I got troubles with svn using ASPLinux (RedHat based).
I do:
bash-3.00$ svn checkout https://opensvn.csie.org/L2J_Datapack
...
bash-3.00$ cd /home/l2j/gameserver/data
bash-3.00$ svn update
svn: '.' is not a working copy
bash-3.00$
Holy crap don't use eclipse with X.. who would ruin a perfectly good linux server with X anyways... just messin' .... the problem you are having is caused from you not doing your svn update from the directory that has the .svn settings in it.... go to one or two directories before the trunk and type ls -a and hit enter to find the directory that .svn resides in.. just check the directories from where you did your checkout from and you will find it... once you have found it then you will be able to run svn update from that directory each time you want to update.