Treatment of ExternalLibraries and dependencies

At the branch nonconservative (for the nonconservative Z4 formulation which requires Kernel modifications) I introduced a standalone ID code by using git submodules, cf. https://gitlab.lrz.de/gi26det/ExaHyPE/tree/nonconservative/Code/ExternalLibraries

We will quickly get more external dependencies at this place. They will all introduce Makefile changes, ie. as in the Makefile at https://gitlab.lrz.de/gi26det/ExaHyPE/blob/4af8a855a1b15ea795ec1d94365421ab0ac4da84/Code/Applications/Z4/Makefile

 # This is to include the dependency to GSL, needed for the TwoPuncture code 
PROJECT_CFLAGS+=-I../../ExternalLibraries/TwoPunctures/libtwopunctures
PROJECT_LFLAGS+=../../ExternalLibraries/TwoPunctures/libtwopunctures/libtwopunctures.a -lgsl -lgslcblas -lm 

There should be a better method, especially because the Makefile will be overwritten everytime I run the toolkit on the application.