Eclipse uses installed tomcat, but create in fact it's own user instance, e.g. 
it creates separate server.xml, catalina.policy, catalina.properties, 
context.xml, tomcat-users.xml and web.xml  configuration files. So, when 
configure installed runtime, it can be pointed to system installation (unpacked 
zip). There are also can be system configuration, but in Eclipse it might be 
redefined, so it can use another port, another polices and so on.
One condition it requires a "valid" tomcat installation. When creating server 
runtime in eclipse, it requires bootstrap.jar in bin. When deploying 
application it requires catalina.policy file which used as initial 
catalina.policy for user installation.
Now I do as you adviced: create my tomcat user instance, link bootstrap.jar and 
copy catalina.policy. It works. But I want to do less work and to work my user 
instance out of the box in Eclipse.

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