Have all header includes put in the file's own cpp if it can

We have some circular dependencies in the system. E.g., the `Map_structure` class includes several files that depend on it. However, the includes of `Map_structure` is done in the CPP file and not in the H/HPP file.

This hides the circular dependency design of the system. This needs to be fixed to make it better manageable and to ease refactoring.