Previously, internalAddGeneratedFile has to depend on old non-nested name for sub-messages.
This creates a hard dependency on old generated code for compatibility usage.
If user's code has custome error handler, the deprecation warning in the old generated code
will also be thrown (even though users haven't explicitly depended on the old message name).

To fix this problem, this change added an additional flag in the generated code to tell run
time that it's safe to use new message name. In this way, internalAddGeneratedFile can safely
depend on new name and don't trigger unnecessary deprecation warning.