Original idea from Zardosht Kasheff to add HA_CLUSTERED_INDEX

- Added a lot of code comments
- Updated get_best_ror_intersec() to prefer index scan on not clustered keys before clustered keys.
- Use HA_CLUSTERED_INDEX to define if one should use HA_MRR_INDEX_ONLY
- For test of using index or filesort to resolve ORDER BY, use HA_CLUSTERED_INDEX flag instead of primary_key_is_clustered()
- Use HA_TABLE_SCAN_ON_INDEX instead of primary_key_is_clustered() to decide if ALTER TABLE ... ORDER BY will have any effect.

sql/ha_partition.h:
  Added comment with warning for code unsafe to use with multiple storage engines at the same time
sql/handler.h:
  Added HA_CLUSTERED_INDEX.
  Documented primary_key_is_clustered()
sql/opt_range.cc:
  Added code comments
  Updated get_best_ror_intersec() to ignore clustered keys.
  Optimized away cpk_scan_used and one instance of current_thd (Simpler code)
  Use HA_CLUSTERED_INDEX to define if one should use HA_MRR_INDEX_ONLY
sql/sql_select.cc:
  Changed comment to #ifdef
  For test of using index or filesort to resolve ORDER BY, use HA_CLUSTERED_INDEX flag instead of primary_key_is_clustered()
  (Change is smaller than what it looks beause of indentation change)
sql/sql_table.cc:
  Use HA_TABLE_SCAN_ON_INDEX instead of primary_key_is_clustered() to decide if ALTER TABLE ... ORDER BY will have any effect.
storage/innobase/handler/ha_innodb.h:
  Added support for HA_CLUSTERED_INDEX
storage/innodb_plugin/handler/ha_innodb.cc:
  Added support for HA_CLUSTERED_INDEX
storage/xtradb/handler/ha_innodb.cc:
  Added support for HA_CLUSTERED_INDEX

sql/ha_partition.h

@@ -877,6 +877,10 @@ public:
   */
   virtual ulong index_flags(uint inx, uint part, bool all_parts) const
   {
+    /*
+      The following code is not safe if you are using different
+      storage engines or different index types per partition.
+    */
     return m_file[0]->index_flags(inx, part, all_parts);
   }
 

sql/handler.h

@@ -161,8 +161,11 @@
 */
 #define HA_KEY_SCAN_NOT_ROR     128 
 #define HA_DO_INDEX_COND_PUSHDOWN  256 /* Supports Index Condition Pushdown */
-
+/*
-
+  Data is clustered on this key. This means that when you read the key
+  you also get the row data in the same block.
+*/
+#define HA_CLUSTERED_INDEX      512
 
 /*
   bits in alter_table_flags:
@@ -2311,9 +2314,22 @@ public:
 
 
  /*
-   @retval TRUE   Primary key (if there is one) is clustered
+   Check if the primary key (if there is one) is a clustered key covering
-                  key covering all fields
+   all fields. This means:
-   @retval FALSE  otherwise
+
+   - Data is stored together with the primary key (no secondary lookup
+     needed to find the row data). The optimizer uses this to find out
+     the cost of fetching data.
+   - The primary key is part of each secondary key and is used
+     to find the row data in the primary index when reading trough
+     secondary indexes.
+   - When doing a HA_KEYREAD_ONLY we get also all the primary key parts
+     into the row. This is critical property used by index_merge.
+
+   For a clustered primary key, index_flags() returns also HA_CLUSTERED_INDEX
+
+   @retval TRUE   yes
+   @retval FALSE  No.
  */
  virtual bool primary_key_is_clustered() { return FALSE; }
  virtual int cmp_ref(const uchar *ref1, const uchar *ref2)

sql/opt_range.cc

@@ -1816,6 +1816,12 @@ QUICK_RANGE_SELECT::~QUICK_RANGE_SELECT()
   DBUG_VOID_RETURN;
 }
 
+/*
+  QUICK_INDEX_SORT_SELECT works as follows:
+  - Do index scans, accumulate rowids in the Unique object 
+    (Unique will also sort and de-duplicate rowids)
+  - Use rowids from unique to run a disk-ordered sweep
+*/
 
 QUICK_INDEX_SORT_SELECT::QUICK_INDEX_SORT_SELECT(THD *thd_param,
                                                  TABLE *table)
@@ -1848,7 +1854,18 @@ QUICK_INDEX_SORT_SELECT::push_quick_back(QUICK_RANGE_SELECT *quick_sel_range)
   if (head->file->primary_key_is_clustered() &&
       quick_sel_range->index == head->s->primary_key)
   {
-   /* A quick_select over a clustered primary key is handled specifically */
+   /*
+     A quick_select over a clustered primary key is handled specifically
+     Here we assume:
+     - PK columns are included in any other merged index
+     - Scan on the PK is disk-ordered.
+       (not meeting #2 will only cause performance degradation)
+
+       We could treat clustered PK as any other index, but that would
+       be inefficient. There is no point in doing scan on
+       CPK, remembering the rowid, then making rnd_pos() call with
+       that rowid.
+    */
     pk_quick_select= quick_sel_range;
     DBUG_RETURN(0);
   }
@@ -4298,11 +4315,19 @@ double get_sweep_read_cost(const PARAM *param, ha_rows records)
   DBUG_ENTER("get_sweep_read_cost");
   if (param->table->file->primary_key_is_clustered())
   {
+    /*
+      We are using the primary key to find the rows.
+      Calculate the cost for this.
+    */
     result= param->table->file->read_time(param->table->s->primary_key,
                                           (uint)records, records);
   }
   else
   {
+    /*
+      Rows will be retreived with rnd_pos(). Caluclate the expected
+      cost for this.
+    */
     double n_blocks=
       ceil(ulonglong2double(param->table->file->stats.data_file_length) /
            IO_SIZE);
@@ -6187,7 +6212,6 @@ TRP_ROR_INTERSECT *get_best_ror_intersect(const PARAM *param, SEL_TREE *tree,
   ROR_SCAN_INFO **cur_ror_scan;
   ROR_SCAN_INFO *cpk_scan= NULL;
   uint cpk_no;
-  bool cpk_scan_used= FALSE;
 
   if (!(tree->ror_scans= (ROR_SCAN_INFO**)alloc_root(param->mem_root,
                                                      sizeof(ROR_SCAN_INFO*)*
@@ -6199,11 +6223,20 @@ TRP_ROR_INTERSECT *get_best_ror_intersect(const PARAM *param, SEL_TREE *tree,
   for (idx= 0, cur_ror_scan= tree->ror_scans; idx < param->keys; idx++)
   {
     ROR_SCAN_INFO *scan;
+    uint key_no;
     if (!tree->ror_scans_map.is_set(idx))
       continue;
+    key_no= param->real_keynr[idx];
+    if (key_no != cpk_no &&
+        param->table->file->index_flags(key_no,0,0) & HA_CLUSTERED_INDEX)
+    {
+      /* Ignore clustering keys */
+      tree->n_ror_scans--;
+      continue;
+    }
     if (!(scan= make_ror_scan(param, idx, tree->keys[idx])))
       return NULL;
-    if (param->real_keynr[idx] == cpk_no)
+    if (key_no == cpk_no)
     {
       cpk_scan= scan;
       tree->n_ror_scans--;
@@ -6289,15 +6322,14 @@ TRP_ROR_INTERSECT *get_best_ror_intersect(const PARAM *param, SEL_TREE *tree,
   {
     if (ror_intersect_add(intersect, cpk_scan, TRUE) && 
         (intersect->total_cost < min_cost))
-    {
-      cpk_scan_used= TRUE;
       intersect_best= intersect; //just set pointer here
   }
-  }
+  else
+    cpk_scan= 0;                                // Don't use cpk_scan
 
   /* Ok, return ROR-intersect plan if we have found one */
   TRP_ROR_INTERSECT *trp= NULL;
-  if (min_cost < read_time && (cpk_scan_used || best_num > 1))
+  if (min_cost < read_time && (cpk_scan || best_num > 1))
   {
     if (!(trp= new (param->mem_root) TRP_ROR_INTERSECT))
       DBUG_RETURN(trp);
@@ -6316,7 +6348,7 @@ TRP_ROR_INTERSECT *get_best_ror_intersect(const PARAM *param, SEL_TREE *tree,
     set_if_smaller(param->table->quick_condition_rows, best_rows);
     trp->records= best_rows;
     trp->index_scan_costs= intersect_best->index_scan_costs;
-    trp->cpk_scan= cpk_scan_used? cpk_scan: NULL;
+    trp->cpk_scan= cpk_scan;
     DBUG_PRINT("info", ("Returning non-covering ROR-intersect plan:"
                         "cost %g, records %lu",
                         trp->read_cost, (ulong) trp->records));
@@ -9511,10 +9543,10 @@ ha_rows check_quick_select(PARAM *param, uint idx, bool index_only,
   bool pk_is_clustered= file->primary_key_is_clustered();
   if (index_only && 
       (file->index_flags(keynr, param->max_key_part, 1) & HA_KEYREAD_ONLY) &&
-      !(pk_is_clustered && keynr == param->table->s->primary_key))
+      !(file->index_flags(keynr, param->max_key_part, 1) & HA_CLUSTERED_INDEX))
      *mrr_flags |= HA_MRR_INDEX_ONLY;
   
-  if (current_thd->lex->sql_command != SQLCOM_SELECT)
+  if (param->thd->lex->sql_command != SQLCOM_SELECT)
     *mrr_flags |= HA_MRR_USE_DEFAULT_IMPL;
 
   *bufsize= param->thd->variables.mrr_buff_size;

sql/sql_select.cc

@@ -8550,17 +8550,19 @@ make_join_readinfo(JOIN *join, ulonglong options, uint no_jbuf_after)
 	  else if (!table->covering_keys.is_clear_all() &&
 		   !(tab->select && tab->select->quick))
 	  {					// Only read index tree
+#ifdef BAD_OPTIMIZATION
 	    /*
               It has turned out that the below change, while speeding things
               up for disk-bound loads, slows them down for cases when the data
               is in disk cache (see BUG#35850):
-	    //  See bug #26447: "Using the clustered index for a table scan
+              See bug #26447: "Using the clustered index for a table scan
-	    //  is always faster than using a secondary index".
+              is always faster than using a secondary index".
+            */
             if (table->s->primary_key != MAX_KEY &&
                 table->file->primary_key_is_clustered())
               tab->index= table->s->primary_key;
             else
-	    */
+#endif
               tab->index=find_shortest_key(table, & table->covering_keys);
 	    tab->read_first_record= join_read_first;
             /* Read with index_first / index_next */
@@ -16525,9 +16527,9 @@ test_if_skip_sort_order(JOIN_TAB *tab,ORDER *order,ha_rows select_limit,
         */
         DBUG_ASSERT (ref_key != (int) nr);
 
-        bool is_covering= table->covering_keys.is_set(nr) ||
+        bool is_covering= (table->covering_keys.is_set(nr) ||
-                          (nr == table->s->primary_key &&
+                           (table->file->index_flags(nr, 0, 1) &
-                          table->file->primary_key_is_clustered());
+                            HA_CLUSTERED_INDEX));
 	
         /* 
           Don't use an index scan with ORDER BY without limit.
@@ -16680,17 +16682,15 @@ test_if_skip_sort_order(JOIN_TAB *tab,ORDER *order,ha_rows select_limit,
     /*
       filesort() and join cache are usually faster than reading in 
       index order and not using join cache, except in case that chosen
-      index is clustered primary key.
+      index is clustered key.
     */
-    if ((select_limit >= table_records) &&
+    if (best_key < 0 ||
+        ((select_limit >= table_records) &&
          (tab->type == JT_ALL &&
           tab->join->tables > tab->join->const_tables + 1) &&
-         ((unsigned) best_key != table->s->primary_key ||
+         !(table->file->index_flags(best_key, 0, 1) & HA_CLUSTERED_INDEX)))
-          !table->file->primary_key_is_clustered()))
       goto use_filesort;
 
-    if (best_key >= 0)
-    {
     if (table->quick_keys.is_set(best_key) && best_key != ref_key)
     {
       key_map map;
@@ -16713,9 +16713,6 @@ test_if_skip_sort_order(JOIN_TAB *tab,ORDER *order,ha_rows select_limit,
     used_key_parts= (order_direction == -1) ?
       saved_best_key_parts :  best_key_parts;
   }
-    else
-      goto use_filesort;
-  } 
 
 check_reverse_order:                  
   DBUG_ASSERT(order_direction != 0);

sql/sql_table.cc

@@ -7983,7 +7983,8 @@ copy_data_between_tables(TABLE *from,TABLE *to,
 
   if (order)
   {
-    if (to->s->primary_key != MAX_KEY && to->file->primary_key_is_clustered())
+    if (to->s->primary_key != MAX_KEY &&
+        to->file->ha_table_flags() & HA_TABLE_SCAN_ON_INDEX)
     {
       char warn_buff[MYSQL_ERRMSG_SIZE];
       my_snprintf(warn_buff, sizeof(warn_buff), 

storage/innobase/handler/ha_innodb.h

@@ -98,10 +98,14 @@ class ha_innobase: public handler
 	Table_flags table_flags() const;
 	ulong index_flags(uint idx, uint part, bool all_parts) const
 	{
+          ulong extra_flag= 0;
+          if (table && idx == table->s->primary_key)
+             extra_flag= HA_CLUSTERED_INDEX;
 	  return (HA_READ_NEXT |
 		  HA_READ_PREV |
 		  HA_READ_ORDER |
 		  HA_READ_RANGE |
+                  extra_flag |
 		  HA_KEYREAD_ONLY);
 	}
 	uint max_supported_keys()	   const { return MAX_KEY; }

storage/innodb_plugin/handler/ha_innodb.cc

@@ -2995,12 +2995,15 @@ UNIV_INTERN
 ulong
 ha_innobase::index_flags(
 /*=====================*/
-	uint,
+	uint index,
 	uint,
 	bool)
 const
 {
-	return(HA_READ_NEXT | HA_READ_PREV | HA_READ_ORDER
+       ulong extra_flag= 0;
+       if (table && index == table->s->primary_key)
+             extra_flag= HA_CLUSTERED_INDEX;
+	return(HA_READ_NEXT | HA_READ_PREV | HA_READ_ORDER | extra_flag
 	       | HA_READ_RANGE | HA_KEYREAD_ONLY);
 }
 

storage/xtradb/handler/ha_innodb.cc

@@ -3408,12 +3408,15 @@ UNIV_INTERN
 ulong
 ha_innobase::index_flags(
 /*=====================*/
-	uint,
+	uint index,
-	uint,
+	uint part,
-	bool)
+	bool all_parts)
 const
 {
-	return(HA_READ_NEXT | HA_READ_PREV | HA_READ_ORDER
+       ulong extra_flag= 0;
+       if (table && index == table->s->primary_key)
+             extra_flag= HA_CLUSTERED_INDEX;
+	return(HA_READ_NEXT | HA_READ_PREV | HA_READ_ORDER | extra_flag 
 	       | HA_READ_RANGE | HA_KEYREAD_ONLY | HA_DO_INDEX_COND_PUSHDOWN);
 }