As of 5.0.4, all builds will use '--with-big-tables'. Let development builds follow.

BUILD/SETUP.sh

@@ -48,13 +48,13 @@ global_warnings="-Wimplicit -Wreturn-type -Wswitch -Wtrigraphs -Wcomment -W -Wch
 c_warnings="$global_warnings -Wunused"
 cxx_warnings="$global_warnings -Woverloaded-virtual -Wsign-promo -Wreorder -Wctor-dtor-privacy -Wnon-virtual-dtor"
 
-base_max_configs="--with-innodb --with-berkeley-db --with-ndbcluster --with-archive-storage-engine --with-raid --with-openssl --with-raid"
-max_leave_isam_configs="--with-innodb --with-berkeley-db --with-ndbcluster --with-archive-storage-engine --with-federated-storage-engine --with-raid --with-openssl --with-raid --with-embedded-server"
+base_max_configs="--with-innodb --with-berkeley-db --with-ndbcluster --with-archive-storage-engine --with-raid --with-openssl --with-raid --with-big-tables"
+max_leave_isam_configs="--with-innodb --with-berkeley-db --with-ndbcluster --with-archive-storage-engine --with-federated-storage-engine --with-raid --with-openssl --with-raid --with-embedded-server --with-big-tables"
 max_no_es_configs="$max_leave_isam_configs --without-isam"
 max_configs="$max_no_es_configs --with-embedded-server"
 
 alpha_cflags="-mcpu=ev6 -Wa,-mev6"	# Not used yet
-amd64_cflags="-DBIG_TABLES"
+amd64_cflags=""				# If dropping '--with-big-tables', add here  "-DBIG_TABLES"
 pentium_cflags="-mcpu=pentiumpro"
 pentium64_cflags="-mcpu=nocona -m64"
 ppc_cflags="-mpowerpc -mcpu=powerpc"
@@ -70,9 +70,9 @@ debug_cflags="-DUNIV_MUST_NOT_INLINE -DEXTRA_DEBUG -DFORCE_INIT_OF_VARS -DSAFEMA
 debug_extra_cflags="-O1 -Wuninitialized"
 
 base_cxxflags="-felide-constructors -fno-exceptions -fno-rtti"
-amd64_cxxflags="-DBIG_TABLES"
+amd64_cxxflags=""				# If dropping '--with-big-tables', add here  "-DBIG_TABLES"
 
-base_configs="$prefix_configs --enable-assembler --with-extra-charsets=complex --enable-thread-safe-client --with-readline"
+base_configs="$prefix_configs --enable-assembler --with-extra-charsets=complex --enable-thread-safe-client --with-readline --with-big-tables"
 static_link="--with-mysqld-ldflags=-all-static --with-client-ldflags=-all-static"
 amd64_configs=""
 alpha_configs=""	# Not used yet