CMake, Makefile: pass the location of arch_flags to the makefile, this way the cmake build does not write to the soruce directory

CMake: only add compiler flags that are actually compatible with the compiler being used - the compiler detection logic in the Makefile is not perfect and that sometime results in weird conflicts

Makefile: Add a CMakeLists.txt that uses the regular Makefile to compute flags and source file. This is a ugly hack, mainly to allow the use of CLion with ABC. Include some changes in the Makefile to support that.