Setup.thread.in was misnamed so it has been replaced by

Setup.config.in.  The latter contains all configure-time selectable
modules; currently thread and gc.

Modules/Setup.thread.in → Modules/Setup.config.in

-# This file is transmogrified into Setup.thread by config.status.
+# This file is transmogrified into Setup.config by config.status.
 
-# Its purpose is to automatically enable the thread module by default
-# unless the the --without-threads argument is given to the configure
-# script.
+# The purpose of this file is to conditionally enable certain modules
+# based on configure-time options.  Currently thread support and
+# garbage collection support are the only two modules so enabled.
 
 # *NOTE*: if the configure script decides it can't support threads,
 # the thread module will still be enabled and cause compile errors.
 # The solution is to use --without-threads on platforms that don't
 # support threads.
-
 @USE_THREAD_MODULE@thread threadmodule.c
 
 # Garbage collection enabled with --with-cycle-gc