Did something change in GNOME 48 (Wayland)? My Chromium PWAs (Edge/Brave Flatpak) stopped grouping under their own icons on Ubuntu 25.04

Hey folks,

Sorry to bother ya'all, but, I am looking for a sanity check and maybe a pointer.

In the last few days my PWAs (Edge/Brave from Flatpak) stopped behaving like separate apps on GNOME 48 (Wayland). When I click the PWA icon (e.g., Outlook), the window now groups under the main Edge/Brave icon instead of the PWA’s own icon. This used to work perfectly, with multiple PWA windows neatly grouped under their own launcher.

Why I think this might be GNOME/Mutter/Wayland-related

• I’m on GNOME 48.0 (Mutter, Wayland) on Ubuntu 25.04.
• Everything was fine until very recently. Now all Chromium-based PWAs seem to be treated as the same app as the parent browser.
• It feels like the window identity/app_id matching changed, or the rules for how Shell picks the .desktop entry.

My setup

• Ubuntu 25.04 (Lobster), GNOME 48.0, Wayland, Kernel 6.14.0-29
• Browsers: com.microsoft.Edge (Flatpak) and com.brave.Browser (Flatpak)
• Example PWA: Outlook (Edge PWA)
• I also have Dash-to-Dock, but I can reproduce this with extensions disabled.

What I tried (short version)

• Wayland vs XWayland: forced both modes per PWA (OZONE_PLATFORM=wayland vs --ozone-platform=x11)
• Desktop file tweaks:
  • Renamed the PWA launcher to match the class/id (crx_<hash>.desktop)
  • Added StartupWMClass/X-GNOME-WMClass to match (crx_<hash>)
  • Made sure only one .desktop exists and updated the desktop database
• Alternate flags:
  • --class=crx_<hash> and also tried --app-id-window-class=crx_<hash>
• Clean launches: quit all Edge/Brave windows before opening the PWA, to avoid inheriting state
• Result: still groups under the parent browser icon instead of the PWA icon

A concrete example (Outlook PWA)

• Filename (as generated by Edge Flatpak): com.microsoft.Edge.flextop.msedge-<hash>-Profile_4.desktop
• Exec looks like: flatpak run --command=/app/bin/edge com.microsoft.Edge --profile-directory='Profile 4' --app-id=<hash> --app-url='https://outlook.office.com/...' --class=crx_<hash> %U
• This used to give Outlook its own icon and grouping. Now it doesn’t.

Asks

• Can anyone else on GNOME 48 (especially Ubuntu 25.04) confirm this started happening in the past few days?
• Did Mutter/Shell tighten app_id/desktop matching rules in 48 that would affect Chromium PWAs?
• Is there a known “right way” now to make PWAs show up as separate apps on Wayland (e.g., the exact app_id that needs to match the .desktop filename)?
• If you’ve got this working on GNOME 48, what Exec/flags/desktop filename combo are you using?

Thank you! I really liked how tidy PWAs used to be in the dock, so I’m hoping this is either a known regression or there’s a new recommended setup I can switch to.