Flatpak updates requiring user confirmation are not handled in GUI (silent failure / refresh loop)

[alockgoy]

When updating Flatpak applications through the Update Manager in Linux Mint, updates that require user interaction (such as replacement of deprecated apps or runtimes) are not handled correctly.
Instead of prompting the user, the Update Manager:

• silently refreshes the update list
• does not show any progress dialog
• leaves the update pending indefinitely

However, running the same operation via terminal:
flatpak update

correctly prompts the user with:
Replace? [Y/n]:

This indicates that the issue is not with Flatpak itself, but with how the GUI handles interactive prompts.

Expected behavior

When a Flatpak update requires confirmation, the Update Manager should:

• display a graphical dialog explaining the action (e.g., app replacement, EOL runtime)
• allow the user to accept or reject the change
• proceed with the update accordingly

Actual behavior

• No dialog is shown
• No error is displayed
• The update remains stuck
• The user must manually run flatpak update in terminal to proceed

Why this matters
This breaks the “no terminal needed” experience that Linux Mint aims to provide.

Less experienced users may:

• not understand why updates never install
• assume the system is broken
• remain on outdated or unsupported software

Suggested solutions

• Detect when Flatpak returns an interactive prompt and surface it in GUI
• Alternatively, run Flatpak updates with automatic confirmation (-y) and show a summary of changes
• Or display a clear error message directing the user

Additional context
This issue appears especially when:

• applications are deprecated and replaced (e.g. Jellyfin Media Player → Jellyfin Desktop) (this was my case)
• runtimes reach end-of-life