I think the 'Tupid is -1' error was actually just fixed in
b45ac0815343 (pushed out around the time you sent this email).
However, your test case did point me to another issue, which was that
include_rules inside a variant was trying to include the top-level
Tuprules.tup file twice. I've changed your test case slightly and
pushed it out in t8061 to fix this.
Thanks for the feedback - let me know if you come across any other
issues with it! I am almost finished with the variants branch, so any
other issues like this are almost certainly bugs :)
-Mike