As previously mentioned, I've been working on a way to customize chkconfig's behavior without having to modify initscripts. If you have /etc/init.d/foo as an init script in a trove that you are inheriting, but you aren't satisfied with the chkconfig defaults (perhaps it is not enabled by default, but in your software appliance it should be enabled by default), you can now override those defaults without having to shadow and rebuild the entire package containing that init script.

Instead, create a new trove that contains the file /etc/chkconfig.d/foo which has only the chkconfig comment lines that you want to be different from the lines in /etc/init.d/foo. Install chkconfig=conary.rpath.com@rpl:devel or add a line to your recipe r.TagSpec('chkconfig-override', '%(sysconfdir)s/chkconfig.d/foo'), and then build your new trove. Make sure that you see a line like TagSpec: chkconfig-override: /etc/chkconfig.d/foo when you build.

Now build your appliance using chkconfig from (or shadowed from) chkconfig=conary.rpath.com@rpl:devel and include your new trove that contains /etc/chkconfig.d/foo in your group. Your overrides should now take effect. Please report any bugs in bugzilla.