I think these should come from the settings by default. We don't need any changes in index.php that way, and can just set them like this:

    [Paths]
    
    ; The path to your navigation structure file.
    ; Note: Leave the leading slash out of the path.
    
    navigation_json = conf/navigation.json
    
    ; The path to your file uploads. Note: Leave
    ; the leading and trailing slashes out of the path.
    
    filemanager_path = files

That way the first call to `conf ('Paths', 'filemanager_path')` or the other one will have the correct default value. And most sites will never change these, so the defaults should keep the existing names intact.