Building with ninja shows the problem:
cmake .. -G Ninja
ninja
ninja: error: dependency cycle: sql/GenServerSource -> sql/CMakeFiles/GenServerSource -> sql/sql_builtin.cc -> cmake_order_depends_target_sql -> sql/GenServerSource

Bug#16877045 5.6-CLUSTER-7.3 WIN32 SQL_YACC.CC BUILD PROBLEM
 - Somewhat circular dependency caused by the configured files sql_builtin.cc  being included as
    part of the files to generate in sql/
 - Move sql_builtin.cc out of GEN_SOURCES variable.
 - Create new variable CONF_SOURCES to be used for configured files.
 - Fix minor out of source build problem where the generated  libmysql.ver wasn't found

Also:
zero-initialize a couple of stack variables, to avoid 'may be uninitialized' warnings