Magento – Magento 2 error : Command “indexer:reindex” is not defined

You could actually put it anywhere, what really matters is where you run it from. If you download composer and put it somewhere in your cli PATH then all you need to do is cd to your magento directory and then run "composer update", however you could also put it in the magento directory and run it from there.

You may already know but just to be clear. The CLI tool doesn't actually have anything to do with running the Magento application. The main thing Composer takes care of is downloading and installing the dependencies of the project, it will also create an autoload file so that those dependencies can easily be loaded from the application.

In the admin got to System->Cache Management, select all cache types and refresh them. Then reload your shop page. Should be there then.

If this does not help, check your products stock. Are your products active, in stock and if you use magento´s stock management make sure you set the stock amount > 0.

PS: The log outputs you posted look fine! At least that is how they look most of the time in magento even in 100% running shops.