In this update I have added a nice splash screen to the application (that's why you now see the manifest.mf file), also the res folder now has the splash screen file and an icon file both in png with transparency.
I have also added MARS.jar an executable that you can download and double click to see what the application is doing so far (and to take a look at the nice splash screen).
I made the src folder reflect the eclipse src folder (added the package folder marsPackage).
Finally I added a GIT cheatsheet text file where I added some git commands for things that are tricky, feel free to add you own commands to that list.

Diego.