Cross-compilation with remote launch from Eclipse is very useful approach to develop RaspberryPi applications. There is a serious security problem however. One who need access to GPIO (ex, using wiringPi) should have root priveleges. Consequently, he has to SSH to RaspberryPi as root user. This is because I can't find the way to tell Eclipse to login as ordinary user and use sudo. So root via SSH seems to be the only solution, am I right? Could you propose any workaround?
The folks at Qucik2Wire agree with your observation regarding security and the need to run any code that accesses the Pi's GPIO pins as root. To address this they have developed a project called gpio-admin which allows non root control of the GPIO pins.