Subentities referenced by BaseFieldDefinition field are not duplicated

I have this issue with cloning custom entity and fixed it with MR 53 and custom code.

With entity_clone 2.0.0-beta6 we have isClonable() method in src/EntityCloneClonableField.php which also checks
$field_definition instanceof FieldConfigInterface
But all custom reference fields are instance of BaseFieldDefinition class.
So we need additional changes to this method.

I tried to remove this FieldConfigInterface check, but it adds a lot of not needed fields and caused recursions and "Circular reference detected" errors.

Finally I managed to clone custom entities with:
1. Apply patch from the MR 53 (attached it)
2. Extend EntityCloneClonableField class in the custom module and add hardcoded custom entity types check.

Example with 2 files:

1. File modules/custom/my_module/src/MyModuleServiceProvider.php

<?php

namespace Drupal\my_module;

use Drupal\Core\DependencyInjection\ContainerBuilder;
use Drupal\Core\DependencyInjection\ServiceProviderBase;

/**
 * Overrides EntityCloneClonableField class.
 */
class MyModuleServiceProvider extends ServiceProviderBase {

  /**
   * {@inheritdoc}
   */
  public function alter(ContainerBuilder $container) {
    if ($container->hasDefinition('entity_clone.clonable_field')) {
      /** @var \Symfony\Component\DependencyInjection\Definition $definition */
      $definition = $container->getDefinition('entity_clone.clonable_field');
      $definition->setClass('Drupal\my_module\EntityCloneClonableField');
    }
  }

}

2. File modules/custom/my_module/src/EntityCloneClonableField.php

<?php

namespace Drupal\my_module;

use Drupal\Core\Field\BaseFieldDefinition;
use Drupal\Core\Field\EntityReferenceFieldItemListInterface;
use Drupal\Core\Field\FieldDefinitionInterface;
use Drupal\Core\Field\FieldItemListInterface;
use Drupal\entity_clone\EntityCloneClonableField as EntityCloneClonableFieldSource;

/**
 * Manage entity clone clonable field.
 */
class EntityCloneClonableField extends EntityCloneClonableFieldSource {

  /**
   * {@inheritDoc}
   */
  public function isClonable(FieldDefinitionInterface $field_definition, FieldItemListInterface $field): bool {
    $isClonable = parent::isClonable($field_definition, $field);

    // Add custom entities fields as clonable.
    $customClonableEntityTypes = [
      'custom_entity_1',
      'custom_entity_2',
    ];
    if (!$isClonable && in_array($field_definition->getTargetEntityTypeId(), $customClonableEntityTypes)
      && $field_definition instanceof BaseFieldDefinition
      && $field instanceof EntityReferenceFieldItemListInterface && $field->count() > 0) {
      return TRUE;
    }

    return $isClonable;
  }

}

There is one more place, where the field key variable needs to be changed: /src/EntityClone/Content/ContentEntityCloneFormBase.php line 205
Or in human terms: The part of the content clone form, which displays referenced entities for which cloning is enforced.

I created a new branch and merge request https://git.drupalcode.org/project/entity_clone/-/merge_requests/102 base on the existing branch and merge request https://git.drupalcode.org/project/entity_clone/-/merge_requests/53.

I adjusted the existing changes and tests and implemented a new test checking this issue's requirement.

The main problem with the fix (1310a610) is that the clone form now also lists fields like uid, revision_uid, and similar. One could explicitly exclude those fields or define it as a feature.

The tests are failing because the action is no longer part of core and the module can't be installed. Maintainers need to decide if they still want to support actions by adding a dependency to contributed action module or not and remove test.
Tested manually with a custom entity and can confirm that without the changes in MR the user only sees the clone and cancel buttons. With the MR applied the child entities are shown. If the checkbox is checked, the fields of the referenced entity (created with Base field definition) are cloned.
When cloning the "standard" content types, nothing changes, the cloning works as before, but I did not test with overly complicated entities.
Will leave status to needs review in case tests do get fixed in the meantime and for somebody else to also test and confirm it's working as expected.

The failing test is for previous major version (should be D10.4.5), D11 is passing. Because of that setting status to needs work.