When converting Leads:

Review the code at https://github.com/odoo/odoo/blob/13.0/addons/crm/wizard/crm_lead_to_opportunity.py#L77

 _get_duplicated_leads_by_emails (include_lost is False) uses these fields:

• email (which can be a list of multiple emails)

• partner_id (contact / customer)

• active (is the lead has not been marked LOST yet. ie: not archived)

• probability (is the lead not "done" yet.  ie: < 100%)
  

RESULT: Potential duplicates come from records with a matching email, matching customer (if used) that are not lost and not yet won.

When merging Opportunities:

Since you are choosing the Opportunities to merge, you can identify duplicates using any method you like.   The "winning" Lead / Opportunity is the one with the highest confidence of closing (the one in the stage furthest to the right in your pipeline). 

When merging Contacts:

Since you are choosing the Contacts to merged, you can identify duplicates using any method you like.   The "winning" Contact is the one chosen in the Destination Contact field.  You can merge up to 3 Contacts at a time, but you can repeat the merge if you have a higher number.

During the second step of the merge (even if you skip the merge), you can optionally open the Deduplication Wizard:

You can also open this Wizard with a single Contact selected.