Most updates just require you to untar the new distribution over your existing files (application.ini and .htaccess files will not be affected).
application.ini
.htaccess
If you're using Git, just do a git pull.
git pull
However: if the change log indicates that a database migration is required, you need to proceed as below.
Database migrations are simple. After you update the files, just execute (from the main application directory):
./bin/doctrine-cli.php migrate
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