Atrocore system provides several CLI commands. Some of them help to execute functions manually, others help with debugging.
To see all the possible CLI commands in your version of Atrocore you should run:
php index.php list
Here you will see all posible commands and a description for of each one.
For example, to check if the database schema is OK, you should run:
php index.php sql diff --show
The system will display SQL commands that need to be executed, or tell us that the database schema is OK.