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refactor: improve code structure based on codeclimate hints

This only restructures the code to be more readable based on hints from
codeclimate analysis:

- simplify MetadataValidator and EntityHelper
- simplify MySqlConnection
- simplify MetadataStorage and discovery process
- introduce EntityAssigner and EntityTransformer helpers
- introduce QueryBuilderHelper and simplify QueryBuilder
- introduce ObjectHydrator
- move common parts of MySQL and Sqlite drivers to their parent

390 of 390 branches covered (100.0%)

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1459 of 1459 relevant lines covered (100.0%)

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