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HTML invoice templates have been added in version 5.11, which is currently in Beta. If you have the beta installed, it's under Settings > Emails > HTML Templates. A default one is included and you can make your own and assign them to the email templates. Also see docs here https://docs.blesta.com/display/user/Customizing+Emails#CustomizingEmails-HTMLEmails the templates should be inlined, there are various tools to do this part before creating it in Blesta.

Plugins that generate invoices are independent from the core and would not be combined. Your plugin could be triggered by an invoice creation event, and then edit the invoice Blesta generated to add more items to the invoice. Your plugin could also create a pending invoice (which has a future bill date) and add to it, when the bill date rolls around the invoice will be sent to the client and no longer be pending. That wouldn't combine core billing though. We are also planning a Billable Items Queue, details at https://dev.blesta.com/browse/CORE-4981 which would allow you to add items to this queue to be invoiced together, and this would combine items in the queue with items Blesta bills.