Update

config/sway/config.d/98-application-defaults.conf

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+# don't show gaps if there's only one window on the desktop
+smart_gaps on
+
+# set floating mode for generated windows
+for_window [title="(?:Open|Save) (?:File|Folder|As)"] floating enable
+for_window [title="(?:Open|Save) (?:File|Folder|As)"] resize set 800 600
+for_window [window_role="pop-up"] floating enable
+for_window [window_role="bubble"] floating enable
+for_window [window_role="task_dialog"] floating enable
+for_window [window_role="Preferences"] floating enable
+for_window [window_type="dialog"] floating enable
+for_window [window_type="menu"] floating enable
+
+# set floating mode for specific applications
+for_window [instance="lxappearance"] floating enable
+for_window [app_id="pamac-manager"] floating enable
+for_window [app_id="blueberry.py"] floating enable
+for_window [app_id="dragon-drop"] floating enable, sticky enable
+for_window [app_id="firefox" title="^Library$"] floating enable, border pixel 1, sticky enable
+for_window [app_id="thunderbird" title=".*Reminder"] floating enable
+for_window [app_id="floating_shell"] floating enable, border pixel 1, sticky enable
+for_window [app_id="Manjaro.manjaro-settings-manager"] floating enable
+for_window [app_id="" title="Picture in picture"] floating enable, sticky enable
+for_window [app_id="" title="Picture-in-Picture"] floating enable, sticky enable
+for_window [instance="around"] floating enable, sticky enable
+for_window [app_id="xsensors"] floating enable
+for_window [title="Save File"] floating enable
+for_window [title="Firefox .*— Sharing Indicator"] floating enable, sticky enable, move to scratchpad
+for_window [app_id="" title=".* is sharing your screen."] floating enable
+for_window [title="^wlay$"] floating enable
+
+# Don't allow applications to inhibit shortcuts, i.e. grab total control of the
+# keyboard. Chrome currently abuses this by enabling it for all "--app=..."
+# shortcuts.
+seat * shortcuts_inhibitor disable

config/sway/config.d/99-autostart-applications.conf

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+# autostart background applications
+# FIXME: exec /usr/lib/polkit-gnome/polkit-gnome-authentication-agent-1
+
+# autostarts
+exec {
+    # $initialize_way_displays
+    $initialize_foot_server
+    # $initialize_mounting_daemon
+    # $initialize_poweralert_daemon
+    # $initialize_idlehack_daemon
+    $initialize_workspace_icons
+    # $initialize_swayr_daemon
+    # $initialize_idle_daemon
+    # $initialize_flashfocus
+
+    $xdg-dirs
+    # $swappy_notify
+    # $autostart_dex
+    # $wlsunset
+    # $autotiling
+    # $cliphist_store
+    # $cliphist_watch
+}
+
+# commands that "reload" something
+exec_always {
+    $initialize_waybar
+
+    $apply_background
+    $help_menu
+    $kanshi
+    # $clip-persist
+    $mako
+    # $auto_xdg_keyboard
+    $watch_playerctl
+    # $calendar_daemon
+    # $enable_noisetorch
+    $onscreen_bar --refresh
+    $disable_nm_applet_autostart
+    $nm_applet
+}