Managing applications with different installers sources and automatic updates: solving the problem

At the same time different versions of the app are installed from different sources one version of the app is installed from flatpak, another from snap and the third from a third party ubuntu repo, i.e. using apt install. all these apps use the same config in ~/.config/ My question is how can i use the bash command line to detect this situation? I mean commands like apt/flatpak/snap list etc. In the current situation I have a problem with applications updating automatically. I would like to mark all applications as manually installed so that they can only be updated with a special command and not automatically. how can I do this for apt | flatpak | snap | applications?