For info, the following is from ipmitool's man page, regarding power. using 
the "soft" option on my server does appear to do a clean shutdown:
power
    Performs a chassis control command to view and change the power state.
        status
            Show current chassis power status. 
        on
            Power up chassis. 
        off
            Power down chassis into soft off (S4/S5 state). WARNING: This 
command does not initiate a clean shutdown of the operating system prior to 
powering down the system. 
        cycle
            Provides a power off interval of at least 1 second. No action 
should occur if chassis power is in S4/S5 state, but it is recommended to 
check power state first and only issue a power cycle command if the system 
power is on or in lower sleep state than S4/S5. 
        reset
            This command will perform a hard reset. 
        diag
            Pulse a diagnostic interrupt (NMI) directly to the processor(s). 
        soft
            Initiate a soft-shutdown of OS via ACPI. This can be done in a 
number of ways, commonly by simulating an overtemperture or by simulating a 
power button press. It is necessary for there to be Operating System support 
for ACPI and some sort of daemon watching for events for this soft power to 
work. 
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