RAII for auto-closing file streams

Small fixes I didn't want to include in unrelated PRs.

There are a few left in `storage.cpp` but since it's a single function
in 600 lines of code, I didn't want to touch the mess. The others are
safe to remove, cucumber and test run on Finland gives 👍.

src/extractor/edge_based_graph_factory.cpp

@@ -476,7 +476,6 @@ void EdgeBasedGraphFactory::GenerateEdgeExpandedEdges(
 
     edge_data_file.seekp(std::ios::beg);
     edge_data_file.write((char *)&original_edges_counter, sizeof(unsigned));
-    edge_data_file.close();
 
     util::SimpleLogger().Write() << "Generated " << m_edge_based_node_list.size()
                                  << " edge based nodes";