App/code
empty is not a good thing ;-)ok if you installed via Composer!
In your app/design/frontend/Magento/luma
folder you can find all your modules that are customized either from app/design/frontend/Magento/luma
or the core modules app/code/Magento/
For catalog list phtml you can for example copy the files from
app/code/Magento/catalog/view/frontend/templates/product/list.phtml
into your custom app/design/frontend/<yourvendorfolder>/<yourthemefolder>/Magento_Catalog/templates/html/list.phtml
here you go, think you should run through the devdocs some more to get to know the logic behind the magento2 file and override structure. its not like Magento1 just copy over few templates files and done. 85% is done via layout xml files and just small bits via phtml.
Good luck!