist knowledge that I couldn't really maintain it. By contrast, when I set it up with SCONS, it took me less than a day and was easily maintainable, however at that stage SCONS didn't handle other platforms very well. So I distribute development versions of clipper with simple build scripts which actually work for me, CCP4 distribute release versions with autoconf because they have enough experience to maintain it, and PHENIX distribute it with SCONS because that's what they use. If you want an autoconf version, use the CCP4 release (granted its always a bit out of date).