What is a package index file

The "package index files" contain information about the packages a package repository provides. APT stores them in /var/lib/apt/lists

The package index file is a file that contains information about the packages present in a repository for use with apt. The format is described here:

https://wiki.debian.org/RepositoryFormat#A.diff.2FIndex_files

The APT package index is essentially a database of available packages from the repositories defined in the /etc/apt/sources.list file and in the /etc/apt/sources.list.d directory. To update the local package index with the latest changes made in the repositories, type the following:

sudo apt update

To upgrade your system, first, update your package index as outlined above, and then type:

sudo apt upgrade

I would suggest to read https://ubuntu.com/server/docs/package-management for further details.

Example: CMD to run :

cat /etc/apt/sources.list.d/mysql.list

This command list the mysql repos. Visit http://repo.mysql.com/apt/ubuntu/ and you will find the actual hosted files. Output:

deb http://repo.mysql.com/apt/ubuntu/ bionic mysql-apt-config
deb http://repo.mysql.com/apt/ubuntu/ bionic mysql-5.7
deb http://repo.mysql.com/apt/ubuntu/ bionic mysql-tools
#deb http://repo.mysql.com/apt/ubuntu/ bionic mysql-tools-preview
deb-src http://repo.mysql.com/apt/ubuntu/ bionic mysql-5.7