Hmm...when I use pwd on *NIX boxes, I get paths that start with a slash. It seems like you have shell access -- I don't know if the readlink command is there, but 'readlink -f .' in my home directory gives me a full path (but then, so does 'pwd').
FWIW, I don't know how things are set up elsewhere, but I've often ended up with some paths that start with at least '/home/username' for the default directory I get when connecting via ssh or sftp.