[everything] Fix circular shared pointer references.

We had a cycle from transaction_manager <-> space_map, and also from
the ref_counters back up to the tm.

This prevented objects being destroyed when various programs exited.

From now on we'll try and only use a shared ptr if ownership is
implied.  Otherwise a reference will be used (eg, for up pointers).

era/restore_emitter.cc

@@ -52,7 +52,7 @@ namespace {
 			in_writeset_ = true;
 			era_ = era;
 
-			bits_.reset(new bitset(md_.tm_));
+			bits_.reset(new bitset(*md_.tm_));
 			bits_->grow(nr_bits, false);
 		}