Made all includes consistent 

I cleaned up all the #includes. Before, they were inconsistent and complicated.

I made the changes according to the suggestions made by the [Google C++ style guide](http://google-styleguide.googlecode.com/svn/trunk/cppguide.html#Names_and_Order_of_Includes), i.e., no "../", all paths fully qualified, etc.

For example, "Helpers.hpp" is included in multiple files, and just from looking at it, it is not clear which one of the four existing Helpers.hpp is included.
Also, many of the subfolders of ./include/ were set as include folders in various ways in the different compile targets. Now, only ./include itself is an include folder.

With this change, cppcheck produces better output. Analyzing and reasoning about the code is much easier now.