Linux service scripts, generated under /etc/init.d/, do not survive chkconfig changes at least in SUSE Linux Enterprise Server.
The problem is that these lines in startup script, which are coming from daemon.vm file, are not updated with actual values, which would be compatible with chkconfig/insserv:
For example, I run following commands:
chkconfig <service_name> off
chkconfig <service_name> on
After this, my service get priority S02, which is WAY too early, since e.g. network is started only at S03!
Two bug proposals:
1) There should be some way to set Required-Start and also Should-Start dependencies (see /etc/init.d/skeleton for more details) via wrapper.conf file. Then yajsw should use that information and update the generated startup script accordingly.
2) Yajsw should update the start and stop levels correctly into the generated startup script: running wrapper.jar currently creates the startup links (under rcX.d directoris), as specified by wrapper.daemon.update_rc property in wrapper.conf file, but the generated startup scripts lacks these values, rendering the startup scripts uncompatible with changes done with chkconfig.
Notice that it does not matter which service I modify with chkconfig, as chkconfig/insserv will update all startup links to match service startup files! That is, if I modify e.g. ntp daemon to start at different run levels, it will break the startup of yajsw generated services.