This extra cleaning up appears to be necessary now

scripts/transform-file.py

@@ -88,6 +88,8 @@ def markdown_to_html(input_file, output_dir):
         pages = []
         for path, subdirs, subfiles in os.walk(site_dir):
             dir = path
+            if dir.startswith(site_dir):
+                dir = path[len(site_dir):]
             if dir.startswith('./'):
                 dir = dir[1:]
             if dir.startswith('/site'):