ardupilot VS MissionPlanner

They are widely used in narrow circles :)

Two of (arguably the best) open source RC aircraft flight controllers (ArduPilot and PX4) are using extended Kalman filters in their state estimators (essentially sensor fusion that provides attitude/position estimate):

https://github.com/ArduPilot/ardupilot/tree/master/libraries...

https://github.com/PX4/PX4-Autopilot/blob/main/src/modules/e...

I'm not that familiar with cleanflight/betaflight/inav scene to know what the FPV racer flight controllers use.

2. https://ardupilot.org/

Trimble also has some nice stuff, I think the BD940 is interesting. I do not know if it's recommended or not, but Ardupilot has a driver for the Septentrio GPS (https://github.com/ArduPilot/ardupilot/blob/master/libraries/AP_GPS/AP_GPS_SBF.cpp), as well for Trimble GPS (https://github.com/ArduPilot/ardupilot/blob/master/libraries/AP_GPS/AP_GPS_GSOF.cpp). So people have used these brands for drones.

For programmable open source autopilot: Arduino > Ardupilot (https://ardupilot.org).

You might also want to look at something like Ardupilot

I'd like to emphasize the reference to Ardupilot bc there is a lot of material already developed there: a lot about navigation and guidance from UAVs, and the low-level stuff. Check this out

Run Mission Planner on a PC, connect it to your flight controller, go to "CONFIG", then "full parameter list", then type the first characters of the one you want in the search box on the right.

To add to this, most of the time one doesn't need to hack on the drone firmware itself. Just configuring/hacking the mission planner alone would go a long way: https://ardupilot.org/planner/

But if you're interested in more readable codebases without too much legacy headaches:

https://github.com/BossHobby/QUICKSILVER (for indoor drones mostly)

And for even less functionality but a good learning tool kind of codebase:

https://github.com/nickrehm/dRehmFlight

I want to build a gui to control a small autonomous boat. My initial plan was to modify this thing: https://github.com/ArduPilot/MissionPlanner

If you want to learn how to build it from scratch, you can still look at Arducopter for the firmware. It's entirely open source, including the GCS's like Mission Planner, and you can look at how they implement control over telemetry radios (using a protocol called Mavlink).

Related feature request, )elevation data from the Norwegian Mapping Authority ): https://github.com/ArduPilot/MissionPlanner/issues/2527