MySQL is funny with catalogs and schemas. It doesn't support schemas like most other databases do. It's just called 'databases'.
When you try to create a reveng.xml file using the Hibernate Reverse Engineering Editor, you can't get multiple databases / schemas to show up.

It looks like the wizard looks at the hibernate.connection.url property in the hibernate-console.properties file. However, when I leave out the name of the database (e.g. jdbc:mysql://localhost:3306) without the database, the wizard does not return any tables.

When you leave out the default database (i.e. schema) name in the connection.url, you should see all databases/ schemas for that one connection.
When a user selects multiple schemas, the resulting reveng.xml file should have one <schema-selection ...> element for each schema the user wants to map tables from.