Success! It seems that a significant number of files were missing. I didn't have the .settings, bin, Galaxy, Particle, PipelineEffect, src, String, TextureAnimations, or Window folders. I also didn't have the .classpath or .project files.
...However I now have a new problem. I can no longer close the game! Several of the buttons on the game menu have now disappeared - Download Updates, Get Entrenchment, Get Diplomacy, and Quit. So I can only close the game via Ctrl Alt Del now!