I think that the simplest way would be by overriding the org.eclipse.sirius.business.internal.session.danalysis.DAnalysisSessionImpl.save(Map<?, ?>, IProgressMonitor) with your own list of options. To do so, you will need to provide your own session factory with the extension point org.eclipse.sirius.sessionFactory.

Meanwhile, what is the goal of modifying this serialization value?

Couldn't it be a parameter to change it the genmodel of your metamodel plugin instead?

I can't find a tutorial so far ( I guess it is not really common to change the doSave), but I don't think it should be that painful. Once you have added the extension to your plugin, you just need to create a class that extends SessionFactoryImpl. In your class, I think you should only need to override createSession so instead of returning a new DAnalysisSessionImpl, you return your own class that overrides DAnalysisSessionImpl. In that class, you will just override the doSave method. 1 extension point, 2 classes, 2 methods :)

If I follow correctly your serialization issue, if in your metamodel you have an EAttribute typed EBoolean with a default value false, you want that information to be serialize in your model even if for an element it is valued as true?

That seems redundant with the metamodel, but I do not know how your M2M tool.

I really think that is an issue that could (and probably should) be handled on the EMF side. I have not done this kind of tweak in a while, but for instance once I wanted to change the serialization of references from being index based to being based on elements URI and I had done it in the genmodel or with some custom code in the generated files (I can't remember at the moment).