I have to agree with frasnow - Netbeans isn't a bug we have to "work around"! That said, you asked a fair question, and it deserves an answer.
Yes, it's absolutely possible. Start by downloading the Netbeans modules for FRC and extracting them. Everything you need to know is in there, you just have to find it.
To compile the code, you probably need to use Ant. This is what Netbeans uses under the hood, and all of the build processes are already written as Ant scripts. The goldmine is in FRCNetbeansUpdateV3077/edu-wpi-first-squawksdk/netbeans/modules/edu-wpi-first-squawksdk/ant.
As you said, Netbeans just FTPs the code to the cRIO. Basic details are
on FIRSTForge. There's an Ant script that does the deploy, too, so that might be even easier than using FTP by itself. But we weren't asking about easy, were we? We're in this to learn... so hack on!
