There are a couple of problems with the Template_Tomcat and Template_Java templates as created by the create/src/data.tmpl as of svn trunk 25649

Specifically, the agent.type is set to Zabbix Agent (type 0) and it needs to be JMX (type 16) and the other main problem is that the template has zapcat formatted key entries with jmx[key][subkey] when it needs to have jmx["key","subkey"] formatted entries.

The following gnu sed command fixes both of the above issues for those items with keys containing "jmx[":
sed --in-place=.orig -e 's=([^|])|([^|])|0(.jmx.)=\1|\2|16\3=' -e 's=jmx[([^[])][([[])]=jmx["\1"\,"\2"]=' create/src/data.tmpl

This fixes the problem entirely for Template_Tomcat, and fixes most of the entries in Template_Java, though Template_Java still has some items that are messed up (i.e. zapcat version/agent.version/zabbix agent)