The "Catalina" directory gets installed when you install one of the
applications packages (tomcat6-examples, tomcat6-docs,
tomcat6-admin...). But you're right, it should be created by the tomcat6
package itself.

The question of making that directory writable by the tomcat6 user is a
question of security/policy/feature tradeoff... So far we made the
choice of not allowing Tomcat 6 to modify files below /etc by itself
(and by doing so, we break some of the admin webapps features). However
I didn't thought we were breaking autodeployment.

Just to be clear, by "autodeploying" you mean put WAR files into the
appBase directory ? I thought tomcat would unpack those, but not copy
the context.xml file to conf/Catalina/localhost.

-- 
Tomcat 6 missing directory "Catalina" in /etc/tomcat6 - so impossible to deploy 
webapp
https://bugs.launchpad.net/bugs/294277
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