src/Pure/Tools/build_process.scala

       using_option(store.open_build_database()) { db =>
         db.transaction {
           Data.all_tables.create_lock(db)
           Data.clean_build(db)
         }
-        db.rebuild()
+        db.vacuum(Data.all_tables)
       }
     }
 
     def store_heap(name: String): Boolean =
       build_heap || Sessions.is_pure(name) ||