Fixed LP bug #999251: Q13 from DBT3 uses table scan instead of covering index scan.

The optimizer chose a less efficient execution plan due to the following
defects of the code:
1. the generic handler function handler::keyread_time did not take into account
   that in clustered primary keys record data is included into each index entry
2. the function make_join_readinfo erroneously decided that index only scan
   could not be used if join cache was empoyed.

Added no additional test case.
Adjusted some of the test results.

mysql-test/r/join_cache.result

@@ -3221,7 +3221,7 @@ explain
 select t1.a, count(t2.p) as count
 from t1 left join t2 on t1.a=t2.a and t2.p % 2 = 1 group by t1.a;
 id	select_type	table	type	possible_keys	key	key_len	ref	rows	Extra
-1	SIMPLE	t1	ALL	NULL	NULL	NULL	NULL	8	Using temporary; Using filesort
+1	SIMPLE	t1	index	NULL	PRIMARY	4	NULL	8	Using index; Using temporary; Using filesort
 1	SIMPLE	t2	ref	i_a	i_a	5	test.t1.a	2	Using where; Using join buffer (flat, BKA join); Key-ordered Rowid-ordered scan
 select t1.a, count(t2.p) as count
 from t1 left join t2 on t1.a=t2.a and t2.p % 2 = 1 group by t1.a;
@@ -4327,15 +4327,15 @@ SELECT t2.v FROM t1, t2, t3
 WHERE t3.v <> t2.v AND t3.pk = t2.i AND t1.v = t3.v AND t1.pk*2<100 
 GROUP BY t2.v ORDER BY t1.pk,t2.v;
 id	select_type	table	type	possible_keys	key	key_len	ref	rows	Extra
-1	SIMPLE	t2	ALL	idx1	NULL	NULL	NULL	20	Using temporary; Using filesort
+1	SIMPLE	t2	index	idx1	idx2	7	NULL	20	Using index; Using temporary; Using filesort
 1	SIMPLE	t3	eq_ref	PRIMARY,idx2	PRIMARY	4	test.t2.i	1	Using where; Using join buffer (flat, BKA join); Key-ordered Rowid-ordered scan
 1	SIMPLE	t1	ref	idx2	idx2	3	test.t3.v	5	Using where; Using join buffer (incremental, BKA join); Key-ordered Rowid-ordered scan
 SELECT t2.v FROM t1, t2, t3 
 WHERE t3.v <> t2.v AND t3.pk = t2.i AND t1.v = t3.v AND t1.pk*2<100 
 GROUP BY t2.v ORDER BY t1.pk,t2.v;
 v
-b
 h
+b
 n
 v
 p
@@ -4345,7 +4345,7 @@ SELECT t2.v FROM t1, t2, t3
 WHERE t3.v <> t2.v AND t3.pk = t2.i AND t1.v = t3.v AND t1.pk*2<100 
 GROUP BY t2.v ORDER BY t1.pk,t2.v;
 id	select_type	table	type	possible_keys	key	key_len	ref	rows	Extra
-1	SIMPLE	t2	ALL	idx1	NULL	NULL	NULL	20	Using temporary; Using filesort
+1	SIMPLE	t2	index	idx1	idx2	7	NULL	20	Using index; Using temporary; Using filesort
 1	SIMPLE	t3	hash_ALL	PRIMARY,idx2	#hash#PRIMARY	4	test.t2.i	20	Using where; Using join buffer (flat, BNLH join)
 1	SIMPLE	t1	hash_ALL	idx2	#hash#idx2	3	test.t3.v	45	Using where; Using join buffer (incremental, BNLH join)
 SELECT t2.v FROM t1, t2, t3

mysql-test/suite/innodb/r/innodb_mysql.result

@@ -2365,8 +2365,8 @@ select_type	SIMPLE
 table	t1
 type	index
 possible_keys	NULL
-key	PRIMARY
-key_len	4
+key	b
+key_len	10
 ref	NULL
 rows	10
 Extra	Using index
@@ -2652,7 +2652,7 @@ select_type	SIMPLE
 table	t1
 type	index
 possible_keys	NULL
-key	PRIMARY
+key	b
 key_len	8
 ref	NULL
 rows	3

sql/handler.cc

@@ -2194,6 +2194,8 @@ double handler::keyread_time(uint index, uint ranges, ha_rows rows)
     The model counts in the time to read index entries from cache.
   */
   ulong len= table->key_info[index].key_length + ref_length;
+  if (index == table->s->primary_key && table->file->primary_key_is_clustered())
+    len= table->s->stored_rec_length;
   double keys_per_block= (stats.block_size/2.0/len+1);
   return (rows + keys_per_block-1)/ keys_per_block +
          len*rows/(stats.block_size+1)/TIME_FOR_COMPARE ;

sql/sql_select.cc

@@ -10080,12 +10080,14 @@ make_join_readinfo(JOIN *join, ulonglong options, uint no_jbuf_after)
       {
         join->need_tmp= 1;
         join->simple_order= join->simple_group= 0;
-        if (sort_by_tab->type == JT_NEXT)
+        if (sort_by_tab->type == JT_NEXT && 
+            !sort_by_tab->table->covering_keys.is_set(sort_by_tab->index))
         {
           sort_by_tab->type= JT_ALL;
           sort_by_tab->read_first_record= join_init_read_record;
         }
-        else if (sort_by_tab->type == JT_HASH_NEXT)
+        else if (sort_by_tab->type == JT_HASH_NEXT &&
+                 !sort_by_tab->table->covering_keys.is_set(sort_by_tab->index))
         {
           sort_by_tab->type= JT_HASH;
           sort_by_tab->read_first_record= join_init_read_record;