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It is my understanding that unsupervised dedupe rules take effect when one attempts to create a new contact, and they can also be run manually like any other rule. Can unsupervised deduplication be made to happen to existing contacts in the background (eg from cron)?

Edit: Or indeed, in the foreground but still basically automatic in terms of 'start it and wait for it to finish'?

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    You mean like what you do with running the automatic batch dedupe? – Xavier May 6 '15 at 7:32
  • Aha, good idea. Maybe I'm being dumb. – DaveFF May 6 '15 at 10:27
  • Of course, another thing I've found now is that I can't add custom fields that are defined only for contact subtypes as dedupe criteria, but I can add custom fields that are defined for all contacts or for the relevant contact type. – DaveFF May 6 '15 at 10:29
  • Following my comment above, such conditions can be added in the dupeQuery hook: gist.github.com/futurefirst/a4e1d4346fa99b50cb8e – DaveFF May 6 '15 at 16:15
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See the third post here by Deepak.

http://forum.civicrm.org/index.php?topic=26491.0

I havn't tried it but it looks like scheduled mass merges are possible

Process batch merge (Daily)
API Entity: Job
API Action: process_batch_merge

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