Pass the root directory to Doxyfilter and thence pythfilter.py so that the latter can get the namespace/packages correct.

docs/Doxyfilter

@@ -1,12 +1,16 @@
 #!/bin/sh
 
+#
+# Doxyfilter <source-root> <filename>
+#
+
 dir=$(dirname "$0")
 
 PYFILTER="$dir/pythfilter.py"
 
-if [ "${1/.py/}" != "$1" ]
+if [ "${2/.py/}" != "$2" ]
 then
-    python "$PYFILTER" -f "$1"
+    python "$PYFILTER" -r "$1" -f "$2"
 else
-    cat "$1"
+    cat "$2"
 fi