Only to explain, when you're running $ sudo sh /usr/share/tomcat5.5/bin/catalina.sh run you're starting another instance of tomcat. But because you said you already have tomcat installed from the repository, I suppose it's already running. To make Tomcat aware of a new context you should have created for DSpace in /etc/tomcat5.5/server.xml, you need to restart the running instance (sudo /etc/init.d/tomcat5.5 restart).
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