Some stuff that was before implicitly checked during deserialization
now need explicit checks, those are introduced here.
This also fixes test failures related to the changed serialization
format (which fields can or cannot be omitted when they have
the default value).
In this commit we instruct the build system to use the unified schema
files instead of collecting the `TUPLE-TREE-YAML` comments.
The fixes to C++ files are necessary because they depend on the order
of the fields in the schema, which was changed.
Alessandro Di Federico