Reverts and fixes from stable

[RobertBColton]

• Reverts changes that I made attempting to fix the progress dialog freezing. It is an issue that can be addressed at a later time, for now the Oracle JDK is sufficient.
• Imports fixes for the event tree in the object from the stable branch that were fixed in Fixes ActionList and EventTree issues. #261
• Removes incorrect fixes, and a related comment, for the previous issue.
• Adds comments to clarify the order of creating the main JFrame and preferences handler. pack() should always be called before making a frame visible. This should make the main frame appear more smoothly now without being shown and then jittering to its size and location.
  https://docs.oracle.com/javase/tutorial/uiswing/components/frame.html