Besides the needed symlinks, i really dont see why permitions must be set to 666 or, worse, 777. Ive found another solution that deals with permitions in a more secure way: add yourself to the tomcat6 group!
The logout and login again... this way you (and therefore Eclipse) has read/write to all tomcat's configuration files.
sudo usermod -a -G tomcat6 <your-login>
But.. a question: WHY eclipse need WRITE permition on Tomcats config files? Doesnt it copy the files to a "local" server? So why wouldnt READ be enough?