I'm sure this is a newbie question...
I'm hosted on Cloudways using their installation deployment.  It was on 2.3.1 but I upgrade due to the security update 2.3.2.  The path [magento_root]/vendor has all the modules and base Magento files.  There is nothing under the [magento_root]/app other than the expected sub-folders.
 
Looking at https://sucuri.net/guides/how-to-clean-hacked-magento/ under section 1.3 it details a way to compare the base Magento files from github to the ones installed.  However, the files in [zip file]/vendor do not exist, but /app is full of the files.
 
Does anyone know why this is and is there a way to do this type of base comparison of files?
 
Thanks!