Prevent false positives when issuing new "dotted filenames" warning.

See #2686.

Cython/Compiler/Main.py

@@ -656,6 +656,7 @@ def search_include_directories(dirs, qualified_name, suffix, pos, include=False)
     for dirname in dirs:
         path = os.path.join(dirname, dotted_filename)
         if os.path.exists(path):
+            if '.' in qualified_name and '.' in os.path.splitext(dotted_filename)[0]:
                 warning(pos, "Dotted filenames ('%s') are deprecated."
                              " Please use the normal Python package directory layout." % dotted_filename, level=1)
             return path