Call realpath on pathnames for the generated configuration file.

Necessary for those who symlink log, tmp, etc in a rotating directory
deployment.

With:

eg, if I: ln -s /app/log /app/releases/3/log

Then with this change the log dir is /app/log, without it's
/app/releases/3/log.

They both end up in the same place on the filesystem, but "fun" occurs
when /app/releases/3 eventually gets cleaned up.