I need to configure default behaviour of EJB3 exporters because:

I need to generate 2 entity beans with @ManyToMany instead of 3 (by default)

There are more cases I'd like to configure exporters defult behaviour, e.g @Embedded class instead of @OneToOne

I guess it is not possible with current Hibernate Tools. Am I right?
What tools can I used instead to get annotated java classes ( I need to be able to configure generation behaviour)?

Second question :
I need to implement business domain but I do not want to modify generated classes directly(and I do not want to use DAO here). First though was to inherit my domain classee from persistance classes and add some methods in subclasses. Does anyone have any better ( and flexible) suggestions?

you can reconfigure all the parts you want.

some of the stuff you talk about sounds more to be related to how the reverse engineering interprets the underlying database; not about how the hbiernate metamodel is converted to annotations.

e.g. creating ManyToMany is something the reverse engineering needs to actually recognize before the java code generator can see it.

But you can redefine all of it if you want. you can even just take the full database model and generate it from there.

it is avaialble in $cfg.getTableMapings().