fixed travis flags and extended doxyfile

The -std=c++11 flag is only set for the CXX compiler flags, avoiding an error
in clang. Modified the Doxyfile a bit as well.
first files of mwc tool

Added the first files that will be used for the mwc tool. The first steps
revolve around managing a repository of source files, detecting changes in each
of them, and tracking dependencies and paths.