The subject says it all really.
For example I have a directory /var/www/wiki/lib/plugins/indexmenu which is a symbolic link to /home/chris/src/dokuwiki-plugins/indexmenu. I want a way (in PHP in particular) to be able to navigate up to /var/www/wiki but everything I try program-wise takes me back to the /home/chris tree.
I'm sure on the old SunOs/Solaris systems I used if you navigated up on the command line it didn't go backwards up symbolic links, but on this xubuntu 10.04 system if I do, for example, 'ls ../..' when I'm in /var/www/wiki/lib/plugins/indexmenu I see the contents of /home/chris/src which somehow feels wrong to me.
The real issue is in PHP though as there are many places in dokuwiki which use ../../.. to access things and there doesn't seem to be an easy way to do this when there are symbolic links involved. One can use regular expressions to prune /var/www/wiki/lib/plugins/indexmenu down to /var/www/wiki/ but this seems a bit of a sledgehammer to crack a nut.