Cleaned up a whole bunch of things

.clang-format

.gitmodules

CMakeLists.txt

README.md

contrib/docopt.cpp

examples/lee_yannakakis_distinguishable.dot

lib/test_suite.cpp

lib/test_suite.hpp

src/complete.cpp

src/distance.cpp

src/generator.cpp

src/learning_graph.cpp

src/main.cpp

src/measure.cpp

src/methods.cpp

src/pre_gephi_tool.cpp

src/reachability.cpp

src/scatter_plot.cpp

src/stats.cpp

src/trees.cpp