As far as I can tell this seems to be for deleting application data (~/.var/app/*), whereas flatpak uninstall --unused is for uninstalling runtimes that are no longer needed.

This app is more equivalent to flatpak uninstall --delete-data

Because there are distros, like fedora for one, that have flat packs installable by the likes of discovery on KDE that doesn’t require CLI useage for install or uninstall of flatpacks

Pretty complicated

#!/bin/bash

# List contents of ~/.var/app/
files=$(ls -1 ~/.var/app/)

# Loop through each element of the folder
for file in $files; do
    # Set the name as a variable
    app_name="${file##*/}"

    # Check if a flatpak app of that name is installed
    if ! flatpak list 2> /dev/null | grep -qw $app_name; then
        # Ask the user to delete the folder
        read -p "The app $app_name is not installed. Do you want to delete its folder? (y/n): " choice
        case "$choice" in
            [Yy]* )
                # Remove the folder recursively
                rm -rf ~/.var/app/$file;;
            [Nn]* )
                echo "Skipping deletion of $app_name folder.";;
            * )
                echo "Invalid input. Skipping deletion of $app_name folder.";;
        esac
    fi
done

echo "All Apps checked."

No, that only deletes the leftover dependencies, it doesn't delete any app data/config left over.

This is kind of a shortcoming of all package management in general; should deleting the package delete your user data? There's an argument to be made that data should be removed with the application, but deleting data irrecoverably as the default isn't necessarily the easiest approach.

There's also another problem, which is that the behaviour of deleting data may make sense for per-user applications, but for system-wide apps, should uninstalling an application start nuking data in people's homedirs?