Fixed many small phpcs issues

This pr fixes many small phpcs issues
@Ocramius Having stricter rules does not forbid us to change these rules to be consistent with PSR-2. The Doctrine CS would then be PSR-2 + Doctrine-specific rules. Currently, it is PSR-2 - negation formatting + Doctrine-specific rules.
For instance, Symfony also applies more rules than PSR-2 (rules which are common to the Doctrine CS for many of them btw), but it builds on top of PSR-2, and we tweaked the Symfony rules a bit when PSR-2 came out to avoid inconsistencies.