flatpak: Use drop-in flatpakrepo for system-wide remotes

[ryonakano]

Fixes the issue I found at elementary/os#783 (comment)

Based on @jumpyvi's work here with two changes:

• Removed Priority=100 from appcenter.flatpakrepo
  • Because I couldn't find such field exist as far as reading man flatpak-remote and man flatpakrepo
• Replaced the value of GPGKey fields using the following command

  base64 -w0 skel/flatpak/repo/flathub.trustedkeys.gpg >> flatpak/flathub.flatpakrepo
  base64 -w0 skel/flatpak/repo/appcenter.trustedkeys.gpg >> flatpak/appcenter.flatpakrepo
  

Checklist

• /var/lib/flatpak/repo is no longer overwritten by default-settings

Details

user@elementary-9-daily:~$ sudo apt purge flatpak elementary-default-settings 
The following package was automatically installed and is no longer required:
  libraw23t64
Use 'sudo apt autoremove' to remove it.

REMOVING:
  elementary-default-settings*  flatpak*  io.elementary.sideload*  pantheon-photos*

Summary:
  Upgrading: 0, Installing: 0, Removing: 4, Not Upgrading: 1
  Freed space: 16.2 MB

Continue? [Y/n] y
(Reading database… 151210 files and directories currently installed.)
Removing elementary-default-settings (8.1.1+r457+pkg326~daily~ubuntu9.1)…
Removing pantheon-photos (8.0.2+r4872+pkg80~daily~ubuntu9.1)…
Removing io.elementary.sideload (6.3.1+r1211+pkg19~daily~ubuntu9.1)…
Removing flatpak (1.18.1-1+elementary3~ubuntu9.1)…
Processing triggers for hicolor-icon-theme (0.18-2build1)…
Processing triggers for doc-base (0.11.2build1)…
Processing 1 removed doc-base file, 27 changed doc-base files...
Processing triggers for man-db (2.13.1-1build1)…
Processing triggers for libglib2.0-0t64:amd64 (2.88.0-1)…
Processing triggers for dbus (1.16.2-2ubuntu4)…
Processing triggers for desktop-file-utils (0.28-1build1)…
(Reading database… 150579 files and directories currently installed.)
Purging configuration files for elementary-default-settings (8.1.1+r457+pkg326~daily~ubuntu9.1)…
Purging configuration files for flatpak (1.18.1-1+elementary3~ubuntu9.1)…
Purging configuration files for pantheon-photos (8.0.2+r4872+pkg80~daily~ubuntu9.1)…
user@elementary-9-daily:~$ ls -la /var/lib/flatpak/repo
ls: cannot access '/var/lib/flatpak/repo': No such file or directory
user@elementary-9-daily:~$ sudo apt install ./elementary-default-settings_8.1.1_all.deb 
Note, selecting 'elementary-default-settings' instead of './elementary-default-settings_8.1.1_all.deb'
The following package was automatically installed and is no longer required:
  libraw23t64
Use 'sudo apt autoremove' to remove it.

Installing:
  elementary-default-settings

Installing dependencies:
  flatpak

Suggested packages:
  malcontent-gui

Summary:
  Upgrading: 0, Installing: 2, Removing: 0, Not Upgrading: 1
  Download size: 1,606 kB / 1,624 kB
  Space needed: 7,076 kB / 52.8 GB available

Continue? [Y/n] y
Get:1 /home/user/elementary-default-settings_8.1.1_all.deb elementary-default-settings all 8.1.1 [18.4 kB]
Get:2 https://ppa.launchpadcontent.net/elementary-os/os-patches/ubuntu resolute/main amd64 flatpak amd64 1.18.1-1+elementary3~ubuntu9.1 [1,606 kB]
Fetched 1,606 kB in 3s (506 kB/s)    
Selecting previously unselected package flatpak.
(Reading database… 153508 files and directories currently installed.)
Preparing to unpack …/flatpak_1.18.1-1+elementary3~ubuntu9.1_amd64.deb…
Unpacking flatpak (1.18.1-1+elementary3~ubuntu9.1)…
Selecting previously unselected package elementary-default-settings.
Preparing to unpack …/elementary-default-settings_8.1.1_all.deb…
Unpacking elementary-default-settings (8.1.1)…
Setting up flatpak (1.18.1-1+elementary3~ubuntu9.1)…
Setting up elementary-default-settings (8.1.1)…
Created symlink '/etc/systemd/system/multi-user.target.wants/flatpak-preinstalld.service' → '/usr/lib/systemd/system/flatpak-
preinstalld.service'.
Processing triggers for dbus (1.16.2-2ubuntu4)…
Processing triggers for desktop-file-utils (0.28-1build1)…
Processing triggers for doc-base (0.11.2build1)…
Processing 1 added doc-base file...
Processing triggers for man-db (2.13.1-1build1)…
Processing triggers for libglib2.0-0t64:amd64 (2.88.0-1)…
Notice: Download is performed unsandboxed as root as file '/home/user/elementary-default-settings_8.1.1_all.deb' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied)
user@elementary-9-daily:~$ ls -la /var/lib/flatpak/repo
total 40
drwxr-xr-x   7 root root 4096 Aug 14 22:57 .
drwxr-xr-x   6 root root 4096 Aug 14 22:57 ..
-rw-r-----   1 root root    0 Aug 14 22:56 .lock
-rw-r--r--   1 root root 1234 Aug 14 22:56 appcenter.trustedkeys.gpg
-rw-r--r--   1 root root 1254 Aug 14 22:57 config
drwxr-xr-x   2 root root 4096 Aug 14 22:56 extensions
-rw-r--r--   1 root root 2888 Aug 14 22:56 flathub.trustedkeys.gpg
drwxr-xr-x 258 root root 4096 Aug 14 22:57 objects
drwxr-xr-x   5 root root 4096 Aug 14 22:56 refs
drwxr-xr-x   2 root root 4096 Aug 14 22:57 state
drwxr-xr-x   3 root root 4096 Aug 14 22:57 tmp
user@elementary-9-daily:~$ ls -la /usr/share/flatpak/remotes.d/
total 20
drwxr-xr-x  2 root root 4096 Aug 14 22:56 .
drwxr-xr-x  5 root root 4096 Aug 14 22:56 ..
-rw-r--r--  1 root root 1990 Feb  6  2026 appcenter.flatpakrepo
-rw-r--r--  1 root root 4100 Feb  6  2026 flathub.flatpakrepo
user@elementary-9-daily:~$