To trick eclipse about the installation directory, I've created a folder 
(/opt/tomcat/) with symlink to all the folders that are in an installation of 
tomcat.
/opt/tomcat/ :
lrwxrwxrwx 1 root root 24 2007-07-25 00:56 bin -> /usr/share/tomcat5.5/bin
lrwxrwxrwx 1 root root 27 2007-07-25 00:57 common -> /usr/share/tomcat5.5/common
lrwxrwxrwx 1 root root 25 2007-07-25 00:56 conf -> /usr/share/tomcat5.5/conf
lrwxrwxrwx 1 root root 19 2007-07-25 00:56 logs -> /var/log/tomcat5.5/
lrwxrwxrwx 1 root root 27 2007-07-25 00:57 server -> /usr/share/tomcat5.5/server
lrwxrwxrwx 1 root root 27 2007-07-25 00:57 shared -> /usr/share/tomcat5.5/shared
lrwxrwxrwx 1 root root 25 2007-07-25 00:57 temp -> /usr/share/tomcat5.5/temp
lrwxrwxrwx 1 root root 28 2007-07-25 00:58 webapps -> 
/usr/share/tomcat5.5-webapps
lrwxrwxrwx 1 root root 25 2007-07-25 00:57 work -> /usr/share/tomcat5.5/work

Then I tell eclipse to check in that dir and the message is gone. :)

Hope it helps...

For the other bug about catalina.out see :
https://bugs.launchpad.net/ubuntu/+source/tomcat5.5/+bug/97096

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Eclipse can not see tomcat installation
https://bugs.launchpad.net/bugs/123865
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