Issue: libsbml crashes JDK when generating sub-model

- After searching the libsbml mailing list. It was a found bug. This bug crashes JDK when software using libsbml to add elements (such as reactions or species etc.) into a model.
- So I have to switch to libsbml 3
- However, there is a bug in JDK1.5 when using libsbml3(error message is "Can't load IA 32-bit.so on a IA 32-bit platform"). To fix this bug, it requires JDK1.5 patch 10. So I bluntly upgraded to JDK1.6

After upgraded to JDK1.6, "Can't load IA 32-bit.so on a IA 32-bit platform" gone.

After Upgraded to libsbml3. Crashing JDK problems solved.

* Honestly, libsbml3 comes on a perfect timing. Otherwise, I have to use other XML parser for generating sub-model.

Known differences between libsbml2 and 3
1. getFatal() and getWarning() deprecated;
2. getNumItems became .size(), which is silly;
3. Add new classes Trigger() and Delay(), which could be gotten by model.getTrigger and model.getDelay(). Therefore, to get math equation, I have to use Trigger.getMath() or Delay.getMath(). Previous. model.getTrigger() and model.getDelay() directly return ASTNode.
4. getNameSpaces repalced getNameSpacesList. And even worse, no class NampSpace anymore. It is less OO.