This is mostly a large collection of report-generating functions which do not depend on each other. plink_common contains convenience functions for file parsing and bit manipulation, plink_matrix encapsulates a few common matrix operations (which are resolved via LAPACK calls under the hood), and plink.c handles command-line parsing and initial dispatch; it's often not necessary to deal with any other files when adding a new command.
When building directly from the code in this repository, you'll probably want to use Makefile.std instead of Makefile; the latter is just aimed at my own OS X and Win64 machines.
Yes, I would like to migrate this codebase to C++11. Unfortunately, the version of GCC currently bundled with Scientific Linux, which we need to build maximally portable Linux binaries, has poor support for it.
Additional discussion is at https://www.cog-genomics.org/plink2/dev .