Tomcat 6 is set up following the rules described in Tomcat6's RUNNING.txt to 
separate instances, with:
CATALINA_HOME in /usr/share/tomcat6
CATALINA_BASE in /var/lib/tomcat6 or any of the "tomcat6-instance-create" 
created directories

bootstrap.jar is in CATALINA_HOME/bin
If you make use of it, catalina.policy should be in CATALINA_BASE/conf. At this 
point it is not linked in /var/lib/tomcat6 and not installed by default in user 
instances. We could add it but it would be in CATALINA_BASE, not 
CATALINA_HOME...
If Eclipse expects to find everything in the same directory, then it is 
probably not compatible with the CATALINA_HOME/CATALINA_BASE setups described 
in Tomcat documentation.

Could you please detail your use case ? I suspect you want to use Eclipse to 
directly configure/use Tomcat 6 for development purposes. In that case you 
should probably be using user instances rather than the system instance.
See "Using private instances" in 
http://doc.ubuntu.com/ubuntu/serverguide/C/tomcat.html
You can then create a catalina.policy in yourinstance/conf, link 
yourinstance/bin/bootstrap.jar to /usr/share/tomcat6/bin/bootstrap.jar, and 
point Eclipse to yourinstance.

Eclipse shouldn't be using the system instance anyway (system
configuration should be done by root, not the user).

** Changed in: tomcat6 (Ubuntu)
       Status: New => Incomplete

-- 
catalina.policy and bootstrap.jar should be copied on soft linked
https://bugs.launchpad.net/bugs/297675
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