Refactor system

The point of this refactor was to to create a new class, AnalysedFile,
to wrap a file's smells, churn and complexity. In the future, this class
will also hold a file's rating.

The Turbulence class changed a lot in this refactor. It now merely
receives a bunch of analysed_files and asks them for their churn and
complexity values. And now it already returns json instead of a hash.

Potential problems:

* I'm thinking in terms of files, not classes

* The AnalysedFilesBuilder#file_smells method is slow
Add `at_pathname?` method to smell and remove `pathnames` reader
Rename method `located_in?` to `at_location?`
Create AnalysedFilesBuilder test
Refactor smell attribute readers tests
Move `has_smells?` logic to its rightful place: AnalysedFile
Move `analysed_file_name` logic to its rightful place: AnalysedFile
Fix Flay tests
Rename method parameter
Move main classes to a new folder named "core"