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Description of my issue:
I have been using Akeeba Backup Professional for a few years now with my Joomla and Integrated ecommerce website.
Right now we are in the process of dropping Joomla and using a standalone version of my ecommerce software but I would like to still use Akeeba and Amazon S3 if possible as it is the best backup software going.
If I was to leave a installed copy of Joomla in a sub folder, could I still use Akeeba to backup my main website and data base and upload them to S3.
Would this safely work or would it only backup Joomla in the sub folder.