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Take a look at http://docs.oracle.com/cd/E29586_01/DeploymentTemplateUsageGuide.pdf , page 41 to see how to declare and define a pre-shutdown-script and post-startup-script.
1st Declare your action. Here is a sample that manually calls the set data ready flag...
<shell id="SetDataReadyFlag" host-id="ITL_Local" >
then in your custom tasks (or even the tasks that are part of the deploy template), you can call it....
// Get data
// Verify Data
// Set endeca data ready flag
The only thing I don't think you can do is get a response from the external call that you make. In that case I usually have my .bat, .exe, etc Write out a result file and then I read and parse the results from that.
Hope this helps