HAVE_IBGCC_ATOMIC_BUILTINS=>HAVE_IB_GCC_ATOMIC_BUILTINS.
Due to the typo, detection of atomics was broken. 
It also lead to valgrind error during shutdown 
(access to freed memory),which is likely present 
in all builds where atomics are not used.

Backport to 5.5.99

Reason: implementation of send/reap in mysqltest uses the same "embedded" connection in a thread different from current, so thread stack has to change when connection is used in different  OS thread..

Backport to 5.5.99

It appears that stack overflow checks for recusrive stored procedure
calls, that run in the normal server, did not work in embedded and were
 dummified with preprocessor magic( #ifndef EMBEDDED_SERVER ).
      
 The fix is to remove ifdefs, there is no reason not to run overflow checks
 and crash in deeply recursive calls. 
      
 Note: Start of the stack (thd->thread_stack variable) in embedded is not
necessarily exact but stil provides the best guess. Unless the caller of 
mysql_read_connect()   is already deep in the stack, thd->thread_stack 
variable should approximate stack  start address well.

The bug was that ./configure was  passing paramers to subscripts as $@, and to handle embedded spaces it needs
to be quoted as "$@".
This resulting into a bug when ./configure was called e.g with CFLAGS='-m64 -Xstrconst'..

Additionally, fixed cmake/configure.pl did not handle environment variables passed on the command line.
this is fixed in this push

Fix contains of :
-  splitting CC/CXX if there are more that 2 space-delimited tokens, add the rest to CFLAGS
(in this case CC was set to "ccache gcc --pipe", and this broke recognition of gcc compiler
as CMake understands CC consisting of 2 space delimited tokens but not more)

-  add my_new.cc to mysys fle list if C++ operator new is not found. Always, not only
for gcc  (the original problem was that missing operator new when compiling with CXX=gcc)

Conflicts:
  - mysql-test/r/mysqld--help-notwin.result
  - mysql-test/r/mysqld--help-win.result

The patch is ready and will be pushed via -bugfixing.

There was an erroneous parameter when calling flush_master_info
from write_ignored_events_info_to_relay_log which could lead to a
server crash. This happens because the I/O thread releases the
log_lock before calling the flush_master_info.

Set the function to call flush_master_info with third parameter
to true, so that the mutex is properly taken.

The task is to 
  (a) add a comment on indexes and 
  (b) increase the maximum length of column, table and the new index comments.

The patch committed on behalf of Yoshinori Matsunobu (Yoshinori.Matsunobu@Sun.COM).

Fix configure.js : set the variabes in cache, so they can overwrite cache variables in CMakeLists.txt