Fix php notices, warnings and deprecated libraries in the project

[ruslanbaidan]

We have plenty of php notices and warnings in the code which can lead to unexpected results, errors in the workflow and other kind of inconsistencies. The goal of the issue is to collect all of the occurrences, report and fix.

For instance during the Anr export process we get bunch the following ones:

PHP Notice: Undefined offset: 5 in /home/ubuntu/monarc/vendor/monarc/core/src/Service/AssetExportService.php on line 94
PHP Warning: array_flip(): Can only flip STRING and INTEGER values! in /home/ubuntu/monarc/vendor/monarc/core/src/Model/Entity/AbstractEntity.php on line 112

Some deprecated classes usages:

PHP Deprecated: The Doctrine\Common\Persistence\Mapping\Driver\MappingDriverChain class is deprecated since doctrine/persistence 1.3 and will be removed in 2.0. Use \Doctrine\Persistence\Mapping\Driver\MappingDriverChain instead. in /home/ubuntu/monarc/vendor/doctrine/persistence/lib/Doctrine/Common/Persistence/Mapping/Driver/MappingDriverChain.php on line 16
PHP Deprecated: The Doctrine\Common\Persistence\Mapping\Driver\AnnotationDriver class is deprecated since doctrine/persistence 1.3 and will be removed in 2.0. Use \Doctrine\Persistence\Mapping\Driver\AnnotationDriver instead. in /home/ubuntu/monarc/vendor/doctrine/persistence/lib/Doctrine/Common/Persistence/Mapping/Driver/AnnotationDriver.php on line 16
PHP Deprecated: The Doctrine\Common\Persistence\ObjectManager class is deprecated since doctrine/persistence 1.3 and will be removed in 2.0. Use \Doctrine\Persistence\ObjectManager instead. in /home/ubuntu/monarc/vendor/doctrine/persistence/lib/Doctrine/Common/Persistence/ObjectManager.php on line 16
PHP Deprecated: The Doctrine\Common\Persistence\Mapping\AbstractClassMetadataFactory class is deprecated since doctrine/persistence 1.3 and will be removed in 2.0. Use \Doctrine\Persistence\Mapping\AbstractClassMetadataFactory instead. in /home/ubuntu/monarc/vendor/doctrine/persistence/lib/Doctrine/Common/Persistence/Mapping/AbstractClassMetadataFactory.php on line 16
PHP Deprecated: The Doctrine\Common\PropertyChangedListener class is deprecated since doctrine/persistence 1.3 and will be removed in 2.0. Use \Doctrine\Persistence\PropertyChangedListener instead. in /home/ubuntu/monarc/vendor/doctrine/persistence/lib/Doctrine/Common/PropertyChangedListener.php on line 16
PHP Deprecated: The Doctrine\Common\Persistence\Mapping\RuntimeReflectionService class is deprecated since doctrine/persistence 1.3 and will be removed in 2.0. Use \Doctrine\Persistence\Mapping\RuntimeReflectionService instead. in /home/ubuntu/monarc/vendor/doctrine/persistence/lib/Doctrine/Common/Persistence/Mapping/RuntimeReflectionService.php on line 16
PHP Deprecated: The Doctrine\Common\Persistence\Event\LoadClassMetadataEventArgs class is deprecated since doctrine/persistence 1.3 and will be removed in 2.0. Use \Doctrine\Persistence\Event\LoadClassMetadataEventArgs instead. in /home/ubuntu/monarc/vendor/doctrine/persistence/lib/Doctrine/Common/Persistence/Event/LoadClassMetadataEventArgs.php on line 16
PHP Deprecated: The Doctrine\Common\Persistence\ObjectRepository class is deprecated since doctrine/persistence 1.3 and will be removed in 2.0. Use \Doctrine\Persistence\ObjectRepository instead. in /home/ubuntu/monarc/vendor/doctrine/persistence/lib/Doctrine/Common/Persistence/ObjectRepository.php on line 16
PHP Deprecated: The Doctrine\Common\Persistence\Event\LifecycleEventArgs class is deprecated since doctrine/persistence 1.3 and will be removed in 2.0. Use \Doctrine\Persistence\Event\LifecycleEventArgs instead. in /home/ubuntu/monarc/vendor/doctrine/persistence/lib/Doctrine/Common/Persistence/Event/LifecycleEventArgs.php on line 16

[ruslanbaidan]

This is a part of the current refactoring task. Can only be completely achieved when all the old components are removed and the code works without deprecaced libraries use.