feat: clean up packages

[NN708]

This PR optimizes the packages by:

1. Removing redundant packages that are already included as dependencies to simplify the recipe.
2. Removing desktop-related packages, as these should be managed in desktop-image.
3. Removing Apx, which can now be installed via Flatpak (Deliver Apx GUI as a Flatpak first-setup#406).

[taukakao]

Why are you removing apx?

[NN708]

Why are you removing apx?

Apx is already packaged in Apx GUI Flatpak, so I think we should remove the duplication here to avoid having multiple versions of Apx on the system. Users could run flatpak run --command=apx org.vanillaos.ApxGUI if they still prefer using the Apx CLI.

The Distrobox bundled with Apx should also be removed, since it's already installed in #116.

[taukakao]

I think not everyone should be expected to install the apx gui. Also, flatpak is not that well suited for CLI programs.

Both apx and distrobox are quite small so removing them doesn't really improve anything.

Including two versions of distrobox was done to more tightly control the version that apx uses, though I didn't make that decision and don't really care.

[NN708]

I think not everyone should be expected to install the apx gui. Also, flatpak is not that well suited for CLI programs.

Both apx and distrobox are quite small so removing them doesn't really improve anything.

The issue is not their size. The Apx in Flatpak won't have access to the configuration on the host system. Instead, it will store its own config at ~/.var/app/org.vanillaos.ApxGUI/data/apx. This could lead to different configurations between GUI and CLI, which would likely confuse users.

I think we should ask users to handle the transition, similar to how they are expected to manually install Showtime (Vanilla-OS/first-setup#397), Papers (Vanilla-OS/first-setup#404), and upcoming changes like Ptyxis (Vanilla-OS/desktop-image#279) and Resources (Vanilla-OS/desktop-image#286). However, we should consider how to better guide users through this process.

Given that this has become more complicated, I have removed that commit from this PR and will open a separate one instead.