// so it should be the first filter to be run
scopedEntityFilterList.add(0, new PublicEntitiesOnlyFilter());
}
// create the module and scoped entity filters from the aggregated lists.
ModuleFilter moduleFilter = CompositeModuleFilter.make(moduleFilterList);
ScopedEntityFilter scopedEntityFilter = CompositeScopedEntityFilter.make(scopedEntityFilterList);
FileSystemFileGenerator fileGenerator = new FileSystemFileGenerator(baseDirectory, logger);
return new HTMLDocumentationGeneratorConfiguration(