Add flatpak update notification and auto proxy config

Automatic proxy config for flatpak in TemplateVMs.
Notify dom0 if system-wide (in TemplateVM) flatpaks are outdated.

A separate patch to `qubes-core-admin-linux` & `vmupdate` will enable
easy update of (in Template) flatpaks via the updater.

related: QubesOS/qubes-issues#2766

Author: alimirjamali

network/update-proxy-configs

@@ -191,3 +191,26 @@ RSYNC_PROXY=\"${PROXY_ADDR_BASE}\""
         update_conf /etc/hosts ""
     fi
 fi
+
+# Flatpak
+if [ -f /usr/bin/flatpak ]; then
+    if [ -n "$PROXY_ADDR" ]; then
+        mkdir -p /run/qubes/bin
+        cat > /run/qubes/bin/flatpak <<EOF
+#!/bin/bash
+### This file is automatically generated by Qubes ($0 script).
+### All modifications here will be lost.
+all_proxy="$PROXY_ADDR" \\
+/usr/bin/flatpak "\$@"
+EOF
+        chmod +x /run/qubes/bin/flatpak
+        cat > /etc/profile.d/qubes-flatpak-proxy.sh << EOF
+### This file is automatically generated by Qubes ($0 script).
+### All modifications here will be lost.
+export PATH=/run/qubes/bin:\$PATH
+EOF
+    else
+        rm -f /run/qubes/bin/flatpak
+        rm -f /etc/profile.d/qubes-flatpak-proxy.sh
+    fi
+fi

package-managers/upgrades-status-notify

@@ -21,6 +21,10 @@ fi
 
 upgrades_installed="$(/usr/lib/qubes/upgrades-installed-check $script_arg)"
 
+if [ "$upgrades_installed" = "true" ] && [ -f "/usr/bin/flatpak" ] && [ -n "$(flatpak remote-ls --system --updates)" ]; then
+    upgrades_installed="false"
+fi
+
 if [ "$upgrades_installed" = "true" ]; then
     /usr/lib/qubes/qrexec-client-vm dom0 qubes.NotifyUpdates /bin/sh -c 'echo 0'
 elif [ "$upgrades_installed" = "false" ]; then