Annotation focused changes and refactoring

runPythonScript now takes an additional argument, the name of the annotation, and the annotation name is also passed when stitching so that resulting images have the original name, the modality, and the annotation name for when there are multiple image areas within a single slide.

src/main/groovy/qupath/ext/qp_scope/QP_scope.groovy

@@ -58,7 +58,7 @@ class QP_scope implements QuPathExtension {
         def menu = qupath.getMenu("Extensions>${name}", true)
 
         // First menu item
-        def qpScope1 = new MenuItem("First scan - Use bounding box")
+        def qpScope1 = new MenuItem("First scan type - Use bounding box")
         // TODO: tooltip
         qpScope1.setOnAction(e -> {
             // TODO: check preferences for all necessary entries, and check for micromanager running+version