I’ve read through this post more fully again, and realised you’re running into the same issue that was discussed further up. That issue hasn’t yet been fixed in ArduSub-stable, so the workaround I originally suggested is likely the best course of action for now.
I spoke with our software team and @williangalvani is working on updating submodules to solve the issue properly for ArduSub >= 4.1, but completing that may take some more time.
I’ve just tried a fresh install of a fresh ardupilot fork on Ubuntu 20.04, and it worked without issues when using that workaround. Combining for a full set of instructions:
git clone https://github.com/your-github-userid/ardupilot
cd ardupilot
# fetch the latest tags
git fetch --tags
# checkout the latest stable tag, and branch off it in your own 'new-branch'
git checkout ArduSub-stable -b new-branch
# manually fix deprecated authentication format
sed -i -e s/git:/https:/ .gitmodules
# initial submodule update and initialisation
git submodule update --init
# fix the same issue within a submodule
sed -i -e s/git:/https:/ modules/mavlink/.gitmodules
# update submodules recursively and continue as normal
git submodule update --init --recursive
# install prerequisites
Tools/environment_install/install-prereqs-ubuntu.sh -y
# reload the path
. ~/.profile
# configure waf for your board (e.g. Pixhawk1)
./waf configure --board Pixhawk1
Note that if you try to initialise submodules before the links have been changed properly then the incorrect link is stored internally, so it’s much easier to start with a fresh ardupilot clone and work through the instructions from the top.