We [will] have two ways of migrating server configuration: the :migrate management operations, which are already described in the Migration Guide, and the WildFly Server Migration tool, for which documentation's there is JBEAP-2646.

They are not equal, as explained at length in the comments in WFLY-5850. We should prominently guide people to the WildFly Server Migration tool, using the :migrate operations directly is more of an advanced use case.

The Migration Guide should explain this at the beginning of the chapter on server upgrade. Then, it should include a warning like this to highlight the difference:

Using the :migrate management operations, you're able to move your EAP 6 configuration files to EAP 7. Still, after the migration, the configuration files will reflect the original EAP 6 configuration (e.g. remoting protocol instead of EAP 7's new http-remoting, port numbers, etc.) and will not contain new EE7 subsystems nor new EAP 7 features (e.g. batch processing, clustered singleton deployments or graceful shutdown). To bring your configuration files fully up to date, while keeping the essential EAP 6 configuration, you must use the WildFly Server Migration tool.

I don't know when the WildFly Server Migration tool will be ready, but even if it won't be ready for 7.0.0.GA, we should provide these explanations and warnings.