finally got the deck migration running - when you start forge, if there's a all-decks2 file, you're asked if you want to import it. this version has all the decks already imported, and the all-decks2 property commented out, so you're not asked again.

src/DeckConverter.java

@@ -0,0 +1,67 @@
+/**
+ * DeckConverter.java
+ * 
+ * Created on 08.11.2009
+ */
+
+import static java.lang.String.*;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JOptionPane;
+
+import forge.Deck;
+import forge.DeckIO;
+import forge.NewDeckIO;
+import forge.properties.ForgeProps;
+import forge.properties.NewConstants;
+
+
+/**
+ * The class DeckConverter. This class uses an {@link OldDeckIO} and a {@link NewDeckIO} to convert the old
+ * all-decks2 file into the new folder structure.
+ * 
+ * @version V0.0 08.11.2009
+ * @author Clemens Koza
+ */
+public class DeckConverter {
+    public static void main(String[] args) {
+        File oldDecks = ForgeProps.getFile(NewConstants.DECKS);
+        File newDecks = ForgeProps.getFile(NewConstants.NEW_DECKS);
+        
+        if(oldDecks == null || !oldDecks.isFile()) return;
+        
+        int choice = JOptionPane.showConfirmDialog(null, format(
+                "This dialog lets you migrate your old decks to the new version of forge.%n"
+                        + "Your old decks file: %s%nYour new decks directory: %s%n%n"
+                        + "If you don't want to see this dialog again, please remove/rename your %1$s file,%n"
+                        + "or otherwise hide it from forge.%n%nDo you want to migrate your decks now?", oldDecks,
+                newDecks), "Deck Migration", JOptionPane.YES_NO_OPTION);
+        
+        if(choice != JOptionPane.YES_OPTION) return;
+        System.out.println("migrating deck file...");
+        
+        DeckIO odio = new OldDeckIO(oldDecks);
+        List<Deck> deckList = new ArrayList<Deck>(Arrays.asList(odio.getDecks()));
+        Map<String, Deck[]> boosterMap = odio.getBoosterDecks();
+        System.out.println("Decks found:");
+        System.out.printf("\t%d normal decks%n", deckList.size());
+        System.out.printf("\t%d booster decks%n", boosterMap.size());
+        
+        //the constructor loads the decks from NEW_DECKS and preserves those from the collections
+        DeckIO ndio = new NewDeckIO(newDecks, deckList, boosterMap);
+        
+        System.out.println("Decks in NewDeckIO:");
+        System.out.printf("\t%d normal decks%n", ndio.getDecks().length);
+        System.out.printf("\t%d booster decks%n", ndio.getBoosterDecks().size());
+        
+        //stores all the decks (new and old) to the directory.
+        ndio.close();
+        
+        JOptionPane.showMessageDialog(null, "Your deck file was successfully migrated!");
+    }
+}