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/extractor/extractor.cpp

@@ -10,7 +10,6 @@
 
 #include "extractor/raster_source.hpp"
 #include "storage/io.hpp"
-#include "storage/io.hpp"
 #include "util/exception.hpp"
 #include "util/exception_utils.hpp"
 #include "util/graph_loader.hpp"
@@ -45,7 +44,6 @@
 #include <atomic>
 #include <bitset>
 #include <chrono>
-#include <chrono>
 #include <fstream>
 #include <iostream>
 #include <iterator>