Books.java

import com.db4o.*;
import com.db4o.activation.ActivationPurpose;
import com.db4o.activation.Activator;
import com.db4o.collections.ArrayList4;
import com.db4o.config.Configuration;
import com.db4o.diagnostic.Diagnostic;
import com.db4o.diagnostic.DiagnosticListener;
import com.db4o.query.*;
import com.db4o.ta.Activatable;
import com.db4o.ta.NotTransparentActivationEnabled;
import com.db4o.ta.TransparentActivationSupport;


class Author implements Activatable {
    private ArrayList4<Book> books;
    private String name;
    private Activator _activator;

    public Author(String name) {
        this.name = name;
        this.books = new ArrayList4<Book>();
    }

    public void addBook(Book book) {
        activate(ActivationPurpose.WRITE);
        if(!books.contains(book)) {
            books.add(book);
        }
    }

    public String getName() {
        activate(ActivationPurpose.READ);
        return name;
    }

    public ArrayList4<Book> getBooks() {
        activate(ActivationPurpose.READ);
        return this.books;
    }

    @Override
    public String toString() {
        return "Author: " + getName() + "; Books: " + getBooks().size();
    }


   /*Bind the class to the specified object container, create the activator*/
   public void bind(Activator activator) {
       if (_activator == activator) {
         return;
       }
       if (activator != null && _activator != null) {
             throw new IllegalStateException();
         }
     _activator = activator;
   }

   /*Call the registered activator to activate the next level,
    * the activator remembers the objects that were already
    * activated and won't activate them twice.
    */
   public void activate(ActivationPurpose purpose) {
     if (_activator == null)
       return;
     _activator.activate(purpose);
   }

}
class Book implements Activatable {
    private String title;
    private Activator _activator;

    public Book(String title) {
        this.title = title;
    }

    /*Bind the class to the specified object container, create the activator*/
   public void bind(Activator activator) {
       if (_activator == activator) {
         return;
       }
       if (activator != null && _activator != null) {
             throw new IllegalStateException();
         }
     _activator = activator;
   }

   /*Call the registered activator to activate the next level,
    * the activator remembers the objects that were already
    * activated and won't activate them twice.
    */
   public void activate(ActivationPurpose purpose) {
     if (_activator == null)
       return;
     _activator.activate(purpose);
   }
}


public class Books {

    public static void clear(ObjectContainer db, Class klass) {
        Query query = db.query();
        query.constrain(klass);
        ObjectSet results = query.execute();
        while(results.hasNext()) {
          db.delete(results.next());
        }
    }

    public static void run(boolean store) {
      ObjectContainer db = Db4o.openFile(configureTA(), "db/test.db4o");

      System.out.println("Clear.");
      //clear database
      clear(db, Author.class);
      clear(db, Book.class);


      Author author = new Author("Philip K. Dick");

      if(store) {
          System.out.println("Store author");
          db.store(author); // this line will screw things up
      }

      Book ubik = new Book("Ubik");
      Book blade = new Book("Blade Runner");

      System.out.println("Add books.");
      author.addBook(ubik);
      author.addBook(blade);

      System.out.println("Second store.");
      db.store(author);

      db.close();
    }

    public static void print() {
        ObjectContainer db = Db4o.openFile(configureTA(), "db/test.db4o");

        Query query = db.query();
        query.constrain(Author.class);
        ObjectSet results = query.execute();

        while(results.hasNext()) {
            System.out.println(results.next());
        }

        db.close();
    }

    public static void main(String[] args) {
      run(false);
      print();
      run(true);
      print();
  }
        private static void activateDiagnostics(Configuration configuration) {
                // Add diagnostic listener that will show all the classes that are not
                // TA aware.
                configuration.diagnostic().addListener(new DiagnosticListener() {
                        public void onDiagnostic(Diagnostic diagnostic) {
                                if (!(diagnostic instanceof NotTransparentActivationEnabled)) {
                                        return;
                                }
                                System.out.println(diagnostic.toString());
                        }
                });
        }
        // end activateDiagnostics
        
    private static Configuration configureTA() {
		Configuration configuration = Db4o.newConfiguration();
		// add TA support
		configuration.add(new TransparentActivationSupport());
		// activate TA diagnostics to reveal the classes that are not TA-enabled.
		//activateDiagnostics(configuration);
		return configuration;
	}
}

results

With first store disabled: 
Author: Philip K. Dick; Books: 2
With first store enabled: 
Author: Philip K. Dick; Books: 0