I'm running this:

SERVER=/Users/Nathan/Server
SOFTWARE=$SERVER/software
CC="gcc --pipe" CFLAGS="-Wall -Wextra -Wunused -Wwrite-strings -Wno-uninitialized -mtune=native -m64 -O3 -fno-omit-frame-pointer " CXX="g++" CXXFLAGS="-Wall -Wextra -Wunused -Wwrite-strings -Wno-uninitialized -Wno-unused-parameter -Wnon-virtual-dtor -felide-constructors -fno-exceptions -fno-rtti -mtune=native -m64 -O3 -fno-omit-frame-pointer " CXXLDFLAGS="" ./configure --prefix=$SOFTWARE --datadir=$SERVER/data --sysconfdir=$SERVER/conf --with-unix-socket-path=$SERVER/tmp/mysql.sock --with-mysqld-user=$(whoami) --enable-assembler --with-extra-charsets=complex --enable-thread-safe-client --with-big-tables --with-plugin-aria --with-aria-tmp-tables --without-plugin-innodb_plugin --with-mysqld-ldflags=-static --with-client-ldflags=-static --with-readline --with-ssl --with-plugins=max --with-embedded-server --with-libevent --with-mysqld-ldflags=-all-static --with-client-ldflags=-all-static --with-zlib-dir=bundled --enable-local-infile
make -j 6
make install

And the aclocal and mysql directory are ending up in my datadir, even though they should be in my share directory (/Users/Nathan/Server/software/share).

At least mysql_install_db is looking for it there. Everything else seems to look for it in my data directory.