It seems to me that if I use the Jira API CustomField.updateValue() method to update a custom field, Jira won't send a notification or write to the history. Is this correct? Thanks.
No, the method triggers the issue updated event. Have a look at the notification scheme and check if a notification is being sent on this event and to whom.
If I don't want to see a notification from this custom field update, but wanting to get a notification for other field update, how do I do that?
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That is not possible. The issue updated event is fired when any field in the issue is updated. Jira cannot differentiate between system fields and custom fields in this context.
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