Explicitely save preferences on startup

Before, the preferences were saved as a side effect of loading files in
the Editor, but it seems better to explicitely save them as well (this
should prevent problems later on, if the Editor class is no longer used
in --verify or --upload mode).

app/src/processing/app/Base.java

@@ -433,6 +433,11 @@ public class Base {
       }
     }
 
+    // Save the preferences. For GUI mode, this happens in the quit
+    // handler, but for other modes we should also make sure to save
+    // them.
+    Preferences.save();
+
     switch (action) {
       case VERIFY:
       case UPLOAD: