I've been deleting the plane and re-cloning every time (to try and avoid caching errors).
I think the problem is case sensitive systems vs not case sensitive systems - on my system, there only ever was one file cloned, and I think windows keeps getting confused between them?
At the moment I have:
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C:\Users\redpa\Documents\FlightGear\Custom Aircraft\AirCrane>git status
[snip]
modified: AirCrane/Nasal/electrical.nas
no changes added to commit (use "git add" and/or "git commit -a")
C:\Users\redpa\Documents\FlightGear\Custom Aircraft\AirCrane>git checkout compaddon
error: Your local changes to the following files would be overwritten by checkout:
AirCrane/Nasal/electrical.nas
Please commit your changes or stash them before you switch branches.
Aborting
It will neither stash nor checkout.
In Windows Explorer, it shows as Electrical.nas, but in Notepad++ its electrical.nas, and it starts as:
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#### AirCrane electrical system ####
#### addapted from the Citation II ####
#### jet engine electrical system ####
I'll try and clone the branch directly
Edit - that worked; it finally didn't gave any git status.
It's now lowercase in both explorer and notepad++ and is the right one.
The only issue remaining is the square particles, which are constant, no matter the altitude above the ground. They even show up if I control U to 10000 feet AGL!