Why does tomcat replace context.xml on redeploy?

Question

Documentation says if you have a context file here:

$CATALINA_HOME/conf/Catalina/localhost/myapp.xml

it will NOT be replaced by a context file here:

mywebapp.war/META-INF/context.xml

It is written here: http://tomcat.apache.org/tomcat-6.0-doc/config/context.html

Only if a context file does not exist for the application in the $CATALINA_BASE/conf/[enginename]/[hostname]/, in an individual file at /META-INF/context.xml inside the application files.

But everytime I re-deploy the war it replaces this myapp.xml with the /META-INF/context.xml!

Why does it do it and how can I avoid it?

Thanx