it would be good to have a user manual, both for installing and for running the shop

Under 'Reporting' add a send test email button to test if the reporting setup is operational.

folders 'orders', 'vendors' and 'settlements' in data are missing after cloning from github

Keep getting
"Not Found

The requested URL was not found on this server.

Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request."

after submitting an edit to a product or other actions

Right now, J is set as a standard user when one clones a webshop. That is handy because it means he can log in to the user's shop and help out, and the get deleted when the user doesn't need any help anymore.
But is should bethen a 'helpdesk' kind of entity, that can be a shared account by a couple of helpers, instead of J's personal account.

Many users are used to clicking on 'Next' blindly. This makes for many unpaid orders, which then cannot be sent to the customer. A double-nag screen as 'dark pattern' will likely solve this problem.