Re-apply the fix for Limits::ponder race

But this time correctly set Threads.ponder

We avoid using 'limits' for passing pondering
flag because we don't want to have 2 ponder
variables in search scope: Search::Limits.ponder
and Threads.ponder. This would be confusing also
because limits.ponder is set at the beginning of
the search and never changes, instead Threads.ponder
can change value asynchronously during search.

No functional change.