Doctrine2 schema tool update fail on many to many relationship - exception

Question

When I need to update my database structure, I do it in PHP using this kind of code :
$tool = new SchemaTool($em);
$classes = array(
$em->getClassMetadata('Entities\Entity1'),
$em->getClassMetadata('Entities\Entity2')
);
$tool->updateSchema($classes);
It works fine until a many to many relation is defined. Consider the following entities as an example :
/**
* Entities\CET\User
*
* #Entity
* #Table(name="tb_user")
*/
class User
{
/**
* #Id
* #Column(type="integer", options={"unsigned"=true})
* #GeneratedValue(strategy="AUTO")
*/
protected $id;
/**
* #ManyToMany(targetEntity="Group", inversedBy="users")
* #JoinTable(name="users_groups")
*/
private $groups;
public function __construct()
{
$this->groups = new ArrayCollection();
}
}
/**
* Entities\CET\Group
*
* #Entity
* #Table(name="tb_group")
*/
class Group
{
/**
* #Id
* #Column(type="integer", options={"unsigned"=true})
* #GeneratedValue(strategy="AUTO")
*/
protected $id;
/**
* #ManyToMany(targetEntity="User", mappedBy="groups")
*/
private $users;
public function __construct()
{
$this->users = new ArrayCollection();
}
}
If my database is empty (no tables) and I update the structure, it works fine. But if tables are already created and I simply want to update them, it breaks and give me the following error :
An exception occurred while executing 'ALTER TABLE tb_group CHANGE id
id INT UNSIGNED AUTO_INCREMENT NOT NULL': SQLSTATE[HY000]: General
error: 1833 Cannot change column 'id': used in a foreign key
constraint 'FK_FF8AB7E0FE54D947' of table 'example.users_groups'
I've tried to manually define join columns and set them to nullable, like this :
/**
* #ManyToMany(targetEntity="Group", inversedBy="users")
* #JoinTable(name="users_groups",
* joinColumns={#JoinColumn(name="user_id", referencedColumnName="id", nullable=true)},
* inverseJoinColumns={#JoinColumn(name="group_id", referencedColumnName="id", nullable=true)}
* )
*/
private $groups;
without much success. Even the simpliest way to define the relation fail to update using Doctrine SchemaTool.
My current workaround is to delete all tables and re-create them, but it's an horrible "solution" on so many levels...