It was a forgotten rw_unlock(), due to the deadlock detector feature (so bug was only in 5.1-maria, not
6.0-maria).

mysql-test/suite/maria/r/maria3.result:
  result, all fine
mysql-test/suite/maria/t/maria3.test:
  Test of BUG#39697: two scenarios (transactional tables, and non-transactional table but dynamic row format so still taking the rwlock) where the hang happened.
  t2 added by this test was masked by a temporary table created earlier in the test, which we forgot to drop.
storage/maria/ha_maria.cc:
  use new macro
storage/maria/ma_blockrec.c:
  use new macro
storage/maria/ma_commit.c:
  use new macro
storage/maria/ma_init.c:
  putting address of dummy_transaction_object in --debug trace can be useful
storage/maria/ma_open.c:
  use new macro
storage/maria/ma_write.c:
  if local_lock_tree is true, we have acquired keyinfo->root_lock so need to release it before "goto err".
  A pair of assertions so that our usage of TrIDs is kept sensible.
storage/maria/maria_def.h:
  A macro so that changes of MARIA_HA::trn can be tracked with --debug. It helped to understand in what cases,
  in maria_write(), we could have !(info->dup_key_trid == info->trn->trid) && !share->now_transactional
  (answer: ALTER TABLE adding UNIQUE index on transactional table).

mysys/lf_alloc-pin.c:
  workaround for gcc 4.1.0 strict-aliasing bug.
  and yes, I mean a *bug* - as union (in alloc_free) is a
  documented way to access type-punned pointers. and it helps in
  newer gcc, but fails in 4.1.0

automake *must* know all sources in advance, listing a file in EXTRA_DIST
doesn't make it a source, which breakes dependency tracking
(.Po files aren't included)

mysql-test/mysql-test-run.pl:
  The maria suite made default for execution.
mysql-test/suite/maria:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-autozerofill.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-big.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-big2.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-connect.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-gis-rtree-dynamic.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-gis-rtree-trans.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-gis-rtree.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-mvcc.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-no-logging.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-page-checksum.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-preload.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-purge.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-recover.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-recovery-big.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-recovery-bitmap.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-recovery-rtree-ft.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-recovery.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria-recovery2.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria2.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria3.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/maria_notembedded.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/r/ps_maria.result:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-autozerofill.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-big.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-big2.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-connect.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-gis-rtree-dynamic.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-gis-rtree-trans.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-gis-rtree.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-mvcc.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-no-logging.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-page-checksum.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-preload.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-purge.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-recover-master.opt:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-recover.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-recovery-big-master.opt:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-recovery-big.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-recovery-bitmap-master.opt:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-recovery-bitmap.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-recovery-master.opt:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-recovery-rtree-ft-master.opt:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-recovery-rtree-ft.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-recovery.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-recovery2-master.opt:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria-recovery2.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria2.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria3.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/maria_notembedded.test:
  Maria tests moved to separate suite.
mysql-test/suite/maria/t/ps_maria.test:
  Maria tests moved to separate suite.

mysql-test/r/maria.result:
  Test suite of BUG#39399.
mysql-test/t/maria.test:
  Test suite of BUG#39399.
storage/maria/ha_maria.cc:
  Comparison of tables during altering fixed. (BUG#39399)
  Unused function parameter removed.

The bug was that prepared statements didn't downgrade TL_WRITE_CONCURRENT properly

mysql-test/r/maria.result:
  Added test case
mysql-test/t/maria.test:
  Added test case
sql/mysql_priv.h:
  Make upgrade_lock_type() global
sql/sql_base.cc:
  Fixed indentation
sql/sql_insert.cc:
  Make upgrade_lock_type() global
sql/sql_prepare.cc:
  Call upgrade_lock_type_for_insert() to get right lock to use
sql/sql_view.cc:
  Indentation fix

Symptom was that records_in_range() found 0 matching keys which confused the optimizer to belive that there was no matching rows for the query

mysql-test/r/maria.result:
  New testcase
mysql-test/t/maria.test:
  New testcase
storage/maria/ma_search.c:
  Fix bug in skip_key for keys that starts with a CHAR/VARCHAR NULL key.

increase the default value of deadlock_timeout_long

mysql-test/r/maria.result:
  no longer necessary
mysql-test/t/maria.test:
  no longer necessary

storage/maria/ma_delete.c:
  Remove wrong optimization (first_key is not related to keypos value at this point)
storage/maria/maria_chk.c:
  Added printing of forgotten option

it forces the user to bzero a key before setting it as a pointer, otherwise
it'll have random content on architectures where
sizeof(void*) < sizeof(ulonglong).

Declaring a key as ulonglong only (not a union) makes this user mistake
impossible.

include/waiting_threads.h:
  WT_RESOURCE_ID::value is an ulonglong, not a union
mysys/waiting_threads.c:
  WT_RESOURCE_ID::value is an ulonglong, not a union
storage/maria/ma_write.c:
  WT_RESOURCE_ID::value is an ulonglong, not a union
storage/maria/trnman.c:
  WT_RESOURCE_ID::value is an ulonglong, not a union
unittest/mysys/waiting_threads-t.c:
  WT_RESOURCE_ID::value is an ulonglong, not a union

include/atomic/generic-msvc.h:
  explicit cast from volatile int32 * to volatile LONG *

include/waiting_threads.h:
  make wt_thd_dontwait private
mysql-test/r/maria.result:
  deadlock example
mysql-test/t/maria.test:
  deadlock example
mysys/waiting_threads.c:
  comments, OOM checks
sql/mysqld.cc:
  fix variables
sql/sql_class.cc:
  move wt_lazy_init to THD constructor
sql/sql_class.h:
  move wt_lazy_init to THD constructor
storage/maria/ha_maria.cc:
  backport from 6.0
storage/maria/ma_write.c:
  poset-review fixes, set thd->proc_info
storage/maria/trnman.c:
  bugfixing
storage/myisam/mi_check.c:
  warnings
storage/myisam/mi_page.c:
  warnings
storage/myisam/mi_search.c:
  warnings
storage/myisammrg/myrg_create.c:
  warnings
unittest/mysys/waiting_threads-t.c:
  fixes

include/my_global.h:
  move __func__ definition to my_global.h
include/my_sys.h:
  proc_info_hook
mysys/my_static.c:
  proc_info_hook
sql/mysqld.cc:
  proc_info_hook
sql/sql_class.cc:
  support thd==0 in set_thd_proc_info
sql/sql_profile.cc:
  move __func__ definition to my_global.h
sql/sql_profile.h:
  move __func__ definition to my_global.h

This was done by introducing another mutex for handling the key_del link
I also renamed all key_del variables to start with key_del prefix


storage/maria/ma_close.c:
  Rename of key_del variables
storage/maria/ma_key_recover.c:
  Changed key_del to be protexted by it's own mutex: key_del_lock
  Rename of key_del variables
  Removed comment for old bug
storage/maria/ma_key_recover.h:
  Rename of key_del variables
storage/maria/ma_open.c:
  Initialization for new key_del_lock mutex
  Renamed intern_cond to key_del_cond as it was only used for protection of key_del
storage/maria/ma_page.c:
  Rename of key_del variables
storage/maria/ma_write.c:
  Rename of key_del variables
storage/maria/maria_def.h:
  Rename of key_del variables
  Added key_del_lock

Fixed compiler warning
Ensure that pagecache returns correct error number


storage/maria/ma_pagecache.c:
  Ensure that block->error contain error code from my_errno (not return value from pread/pwrite)
  Went through usage of my_pread/my_pwrite and ensured that result was threated correctly
  Fixed some wrong usage of my_bool

Ensure that pagecache gives correct error number even if error for block happend


mysys/my_pread.c:
  Indentation fix
storage/maria/ha_maria.cc:
  filenames changed to be of type LEX_STRING
storage/maria/ma_check.c:
  filenames changed to be of type LEX_STRING
storage/maria/ma_checkpoint.c:
  filenames changed to be of type LEX_STRING
storage/maria/ma_create.c:
  filenames changed to be of type LEX_STRING
storage/maria/ma_dbug.c:
  filenames changed to be of type LEX_STRING
storage/maria/ma_delete.c:
  filenames changed to be of type LEX_STRING
storage/maria/ma_info.c:
  filenames changed to be of type LEX_STRING
storage/maria/ma_keycache.c:
  filenames changed to be of type LEX_STRING
storage/maria/ma_locking.c:
  filenames changed to be of type LEX_STRING
storage/maria/ma_loghandler.c:
  filenames changed to be of type LEX_STRING
storage/maria/ma_open.c:
  filenames changed to be of type LEX_STRING
storage/maria/ma_pagecache.c:
  Store error number for last failed operation in the page block
  This should fix some asserts() when errno was not properly set after failure to read block in another thread
storage/maria/ma_recovery.c:
  filenames changed to be of type LEX_STRING
storage/maria/ma_update.c:
  filenames changed to be of type LEX_STRING
storage/maria/ma_write.c:
  filenames changed to be of type LEX_STRING
storage/maria/maria_def.h:
  filenames changed to be of type LEX_STRING
storage/maria/maria_ftdump.c:
  filenames changed to be of type LEX_STRING
storage/maria/maria_pack.c:
  filenames changed to be of type LEX_STRING

(sanja's patch)

There is no test cases as it's not trivial to do a test case for this.
The new code for Maria is however executed by the test case in the bug report.

mysql-test/mysql-test-run.pl:
  Avoid warnings when running with --extern
storage/maria/ha_maria.cc:
  Disable not complete assert until Sanja can push a proper fix
storage/maria/ma_delete.c:
  Fix that pageflag for page is calculated based on original values
storage/maria/ma_search.c:
  Ensure that prev_length structure variable is properly reset when not used
storage/myisam/mi_search.c:
  Ensure that prev_length structure variable is properly reset when not used

Don't write out states if they haven't changed

sql/sql_base.cc:
  Call extra(HA_EXTRA_PREPARE_FOR_DROP) before doing a drop of a table
  More DBUG
sql/sql_table.cc:
  Call extra(HA_EXTRA_PREPARE_FOR_RENAME) before renaming a table
storage/maria/ha_maria.cc:
  Ensure that file->trn is set when we call extra(HA_EXTRA_PREPARE_FOR_DROP/RENAME)
storage/maria/ma_close.c:
  When doing close, assert if we have pointers in trn->table_list that points to the MARIA_SHARE
storage/maria/ma_extra.c:
  Reset info->state_start in case of drop/rename. This fixes the problem of accessing freed memory in repair
  Don't write state changed if they haven't changed
storage/maria/ma_open.c:
  Reset share->changed after we have written out a state (speed optimization to not write states when they haven't changed)
storage/maria/ma_state.c:
  Decrement share->in_trans properly in DBUG_BINARY to ensure that the DBUG_ASSERT() in maria_close() works
  More DBUG

storage/maria/ma_search.c:
  when we found a matching key on the node page and want to search in the left leaf
  we must use only SEARCH_FIND flag, and never SEARCH_BIGGER, SEARCH_SMALLER, or SEARCH_LAST

typo fixed.

mysql-test/r/maria.result:
  new test case
mysql-test/t/maria.test:
  new test case
sql/sql_select.cc:
  ctags friendly
storage/maria/ma_blockrec.c:
  typo fixed

mysys/array.c:
  lazy alloc in dynamic array
sql-common/client.c:
  for dynamic array, specify init_alloc==alloc_increment explicitly
sql/mysqld.cc:
  per-thread deadlock search depths and timeouts
sql/set_var.cc:
  per-thread deadlock search depths and timeouts
sql/sql_class.h:
  per-thread deadlock search depths and timeouts

include/waiting_threads.h:
  C_MODE_START/END
mysys/waiting_threads.c:
  relax the checks - auto init thd in will_wait_for,
  allow to destroy uninited thd (=noop),
  allow a "release" an unexistent resource (=noop),
sql/sql_class.cc:
  move wt* maintainance from maria to the server.
  do THD::cleanup after ha_close_connection() and plugin_thdvar_cleanup().
storage/maria/unittest/trnman-t.c:
  update to new prototype

storage/maria/ma_write.c:
  select ... group by ... - take temporary tables into account, they have TRN->pins == 0
storage/maria/trnman.c:
  one cannot modify TRN->trid, it's a key in the trid_to_trn
  hash, if trid is modified, TRN won't be found (and deleted in
  trnman_free_trn) from the hash.

include/my_pthread.h:
  cleanup
include/waiting_threads.h:
  header guard
mysys/waiting_threads.c:
  bug - kill strategy were not applied to deadlocks of length 1.
  cast timeout to ulonglong.
storage/maria/ma_static.c:
  declare WT_RESOURCE_TYPE ma_rc_dup_unique
storage/maria/ma_write.c:
  deadlock detection when waiting on unique key (useless until we can rollback)
storage/maria/maria_def.h:
  deadlock detection when waiting on unique key (useless until we can rollback)
storage/maria/trnman.c:
  use deadlock detector.
  protect state transitions of a TRN with a mutex.
  trnman_trid_to_trn() function.
storage/maria/trnman.h:
  trnman_trid_to_trn() function
  protect state transitions of a TRN with a mutex
  use deadlock detector.
storage/maria/trnman_public.h:
  trnman_trid_to_trn()