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Refactor includes of files and libraries #13

Description

@tanya-kta

Check all includes and rewrite them to follow the rule: all files and libraries used in file A has to be included in file A, even if some of them are already included through other files. Also check for other problems such as unused includes. For example:

Incorrect:

//a.cpp
#include <cmath>

//using `cmath` functions
//b.cpp
#include "a.cpp"

//using `cmath` and `a.cpp` functions

Correct:

//a.cpp
#include <cmath>

//using `cmath` functions
//b.cpp
#include <cmath>

#include "a.cpp"

//using `cmath` and `a.cpp` functions

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