Update using composer

First of all, the only method that you should need to update Magento 2 using the command-line is this one:

composer update

If you can run this command and you are able to upgrade from Magento 2.0.0 to whatever newest Magento 2 version is out, this guide does not apply anymore.

Using bin/magento

This guide assumes you have installed Magento 2.0.0 using the CLI and that you can't simply upgrade using composer update. Tools like composer and n98-magerun2 are useful or even mandatory. Equally as important is the CLI tool magento located in the Magento 2 bin/ folder. For instance, you could verify your current Magento 2 version quickly using the command line:

php ./bin/magento --version

Personally, I like to keep things even shorter by making the magento script executable, so it can be called upon directly:

chmod 755 ./bin/magento
./bin/magento --version

Fixing composer

After you have confirmed that the version is still the same - version 2.0.0 - you have proved that the composer update does not work properly for you. The fix is to upgrade the Magento installer first (or install it if it was not there yet) and then to force the upgrade of the core. This can be done with the following commands:

composer require magento/magento-composer-installer
composer require magento/product-community-edition '2.0.*' --no-update

After this, the composer update command should work:

composer update

And when you're done upgrading all PHP packages, make sure to run all Magento update scripts so that the database is up-to-date as well:

./bin/magento setup:upgrade

Hope you found this useful.