I created a project with following structure:

HibernateUtil:
        
Give the path relative to your project.
Create a folder called resources in your  src  and put your config file there.
   configuration.configure("/resources/hibernate.cfg.xml");
And If you check your code
Configuration  configuration = new Configuration().configure( "C:\\Users\\Nikolay_Tkachev\\workspace\\hiberTest\\src\\logic\\hibernate.cfg.xml");
return new Configuration().configure().buildSessionFactory();
In two lines you are creating two configuration objects.
That should work(haven't tested) if you write,
Configuration  configuration = new Configuration().configure( "C:\\Users\\Nikolay_Tkachev\\workspace\\hiberTest\\src\\logic\\hibernate.cfg.xml");
return  configuration.buildSessionFactory();
But It fails after you deploy on the server,Since you are using system path than project relative path.