I was am going to use both Raspberry Pi, 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 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 may even buy this package when the time comes.

It arrived in the mail via FedEx today.

I connected it to my Linux box and was able to talk to it over the COM port.
Then I went into Windows and flashed the thing with the ArduPilot firmware.

I really should look into the code of ArduPilot. It seems like I can write my own waypoint manager if I put the thing into the correct mode.

I played with the features and then went back into Linux.
The COM is spitting out binary data now. I'll look into that later.

For now, I know that I can use it out-of-the-box to put into an RC plane to program it to perform the actions I want it to do.
That's good enough for now.

I'm going to get some connectors tomorrow to wire it up to my RC controls properly. It connects with a simulator, so that will be useful for
trying out a few things. I'm actually curious if the simulator data will be fed into the chip, and if I can read what it's reading. I doubt it though.
Putting it in Simulator mode will probably make it so I can't read the COM port. In the end, my drone override won't need to do anything too fancy.
It will just be another component in the chain. Now to buy a Raspberry Pi!

I did acquire a Raspberry Pi. I do like it, although it's been given the job of acting as a server for the time being.

I also have used the ArduPilot in the air, and the air sensor is giving me issues.
It seems like a common problem though. I'll have to stop using it for now.