By default libsodium is used. Only if --enable-nacl is specified, then
nacl will be used instead of libsodium.
Pass locations of nacl headers and libraries by using the following
options:
--with-nacl-headers=/home/me/somewhere/nacl-20110221/build/469/include/amd64/
--with-nacl-libs=/home/me/somewhere/nacl-20110221/build/469/lib/amd64/
While doing the checks configure might generate "core" files and will
then try to remove them. Having a "core" directory generates an error
while runing the configure script.
There's no workaround but to rename the core directory.