Since most (or all) make implementations have their own extensions, staying within this subset is a continual challenge. The CCNx build is tested with GNU make, BSD make, and Solaris make.
The ./configure script's main job is to build the conf.mk file that defines the configurable make macros. This is done largely just by using the output of the uname command, but scripted configuration is possible as well. The csrc/conf/ directory contains the system-specific make fragments and scripts.
If you need to override the configured values, put them into a file named csrc/conf/local.mk before you execute ./configure in csrc/.
For convenience, there is a Makefile link placed into the subdirectories of csrc/ so that you can easily rebuild just part of the world.