made #include organization consistent
now output to both file and console
cleaned up log code a bit
using boost logging in part of code now
more boost logging in dynamix.cpp
Merge commit '0accb0987cd10eb80d53cb8fcbce7f1b2697d2e9' into wavefunction_and_dm

* commit '0accb0987cd10eb80d53cb8fcbce7f1b2697d2e9':
  cleaned up Makefile