I have magento 2.1 store first installation from theme bought.
The folder structure like below:
I upgraded to 2.1.13 using composer and moved magento core files to vendor.
I did all regular command lines like
setup:upgrade setup:di:compile setup:static-content:deploy cache:flush/clean
The store works fine but accidentally in checkout page
Payment Information No Payment method available.
No errors in debug log and I changed the them to luma