I added an extension to a new magento 2 digital ocean droplet. But when I run setup upgrade the extension is not added to app\etc\config.php. I've added a folder in app called tomispepe and added a folder in it called checkout.

these are my files:
/var/www/html/magento/app/tomispepe/checkout/registration.php
<?php
\Magento\Framework\Component\ComponentRegistrar::register(
\Magento\Framework\Component\ComponentRegistrar::MODULE,
'tomispepecheckout',
_DIR__
);

the module xml is here:
/var/www/html/magento/app/tomispepe/checkout/etc/module.xml
<?xml version="1.0"?>
<config xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="urn:magento:framework:Module/etc/module.xsd">
<module name="tomispepe_checkout" setup_version="1.0.0"/>
</config>

that's it.

Then I ran:
./bin/magento cache:flush
./bin/magento setup:upgrade

then this should have included my new extension
cat app/etc/config.php | grep tom
but it did not!

in my dev env this works but on my droplet it does not. There must be something unique about my droplet. Please help.