[Doctrine] ManyToMany Relationships not persisted in database with haveInRepository nested entity creation

#### What are you trying to achieve?

I am running a functional test on a Symfony 4 + Doctrine 2 with two entities with a ManyToMany relationship. I create the entities using haveInRepository nested functionality and I expect to have the two entities created on the database and related on the join table.

#### What do you get instead?

The entities are created but relationships in join tables are not, so the test fails due to missing information on database.

> Provide console output if related. Use `-vvv` mode for more details.

```bash
vagrant@symfonyvm:/var/www/mtm$ php vendor/bin/codecept run
Codeception PHP Testing Framework v3.1.2
Powered by PHPUnit 8.5.0 by Sebastian Bergmann and contributors.
Running with seed:

App\Tests.acceptance Tests (0) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

App\Tests.functional Tests (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Testing App\Tests.functional
✖ ManytoManyEntitiesCest: Try to test (0.07s)
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

App\Tests.unit Tests (0) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Time: 326 ms, Memory: 28.25 MB

There was 1 failure:

---------
1) ManytoManyEntitiesCest: Try to test
Test tests/functional/ManytoManyEntitiesCest.php:tryToTest
Step See in repository "App\Entity\EntityA",{"entityB":{"name":"Name B"}}
Fail App\Entity\EntityA with {"entityB":{"name":"Name B"}}
Failed asserting that false is true.

Scenario Steps:

4. $I->seeInRepository("App\Entity\EntityA",{"entityB":{"name":"Name B"}}) at tests/functional/ManytoManyEntitiesCest.php:24
3. $I->seeInRepository("App\Entity\EntityA",{"name":"Name A"}) at tests/functional/ManytoManyEntitiesCest.php:23
2. $I->seeInRepository("App\Entity\EntityB",{"name":"Name B"}) at tests/functional/ManytoManyEntitiesCest.php:22
1. $I->haveInRepository("App\Entity\EntityA",{"name":"Name A","entityB":[{"name":"Name B"}]}) at tests/functional/ManytoManyEntitiesCest.php:19

FAILURES!
Tests: 1, Assertions: 3, Failures: 1.
```
> Provide test source code if related

```php
haveInRepository(
EntityA::class,
[
'name' => 'Name A',
'entityB' =>[[ 'name' => 'Name B' ]],
]);
$I->seeInRepository(EntityB::class, ['name' => 'Name B']);
$I->seeInRepository(EntityA::class, ['name' => 'Name A']);
$I->seeInRepository(EntityA::class, ['entityB' => ['name' => 'Name B']]);
}
```
### Details

With that setup, the two first seeInRepository pass but the third does not. It could be due to the syntax of the array not being correct on the last assertion as it should really be an array, but if you look into the database you can see that the join table has not been filled.

It may be due a syntax problem, but in that case it should be an issue with docs as it doesn't specify how to work with ManyToMany relationships.

I have created a complete example in this repo: https://github.com/Pryrios/test-manytomany

* Codeception version: Codeception PHP Testing Framework v3.1.2
* PHP Version: 7.2
* Operating System: Ubuntu 18.04
* Installation type: Composer

functional.suite.yml
```yml
actor: FunctionalTester
modules:
enabled:
- Symfony:
app_path: 'src'
environment: 'test'
- Doctrine2:
depends: Symfony
cleanup: true
- \App\Tests\Helper\Functional
```

Start with tests/functional/ManytoManyEntitiesCest.php and the Doctrine2 configuration in functional.suite.yml, then trace how haveInRepository handles the nested entityB data. Verify the expected ManyToMany mapping and assertion syntax against the reported database state. Done means the entities are created, the join table contains the relationship, and the final seeInRepository assertion passes.

Written by the indexing model from the issue text.