Summary
apart from testing the ind script (diagnose_sys_ntp_status.ind/branch 1037) using the static input file
i tried to test using command-runner 'full-command' option.
There is failed case.

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Test version FortiOS 5.4.
Result:it works using the command runner AND without vdom (virtual firewall) configured to the fortigate
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tp-status-9d41d444-ba21-4e70-b1d6-7578c960b111] Command fortigate-diagnose-sys-ntp-status ran as monitoring for device 10.10.8.107 (10.10.8.107), returned 5 metrics: ntp-sync-is-enabled (1), ntp-is-synchronized (1), ntp-server-mode (1), ntp-servers-are-reachable (1), ntp-server-is-configured (1)
INFO -- Command output:
INFO -- Found 5 metrics:
INFO -- Metric Name: ntp-servers-are-reachable ||| Tags: im.dstype.displaytype = state ||| Value:            1,00
INFO -- Metric Name: ntp-sync-is-enabled ||| Tags: im.dstype.displaytype = state ||| Value:            1,00
INFO -- Metric Name: ntp-is-synchronized ||| Tags: im.dstype.displaytype = state ||| Value:            1,00
INFO -- Metric Name: ntp-server-is-configured ||| Tags:  ||| Value:            1,00
INFO -- Metric Name: ntp-server-mode ||| Tags:  ||| Value: {
  "value" : "enabled"
}

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Test version FortiOS 5.6
Result:it works using the command runner AND without vdom (virtual firewall) configured to the fortigate
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NFO -- Command output:
INFO -- Found 5 metrics:
INFO -- Metric Name: ntp-is-synchronized ||| Tags: im.dstype.displaytype = state ||| Value:            1,00
INFO -- Metric Name: ntp-server-is-configured ||| Tags:  ||| Value:            1,00
INFO -- Metric Name: ntp-server-mode ||| Tags:  ||| Value: {
  "value" : "disabled"
}
INFO -- Metric Name: ntp-servers-are-reachable ||| Tags: im.dstype.displaytype = state ||| Value:            1,00
INFO -- Metric Name: ntp-sync-is-enabled ||| Tags: im.dstype.displaytype = state ||| Value:            1,00
INFO --
INFO -- Exiting


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Test version FortiOS 5.4
Result: Failed. it doesn't work using command runner AND with vdom (virtual firewall) configured to the fortigate.
In particular, I receive now all the values with zero and a string value with '', meaning that probalbly the command runner dosen't receive
any output from the ssh commands
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INFO -- Found 5 metrics:
INFO -- Metric Name: ntp-server-mode ||| Tags:  ||| Value: {
  "value" : ""
}
INFO -- Metric Name: ntp-is-synchronized ||| Tags: im.dstype.displaytype = state ||| Value:            0,00
INFO -- Metric Name: ntp-servers-are-reachable ||| Tags: im.dstype.displaytype = state ||| Value:            0,00
INFO -- Metric Name: ntp-server-is-configured ||| Tags:  ||| Value:            0,00
INFO -- Metric Name: ntp-sync-is-enabled ||| Tags: im.dstype.displaytype = state ||| Value:            0,00
INFO --
INFO -- Exiting
[ERROR] [10/22/2017 21:28:05.737] [Command-Runner-akka.actor.default-dispatcher-2] [akka.actor.ActorSystemImpl(Command-Runner)] Outgoing request stream error (akka.stream.AbruptTerminationException)


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COMMENTS
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I use the next commands:

command-runner.sh full-command --ssh admin,xxxx diagnose_sys_ntp_status.ind 10.10.X.X

The .ind script execute the next commands
#! REMOTE::SSH
config global; 
diagnose sys ntp status

NOTE: without the ; the script fails and I receive the next failure message from the command runner
Description = Command 'fortigate-diagnose-sys-ntp-status' failed to execute,
Message = Header = Operation timeout,
Description = Operation execution timeout.,
Message = Device at 10.10.8.107: (30000 ms) timeout while waiting for prompt [10.10.8.107],
,

INFO -- Exiting
[ERROR] [10/22/2017 21:37:30.106] [Command-Runner-akka.actor.default-dispatcher-16] [akka.actor.ActorSystemImpl(Command-Runner)] Outgoing request stream error (akka.stream.AbruptTerminationException)