I was am going to use both gumstix, and DIYdrones for this.

Initially it will all be the DIYdrones hardware.

This hardware does almost everything. Autonomous flight, GPS navigation, RC control hybrid.

I've gone with the APM 2.5 system. I went with the uBlox LEA-6H GPS upgrade.
It has the following challenges: - Ground based management - programmed to stay within range of your remote control (1km or so) - Unsure how it will work on a glider

I want to get this and do some testing with the CLI.

If I can get this to accept commands from a gumstix PC, then I can put all of them into one glider and have a completely programmable brain.

You'll notice that the connectors to the ARM2 are compatible with the robostix outputs.
In this way I will chain the devices:
RC 5CH reciever → robostix brain → APM 2.5

This way, when the unit is within range of the remote control, I can send signals to the robostix. It, in turn, can decide if it should pass them on to the APM chip.

I will likely buy this package when the time comes.