InnoDB Plugin locks table

This is a pre fix update that does the change to the handler api.

This is done since there are already changes in this version,
so the real fix does not need to change the api.

sql/handler.h:
  Bug#37453: Dropping/creating index on partitioned table with
  InnoDB Plugin locks table
  
  The check for which alter table flags a handler have is done through the
  handlerton, which will not work correctly for any partitioned table.
  It must be through the handler interface.
  
  To be able to fix this I have to add a virtual function to the handler class.

          ``FLUSH TABLES WITH READ LOCK''

Concurrent execution of 1) multitable update with a
NATURAL/USING join and 2) a such query as "FLUSH TABLES
WITH READ LOCK" or "ALTER TABLE" of updating table led
to a server crash.


The mysql_multi_update_prepare() function call is optimized
to lock updating tables only, so it postpones locking to
the last, and if locking fails, it does cleanup of modified
syntax structures and repeats a query analysis.  However,
that cleanup procedure was incomplete for NATURAL/USING join
syntax data: 1) some Field_item items pointed into freed
table structures, and 2) the TABLE_LIST::join_columns fields
was not reset.

Major change:
  short-living Field *Natural_join_column::table_field has
  been replaced with long-living Item*.


mysql-test/r/lock_multi.result:
  Added test case for bug #38691.
mysql-test/t/lock_multi.test:
  Added test case for bug #38691.
sql/item.cc:
  Bug #38691: segfault/abort in ``UPDATE ...JOIN'' while
            ``FLUSH TABLES WITH READ LOCK''
  
  The Item_field constructor has been modified to allocate
  and copy original database/table/field names always (not
  during PS preparation/1st execution only), because
  an initialization of Item_field items with a pointer to
  short-living Field structures is a common practice.
sql/sql_base.cc:
  Bug #38691: segfault/abort in ``UPDATE ...JOIN'' while
            ``FLUSH TABLES WITH READ LOCK''
  
  1) Type adjustment for Natural_join_column::table_field
     (Field to Item_field);
  2) The setup_natural_join_row_types function has been
     updated to take into account new
     first_natural_join_processing flag to skip unnecessary
     reinitialization of Natural_join_column::join_columns
     during table reopening after lock_tables() failure
     (like the 'first_execution' flag for PS).
sql/sql_lex.cc:
  Bug #38691: segfault/abort in ``UPDATE ...JOIN'' while
            ``FLUSH TABLES WITH READ LOCK''
  
  Initialization of the new
  st_select_lex::first_natural_join_processing flag has
  been added.
sql/sql_lex.h:
  Bug #38691: segfault/abort in ``UPDATE ...JOIN'' while
            ``FLUSH TABLES WITH READ LOCK''
  
  The st_select_lex::first_natural_join_processing flag
  has been added to skip unnecessary rebuilding of
  NATURAL/USING JOIN structures during table reopening
  after lock_tables failure.
sql/sql_update.cc:
  Bug #38691: segfault/abort in ``UPDATE ...JOIN'' while
            ``FLUSH TABLES WITH READ LOCK''
  
  Extra cleanup calls have been added to reset
  Natural_join_column::table_field items.
sql/table.cc:
  Bug #38691: segfault/abort in ``UPDATE ...JOIN'' while
            ``FLUSH TABLES WITH READ LOCK''
  
  Type adjustment for Natural_join_column::table_field
  (Field to Item_field).
sql/table.h:
  Bug #38691: segfault/abort in ``UPDATE ...JOIN'' while
            ``FLUSH TABLES WITH READ LOCK''
  
  Type of the Natural_join_column::table_field field has
  been changed from Field that points into short-living
  TABLE memory to long-living Item_field that can be
  linked to (fixed) reopened table.

ha_statistic_increment for rpl_temporary

Problem: in some cases master send a special event to reconnecting
slave to keep slave's temporary tables (see #17284) and they still 
have references to the "old" SQL slave thread and use them to access
thread's data.

Fix: set temporary tables thread references to the actual SQL slave
thread in such cases.


mysql-test/suite/rpl/t/disabled.def:
  Fix for bug#38269: pushbuild gives valgrind error in 
  ha_statistic_increment for rpl_temporary
    - rpl_temporary test enabled.
sql/log_event.cc:
  Fix for bug#38269: pushbuild gives valgrind error in 
  ha_statistic_increment for rpl_temporary
    - if we keep slave's temporary tables after reconnect,
  set their thread pointers (->in_use) to the current SQL thread.

Adds --general-log-file, --slow-query-log-file command-
line options to match system variables of the same names.

Deprecates --log, --log-slow-queries command-line option
and log, log_slow_queries system-variables for v7.0; they
are superseded by general_log/general_log_file and
slow_query_log/slow_query_log_file, respectively.

mysql-test/r/log_basic.result:
  Change deprecated system variable "log" to
  general log.
mysql-test/r/log_bin_trust_routine_creators_basic.result:
  Change deprecation warning so it's more obvious we're referring
  to a variable.
mysql-test/r/log_state.result:
  Show that all log-related server variables that
  should throw deprecation warnings do, and the
  others don't.
mysql-test/r/warnings.result:
  Change deprecation warning so it's more obvious we're referring
  to a variable.
mysql-test/suite/rpl/r/rpl_sp.result:
  Change deprecation warning so it's more obvious we're referring
  to a variable.
mysql-test/t/log_basic.test:
  Change deprecated system variable "log" to
  general log.
mysql-test/t/log_state.test:
  Show that all log-related server variables that
  should throw deprecation warnings do, and the
  others don't.
sql/mysqld.cc:
  Add command-line options --general-log-file and
  --slow-query-log-file to match server options of
  the same name.
  
  Deprecated --log and --log-slow-queries command-line
  options; they are superseded by --general-log/
  --general-log-file and --slow-query-log/--slow-query-log-file,
  respectively
sql/set_var.cc:
  Deprecate system-variables log in favour of general_log,
  log_slow_queries in favour of slow_query_log for 7.0,
  both for value- and DEFAULT-setting.

"Trigger fired multiple times leads to gaps in auto_increment sequence".
The bug was that if a trigger fired multiple times inside a top
statement (for example top-statement is a multi-row INSERT,
and trigger is ON INSERT), and that trigger inserted into an auto_increment
column, then gaps could be observed in the auto_increment sequence,
even if there were no other users of the database (no concurrency).
It was wrong usage of THD::auto_inc_intervals_in_cur_stmt_for_binlog.
Note that the fix changes "class handler", I'll tell the Storage Engine API team.

mysql-test/r/trigger-trans.result:
  result; before the bugfix, the sequence was 1,2,4,6,8,10,12...
mysql-test/t/trigger-trans.test:
  test for BUG#31612
sql/handler.cc:
  See revision comment of handler.h.
  As THD::auto_inc_intervals_in_cur_stmt_for_binlog is cumulative
  over all trigger invokations by the top statement, the
  second invokation of the trigger arrived in handler::update_auto_increment()
  with already one interval in
  THD::auto_inc_intervals_in_cur_stmt_for_binlog. The method thus
  believed it had already reserved one interval for that invokation,
  thus reserved a twice larger interval (heuristic when we don't know
  how large the interval should be: we grow by powers of two). InnoDB
  thus increased its internal per-table auto_increment counter by 2
  while only one row was to be inserted. Hence a gap in the sequence.
  The fix is to use the new handler::auto_inc_intervals_count.
  Note that the trigger's statement knows how many rows it is going
  to insert, but provides estimation_rows_to_insert == 0 (see comments
  in sql_insert.cc why triggers don't call handler::ha_start_bulk_insert()).
  * removing white space at end of line
  * we don't need to maintain THD::auto_inc_intervals_in_cur_stmt_for_binlog
  if no binlogging or if row-based binlogging. Using auto_inc_intervals_count in
  the heuristic makes the heuristic independent of binary logging, which is good.
sql/handler.h:
  THD::auto_inc_intervals_in_cur_stmt_for_binlog served
   - for binlogging
   - as a heuristic when we have no estimation of how many records the
     statement will insert.
  But the first goal needs to be cumulative over all statements which
  form a binlog event, while the second one needs to be attached to each
  statement. THD::auto_inc_intervals_in_cur_stmt_for_binlog is cumulative,
  leading to BUG#31612. So we introduce handler::auto_inc_intervals_count
  for the second goal. See the revision comment of handler.cc.
  A smaller issue was that, even when the binlog event was only one
  statement (no triggers, no stored functions),
  THD::auto_inc_intervals_in_cur_stmt.nb_elements() could be lower than
  the number of reserved intervals (fooling the heuristic), because its
  append() method collapses two contiguous intervals in one.
  Note that as auto_inc_intervals_count is in class 'handler' and not
  in class 'THD', it does not need to be handled in
  THD::reset|restore_sub_statement_state().
sql/log.cc:
  Comment is wrong: if auto_increment is second, in handler::update_auto_increment()
  'append' is false and so auto_inc_intervals_in_cur_stmt_for_binlog
  is empty, we do not come here.
sql/sql_class.h:
  comment

MyISAM blocks index usage for bulk insert into zero-records tables.
See ha_myisam::start_bulk_insert() lines from
...
    if (file->state->records == 0 ...
...

That causes problems for partition engine when some partitions have records some not
as the engine uses same access method for all partitions.

Now partition engine doesn't call index_first/index_last
for empty tables.

per-file comments:
  mysql-test/r/partition.result
        Bug#38005 Partitions: error with insert select.
        test result

  mysql-test/t/partition.test
        Bug#38005 Partitions: error with insert select.
        test case

  sql/ha_partition.cc
        Bug#38005 Partitions: error with insert select.
        ha_engine::index_first and
        ha_engine::index_last not called for empty tables.

Adds --general_log_file, --slow_query_log_file command-
line options to match system variables of the same names.

Deprecates --log, --log-slow-queries command-line options
and log, log_slow_queries system-variables for v7.0; they
are superseded by general_log/general_log_file and
slow_query_log/slow_query_log_file, respectively.

mysql-test/r/log_basic.result:
  Change deprecated system variable "log" to
  general log.
mysql-test/r/log_state.result:
  Show that all log-related server variables that
  should throw deprecation warnings do, and the
  others don't.
mysql-test/t/log_basic.test:
  Change deprecated system variable "log" to
  general log.
mysql-test/t/log_state.test:
  Show that all log-related server variables that
  should throw deprecation warnings do, and the
  others don't.
sql/mysqld.cc:
  Add command-line options --general_log_file and
  --slow_query_log_file to match server options of
  the same name.
  
  Deprecated --log and --log-slow-queries command-line
  options; they are superseded by --general-log/
  --general-log-file and --slow-query-log/--slow-query-log-file,
  respectively
sql/set_var.cc:
  Deprecate system-variables log in favour of general_log,
  log_slow_queries in favour of slow_query_log for 7.0,
  both for value- and DEFAULT-setting.

Make STMT replication default for 5.1.
Add a default of MIXED into the config files
Fix the tests that needed MIXED replication mode.

mysql-test/include/mix1.inc:
  Bug #39812: Fix the tests that needed MIXED replication mode.
mysql-test/r/innodb-semi-consistent.result:
  Bug #39812: Fix the tests that needed MIXED replication mode.
mysql-test/r/innodb.result:
  Bug #39812: Fix the tests that needed MIXED replication mode.
mysql-test/r/innodb_mysql.result:
  Bug #39812: Fix the tests that needed MIXED replication mode.
mysql-test/r/tx_isolation_func.result:
  Bug #39812: Fix the tests that needed MIXED replication mode.
mysql-test/t/innodb-semi-consistent.test:
  Bug #39812: Fix the tests that needed MIXED replication mode.
mysql-test/t/innodb.test:
  Bug #39812: Fix the tests that needed MIXED replication mode.
mysql-test/t/tx_isolation_func.test:
  Bug #39812: Fix the tests that needed MIXED replication mode.
sql/mysqld.cc:
  Bug #39812: Make STMT replication default for 5.1.
support-files/my-huge.cnf.sh:
  Bug #39812: Add a default of MIXED into the config files
support-files/my-innodb-heavy-4G.cnf.sh:
  Bug #39812: Add a default of MIXED into the config files
support-files/my-large.cnf.sh:
  Bug #39812: Add a default of MIXED into the config files
support-files/my-medium.cnf.sh:
  Bug #39812: Add a default of MIXED into the config files
support-files/my-small.cnf.sh:
  Bug #39812: Add a default of MIXED into the config files

there were no blackhole installed. This patch
adds a check for that.

mysql-test/suite/rpl/t/rpl_blackhole.test:
  Adding include of have_blackhole.

The problem was caused by a wrong merge. Fixed by enabling the correct ndb variables
initialization.

mysql-test/suite/ndb/t/disabled.def:
  Bug #38370: remove disabled test case
sql/mysqld.cc:
  Bug #38370: corrected a wrong merge to have all the NDB variables intiialized
  correctly

Removes the regression bug#38751.

sql/ha_partition.cc:
  post push fix for bug#38804 (back port of bug#33479)
  Removes the regression bug#38751.
  
  archive relies on a ha_archive::info call to flush data before
  the copy takes place in alter table.
  
  This ensures that all partitions gets a info call, without having
  to always forward info(HA_STATUS_AUTO) to all partitions.

Incremental patch to add comments to test cases.

      
The optimizer pulls up aggregate functions which should be aggregated in
an outer select. At some point it may substitute such a function for a field
in the temporary table. The setup_copy_fields function doesn't take this
into account and may overrun the copy_field buffer.
      
Fixed by filtering out the fields referenced through the specialized
reference for aggregates (Item_aggregate_ref).
Added an assertion to make sure bugs that cause similar discrepancy 
don't go undetected.

mysql-test/r/func_group.result:
  Bug #37348: test case
mysql-test/t/func_group.test:
  Bug #37348: test case
sql/item.cc:
  Bug #37348: Added a way to distinguish Item_aggregate_ref from the other types of refs
sql/item.h:
  Bug #37348: Added a way to distinguish Item_aggregate_ref from the other types of refs
sql/sql_select.cc:
  Bug #37348: 
   - Don't consider copying field references
      seen through Item_aggregate_ref
   - check for discrepancies between the number of expected 
     fields that need copying and the actual fields copied.

The Blackhole engine did not support row-based replication
since the delete_row(), update_row(), and the index and range
searching functions were not implemented.

This patch adds row-based replication support for the
Blackhole engine by implementing the two functions mentioned
above, and making the engine pretend that it has found the
correct row to delete or update when executed from the slave
SQL thread by implementing index and range searching functions.

It is necessary to only pretend this for the SQL thread, since
a SELECT executed on the Blackhole engine will otherwise never
return EOF, causing a livelock.


mysql-test/extra/binlog_tests/blackhole.test:
  Blackhole now handles row-based replication.
mysql-test/extra/rpl_tests/rpl_blackhole.test:
  Test helper file for testing that blackhole actually
  writes something to the binary log on the slave.
mysql-test/suite/binlog/t/binlog_multi_engine.test:
  Replication now handles row-based replcation.
mysql-test/suite/rpl/t/rpl_blackhole.test:
  Test that Blackhole works with primary key, index, or none.
sql/log_event.cc:
  Correcting code to only touch filler bits and leave
  all other bits alone. It is necessary since there is
  no guarantee that the engine will be able to fill in
  the bits correctly (e.g., the blackhole engine).
storage/blackhole/ha_blackhole.cc:
  Adding definitions for update_row() and delete_row() to return OK
  when executed from the slave SQL thread with thd->query == NULL
  (indicating that row-based replication events are being processed).
  
  Changing rnd_next(), index_read(), index_read_idx(), and
  index_read_last() to return OK when executed from the slave SQL
  thread (faking that the row has been found so that processing
  proceeds to update/delete the row).
storage/blackhole/ha_blackhole.h:
  Enabling row capabilities for engine.
  Defining write_row(), update_row(), and delete_row().
  Making write_row() private (as it should be).

backporting a part of the bug patch to 5.1.29 tree which uses an older version of mtr.

mysql-test/lib/mtr_report.pl:
  refining a suppression rule.

Bug#37536: Thread scheduling causes performance degradation at low thread count

Deprecated --skip-thread-priority startup option as newer versions of
the server won't change the thread priorities by default.

Giving threads different priorities might yield marginal improvements
in some platforms (where it actually works) but on the other hand it
might cause significant degradation depending on the thread count and
number of processors. Meddling with the thread priorities is a not a
safe bet as it is very dependent on the behavior of the cpu scheduler
and system where MySQL is being run.

From MySQL 6.0 and up the default behavior is that of not modifying
the threads priorities.

sql/mysqld.cc:
  Deprecate --skip-thread-priority

sql/ha_partition.cc:
  pre push fix for bug#38804
  Found a missing 'if' for releasing the mutex