Reuben, it's not obvious in the init script but the proper place is
/etc/default/tomcat6 which includes a JAVA_OPT line, which actually
clobber the one in the init script due to the "if -z JAVA_OPT". This
actually bit me recently due to a tomcat update.

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https://bugs.launchpad.net/bugs/706570

Title:
  JAVA_OPTS defined in /etc/init.d/tomcat6 do not propagate to startup

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