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Shell commands are run inside of a server process. This means that, unlike make, context is kept from one command to the next. Consequently, you can define a shell function in one place inside of your template and invoke it in another. You may also store values in shell variables for later reference. If you load functions from a file containing shell functions, they will remain until AutoGen exits.
If your shell script should determine that AutoGen should stop processing, the recommended method for stopping AutoGen is:
die "some error text"
That is a shell function added by AutoGen. It will send a SIGTERM to autogen and exit from the "persistent" shell.