clean-up guidance code/code in general

removes duplicated includes
removes unused includes
eliminates dedicated toolkits that resulted in circular dependencies
moves functionality close to data, where possible

src/contractor/contractor.cpp

@@ -6,7 +6,6 @@
 #include "extractor/edge_based_graph_factory.hpp"
 #include "extractor/node_based_edge.hpp"
 
-#include "storage/io.hpp"
 #include "storage/io.hpp"
 #include "util/exception.hpp"
 #include "util/exception_utils.hpp"