In the Save/Load screen, there is an option on the bottom to Save as a file. Then when you run the new version of the game you can Load or Quickload a file (you can work through the directory tree to wherever you saved it.) As far as I can tell, the save I had from 0.8.2.1 was compatible. This is also what you need to do at the end of a game session if your browser is set to delete cookies and such.