A simple example showing how doctrine behaviours (in this chase (nested) tree and soft-delete) can be used within TYPO3 Flow.

AbstractTreeRepository.php

<?php
namespace Your\Package\Domain\Repository;

use TYPO3\Flow\Annotations as Flow;

/**
 * @Flow\Scope("singleton")
 */
abstract class AbstractTreeRepository extends \Gedmo\Tree\Entity\Repository\NestedTreeRepository implements \TYPO3\Flow\Persistence\RepositoryInterface {

        /**
	 * @var \TYPO3\Flow\Persistence\PersistenceManagerInterface
	 */
	protected $persistenceManager;

	/**
	 * @var \Doctrine\ORM\EntityManager
	 */
	protected $entityManager;

	/**
	 * Warning: if you think you want to set this,
	 * look at RepositoryInterface::ENTITY_CLASSNAME first!
	 *
	 * @var string
	 */
	protected $objectType;

	/**
	 * @var array
	 */
	protected $defaultOrderings = array();

	/**
	 * Initializes a new Repository.
	 *
	 * @param \Doctrine\Common\Persistence\ObjectManager $entityManager The EntityManager to use.
	 * @param \Doctrine\Common\Persistence\Mapping\ClassMetadata $classMetadata The class descriptor.
	 */
	public function __construct(\Doctrine\Common\Persistence\ObjectManager $entityManager, \Doctrine\Common\Persistence\Mapping\ClassMetadata $classMetadata = NULL) {
		if ($classMetadata === NULL) {
			if (static::ENTITY_CLASSNAME === NULL) {
				$this->objectType = str_replace(array('\\Repository\\', 'Repository'), array('\\Model\\', ''), get_class($this));
			} else {
				$this->objectType = static::ENTITY_CLASSNAME;
			}
			$classMetadata = $entityManager->getClassMetadata($this->objectType);
		}
		parent::__construct($entityManager, $classMetadata);
		$this->entityManager = $this->_em;
	}

	/**
	 * Injects the persistence manager
	 *
	 * @param \TYPO3\Flow\Persistence\PersistenceManagerInterface $persistenceManager
	 * @return void
	 */
	public function injectPersistenceManager(\TYPO3\Flow\Persistence\PersistenceManagerInterface $persistenceManager) {
		$this->persistenceManager = $persistenceManager;
	}

	/**
	 * Returns the classname of the entities this repository is managing.
	 *
	 * @return string
	 * @api
	 */
	public function getEntityClassName() {
		return $this->objectType;
	}

	/**
	 * Adds an object to this repository.
	 *
	 * @param object $object The object to add
	 * @return void
	 * @api
	 */
	public function add($object) {
		$this->entityManager->persist($object);
	}

	/**
	 * Removes an object from this repository.
	 *
	 * @param object $object The object to remove
	 * @return void
	 * @api
	 */
	public function remove($object) {
		$this->entityManager->remove($object);
	}

	/**
	 * Finds all entities in the repository.
	 *
	 * @return \TYPO3\Flow\Persistence\QueryResultInterface The query result
	 * @api
	 */
	public function findAll() {
		return $this->createQuery()->execute();
	}

	/**
	 * Finds an object matching the given identifier.
	 *
	 * @param mixed $identifier The identifier of the object to find
	 * @return object The matching object if found, otherwise NULL
	 * @api
	 */
	public function findByIdentifier($identifier) {
		return $this->entityManager->find($this->objectType, $identifier);
	}

	/**
	 * Returns a query for objects of this repository
	 *
	 * @return \TYPO3\Flow\Persistence\Doctrine\Query
	 * @api
	 */
	public function createQuery() {
		$query = new \TYPO3\Flow\Persistence\Doctrine\Query($this->objectType);
		if ($this->defaultOrderings) {
			$query->setOrderings($this->defaultOrderings);
		}
		return $query;
	}

	/**
	 * Counts all objects of this repository
	 *
	 * @return integer
	 * @api
	 */
	public function countAll() {
		return $this->createQuery()->count();
	}

	/**
	 * Removes all objects of this repository as if remove() was called for
	 * all of them.
	 *
	 * @return void
	 * @api
	 * @todo maybe use DQL here, would be much more performant
	 */
	public function removeAll() {
		foreach ($this->findAll() AS $object) {
			$this->remove($object);
		}
	}

	/**
	 * Sets the property names to order results by. Expected like this:
	 * array(
	 *  'foo' => \TYPO3\Flow\Persistence\QueryInterface::ORDER_ASCENDING,
	 *  'bar' => \TYPO3\Flow\Persistence\QueryInterface::ORDER_DESCENDING
	 * )
	 *
	 * @param array $defaultOrderings The property names to order by by default
	 * @return void
	 * @api
	 */
	public function setDefaultOrderings(array $defaultOrderings) {
		$this->defaultOrderings = $defaultOrderings;
	}

	/**
	 * Schedules a modified object for persistence.
	 *
	 * @param object $object The modified object
	 * @return void
	 * @throws \TYPO3\Flow\Persistence\Exception\IllegalObjectTypeException
	 * @api
	 */
	public function update($object) {
		if (!($object instanceof $this->objectType)) {
			throw new \TYPO3\Flow\Persistence\Exception\IllegalObjectTypeException('The modified object given to update() was not of the type (' . $this->objectType . ') this repository manages.', 1249479625);
		}
		$this->persistenceManager->update($object);
	}
}

?>

Category.php

<?php
namespace Your\Package\Domain\Model;

use TYPO3\Flow\Annotations as Flow;
use Doctrine\ORM\Mapping as ORM;
use Gedmo\Mapping\Annotation as Gedmo;

/**
 * A Category (Nested tree structure)
 *
 * @Flow\Entity
 * @Gedmo\Tree(type="nested")
 */
class Category {

        /**
	 * @var string
	 */
	protected $title;

	/**
	 * @Gedmo\TreeLeft
	 * @var integer
	 */
	protected $treeLeft;

	/**
	 * @Gedmo\TreeLevel
	 * @var integer
	 */
	protected $treeLevel;

	/**
	 * @Gedmo\TreeRight
	 * @var integer
	 */
	protected $treeRight;

	/**
	 * @Gedmo\TreeRoot
	 * @ORM\Column(nullable=true)
	 * @var integer
	 */
	protected $treeRoot;

	/**
	 * @Gedmo\TreeParent
	 * @ORM\ManyToOne(inversedBy="treechildren")
	 * @ORM\Column(nullable=true)
	 * @var \Your\Package\Domain\Model\Category
	 */
	protected $treeParent;

	/**
	 * @ORM\OneToMany(mappedBy="treeparent")
	 * @ORM\OrderBy({"left" = "ASC"})
	 * @var \Doctrine\Common\Collections\ArrayCollection<\Your\Package\Domain\Model\Category>
	 */
	protected $treeChildren;

	/**
	 * @param string $title
	 */
	public function setTitle($title) {
		$this->title = $title;
	}

	/**
	 * @return string
	 */
	public function getTitle() {
		return $this->title;
	}

	/**
	 * @param \Your\Package\Domain\Model\Category $treeParent
	 */
	public function setTreeParent(\Your\Package\Category $treeParent) {
		$this->treeParent = $treeParent;
	}

	/**
	 * @return \Your\Package\Domain\Model\Category
	 */
	public function getTreeParent() {
		return $this->treeParent;
	}

}
?>

CategoryController.php

<?php
namespace Your\Package\Controller;

use TYPO3\Flow\Annotations as Flow;
use Your\Package\Domain\Model\Category;

/**
 * Category controller
 */
class CategoryController extends \TYPO3\Flow\Mvc\Controller\ActionController {

        /**
	 * @var \Your\Package\Domain\Repository\CategoryRepository
	 * @Flow\Inject
	 */
	protected $categoryRepository;

	/**
	 * @return void
	 */
	public function indexAction() {
		$this->view->assign('categories', $this->categoryRepository->childrenHierarchy());
	}

	/**
	 * @return void
	 */
	public function addAction() {
		$food = new Category();
		$food->setTitle('Food');
		$this->categoryRepository->add($food);

		$fruits = new Category();
		$fruits->setTitle('Fruits');
		$fruits->setTreeParent($food);
		$this->categoryRepository->add($fruits);

		$vegetables = new Category();
		$vegetables->setTitle('Vegetables');
		$vegetables->setTreeParent($food);
		$this->categoryRepository->add($vegetables);

		$carrots = new Category();
		$carrots->setTitle('Carrots');
		$carrots->setTreeParent($vegetables);
		$this->categoryRepository->add($carrots);

		$this->redirect('index');
	}

}

?>

CategoryRepository.php

<?php
namespace Your\Package\Domain\Repository;

use TYPO3\Flow\Annotations as Flow;

/**
 * @Flow\Scope("singleton")
 */
class CategoryRepository extends \Your\Package\Domain\Repository\AbstractTreeRepository {

}

?>

composer.json

{
    ...
    "require": {
        "typo3/flow": "2.0.*",
        "gedmo/doctrine-extensions": "dev-master"
    },
    ...
}

EntityManagerFactoryAspect.php

<?php
namespace Your\Package\Aop;

use TYPO3\Flow\Annotations as Flow;

/**
 * "Hooks into" creation of doctrine EntityManager in order to register Behaviours
 * from the "gedmo/doctrine-extensions" package.
 * Note: Currently only "soft-delete" and "tree" behaviours are supported
 *
 * @Flow\Aspect
 */
class EntityManagerFactoryAspect {

	/**
	 * @var \TYPO3\Flow\Reflection\ReflectionService
	 * @Flow\Inject
	 */
	protected $reflectionService;

	/**
	 * @Flow\Around("method(TYPO3\Flow\Persistence\Doctrine\EntityManagerFactory->create())")
	 * @param \TYPO3\Flow\Aop\JoinPointInterface $joinPoint The current join point
	 * @return \Doctrine\ORM\EntityManager
	 */
	public function registerDoctrineBehaviors(\TYPO3\Flow\Aop\JoinPointInterface $joinPoint) {
		/** @var $entityManager \Doctrine\ORM\EntityManager */
		$entityManager = $joinPoint->getAdviceChain()->proceed($joinPoint);
		/** @var $eventManager \Doctrine\Common\EventManager */
		$eventManager = $entityManager->getEventManager();

		$classNamesAnnotatedAsDeletable = $this->reflectionService->getClassNamesByAnnotation('Gedmo\Mapping\Annotation\SoftDeleteable');
		$classNamesAnnotatedAsTree = $this->reflectionService->getClassNamesByAnnotation('Gedmo\Mapping\Annotation\Tree');
		if (!is_array($classNamesAnnotatedAsDeletable) && !is_array($classNamesAnnotatedAsTree)) {
			return $entityManager;
		}

		foreach ($classNamesAnnotatedAsDeletable as $index => $className) {
			if (!$this->reflectionService->isClassAnnotatedWith($className, 'TYPO3\Flow\Annotations\Entity')) {
				unset($classNamesAnnotatedAsDeletable[$index]);
			}
		}
		foreach ($classNamesAnnotatedAsTree as $index => $className) {
			if (!$this->reflectionService->isClassAnnotatedWith($className, 'TYPO3\Flow\Annotations\Entity')) {
				unset($classNamesAnnotatedAsTree[$index]);
			}
		}

		if ($classNamesAnnotatedAsDeletable !== array()) {
			$doctrineConfiguration = $entityManager->getConfiguration();
			$doctrineConfiguration->addFilter('soft-deletable', 'Gedmo\SoftDeleteable\Filter\SoftDeleteableFilter');
			$entityManager->getFilters()->enable('soft-deletable');

			$softDeletableListener = new \Gedmo\SoftDeleteable\SoftDeleteableListener();
			$eventManager->addEventSubscriber($softDeletableListener);
		}
		if ($classNamesAnnotatedAsTree !== array()) {
			$treeListener = new \Gedmo\Tree\TreeListener();
			$eventManager->addEventSubscriber($treeListener);
		}

		return $entityManager;
	}

}

?>

Index.html

<!DOCTYPE html>
<html>
<body>
<h1>Categories</h1>
<ul class="t3-content-navigation">
        <f:render section="categoryTree" arguments="{categories: categories}" />
</ul>
<f:section name="categoryTree">
	<f:for each="{categories}" as="category">
		<li>
			{category.title} ({category.treeLevel})
			<f:if condition="{category.__children}">
				<ul>
					<f:render section="categoryTree" arguments="{categories: category.__children}" />
				</ul>
			</f:if>
		</li>
	</f:for>
</f:section>

<f:link.action action="add">Add new tree</f:link.action>
</body>
</html>

Settings.yaml

TYPO3:
  Flow:

     # disable reflection for non psr-0 compliant 3rd party packages
    object:
      excludeClasses:
       'gedmo.doctrineextensions' : ['Gedmo\\.*']

SoftDeletableEntity.php

<?php
namespace Your\Package\Domain\Model;

use TYPO3\Flow\Annotations as Flow;
use Doctrine\ORM\Mapping as ORM;
use Gedmo\Mapping\Annotation as Gedmo;

/**
 * An example entity with soft-delete behaviour
 *
 * @Flow\Entity
 * @Gedmo\SoftDeleteable(fieldName="deletedAt")
 */
class SoftDeletableEntity {

	/**
	 * @var string
	 */
	protected $title;

	/**
	 * DateTime when this entity was deleted (used for "Soft-Delete behaviour")
	 *
	 * @var \DateTime
	 * @ORM\Column(nullable=true)
	 */
	protected $deletedAt;

	/**
	 * @return \DateTime
	 */
	public function getDeletedAt() {
		return $this->deletedAt;
	}

	/**
	 * @param \DateTime $deletedAt
	 * @return void
	 */
	public function setDeletedAt(\DateTime $deletedAt) {
		$this->deletedAt = $deletedAt;
	}

	/**
	 * @return string The Document's title
	 */
	public function getTitle() {
		return $this->title;
	}

	/**
	 * Sets this Document's title
	 *
	 * @param string $title The Document's title
	 * @return void
	 */
	public function setTitle($title) {
		$this->title = $title;
	}

}
?>

@svparijs sorry, only saw your comment now.. If this is still a problem please flush the caches (if that gives the same exception use ./flow typo3.flow:cache:flush --force
Those annotations should be ignored with the provided Settings.yaml

FYI: With the latest version of Flow (and a change that is currently still under review) this will get very easy: https://gist.github.com/bwaidelich/9617211