I’m guessing this is a simple one… but for some reason I lost all the references in my project. I readded all the jar’s, but for some reason when I right click and go to run as, all I get is java application choice. I don’t get the wpilib java deploy option. I can create a new project and get the option there, but not on my old project. Any suggestions on how to get that back? Thanks!
Did something get messed up in the Eclipse .project file? Try comparing it with a new project.
I feel like re-installing the FRC plugin would be something to try.
Ah, I think it was the .project file. It was missing an entry in the natures section, added it back in and it looks like it’s working again. Thanks! 
I’m having the same problem. On my old laptop my git repository has the option run as WPILib Java Deploy, but on my new laptop it only shows run as Java Application. The .project file matches of course because it’s the same code. Any other suggestions on how to fix this?
The posts above imply that you’ll require an Eclipse FRC plugin on the new laptop in order to do this. If you Google “screensteps wpilib” and hunt around that website, you’ll probably find links to this plugin. I saw a few mentions of Eclipse plugins when I was on there earlier tonight.