Loading machine from AST does not work with referenced definition files

[cobizobi]

Loading a machine from a Java AST currently fails if a definition from a referenced definition file is used in the machine. This is probably because the PreParser is not executed and definitions from definition files are not collected by the DefinitionCollector (which is required for typing of definitions).

[iTitus]

Added a workaround, although the core issue is not fixed

EDIT: workaround costs too much performance-wise, added javadoc warning instead