It seems like apt autoremove really removed the package I just installed in the previous step.
So what worked for me was:
git clone https://github.com/doxygen/doxygen.git
cd doxygen
mkdir build
cd build
These are new:
sudo apt-get install flex
sudo apt-get install bison
cmake -G "Unix Makefiles" ..
make
…but of course the horror wouldn’t end there, see my next question 😀