Don't generate code in CubeIDE or CubeMX from the .ioc, it will overwrite stuff.
If you use the IntelliSense configuration in
.vscode/, add a symlinkTools/STM32CubeCLTto yourSTM32CubeCLT_*installation.
$ ln -s /opt/ST/STM32CubeCLT_1.19.0 Tools/STM32CubeCLT