Index: trunk/src_plugins/lib_gtk_common/dlg_command.c
===================================================================
--- trunk/src_plugins/lib_gtk_common/dlg_command.c	(revision 18823)
+++ trunk/src_plugins/lib_gtk_common/dlg_command.c	(revision 18824)
@@ -292,7 +292,7 @@
 	 */
 void ghid_command_window_show(pcb_gtk_command_t *ctx, pcb_bool raise)
 {
-	GtkWidget *vbox, *vbox1, *hbox, *button, *expander, *text;
+	GtkWidget *vbox, *vbox1, *hbox, *button, *expander, *text, *warn;
 	gint i;
 
 	if (command_window != NULL) {
@@ -311,6 +311,9 @@
 	gtk_container_set_border_width(GTK_CONTAINER(vbox), 6);
 	gtk_container_add(GTK_CONTAINER(command_window), vbox);
 
+	warn = gtk_label_new("WARNING: separate command window is deprecated.\nPlease consider turning it off in the preferences.\n\n");
+	gtk_box_pack_start(GTK_BOX(vbox), warn, FALSE, FALSE, 0);
+
 	ctx->prompt_label = gtk_label_new(pcb_cli_prompt(":"));
 	gtk_box_pack_start(GTK_BOX(vbox), ctx->prompt_label, FALSE, FALSE, 0);
 
Index: trunk/src_plugins/lib_gtk_config/gui-config.c
===================================================================
--- trunk/src_plugins/lib_gtk_config/gui-config.c	(revision 18823)
+++ trunk/src_plugins/lib_gtk_config/gui-config.c	(revision 18824)
@@ -511,7 +511,7 @@
 
 	pcb_gtk_check_button_connected(vbox, NULL, conf_hid_gtk.plugins.hid_gtk.use_command_window,
 																 TRUE, FALSE, FALSE, 2,
-																 config_command_window_toggle_cb, com, _("Use separate window for command entry"));
+																 config_command_window_toggle_cb, com, _("Use separate window for command entry (DEPRECATED)"));
 
 	pcb_gtk_check_button_connected(vbox, NULL, conf_hid_gtk.plugins.hid_gtk.compact_horizontal,
 																 TRUE, FALSE, FALSE, 2,