Fix upgrade from 2.5 to 2.6 to 2.7

CURA-3975

- Set Preferences setting_version in CuraApplication so Preferences can
  get upgraded correctly
- Fix upgrade script for 2.5 to 2.6
- Fix upgrade script for 2.6 to 2.7 which relies on the upgrade of 2.5
  to 2.6

plugins/VersionUpgrade/VersionUpgrade25to26/VersionUpgrade25to26.py

@@ -61,8 +61,13 @@ class VersionUpgrade25to26(VersionUpgrade):
             parser["general"]["visible_settings"] = ";".join(new_visible_settings)
 
         #Change the version number in the file.
+        if "general" not in parser:
+            parser["general"] = {}
         parser.set("general", "version", "4")
-        parser.set("general", "setting_version", "1")
+
+        if "metadata" not in parser:
+            parser["metadata"] = {}
+        parser.set("metadata", "setting_version", "1")
 
         #Re-serialise the file.
         output = io.StringIO()