I’ve worked it out, thanks for the responses, maybe I didn’t word the question properly or something, but here’s what I did for anyone interested in the future:
You only need to do this once for every machine you want to work on.
Add the llvm freedesktop sdk extensions to get a clangd executable to your flatpak manifest:
Run the Flatpak: Build command in the command palette (Ctrl+Shift+P) this might take a minute. Make sure you have the required sdks installed (see the manifest for details).
There should now be two folders: .flatpak and _build. There should also be a script generated at .flatpak/meson.sh. Run: