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The commands in the "container_commands" section of an .ebextensions file are executed after the application version file is extracted. This phase occurs in the Elastic Beanstalk deployment process where the application code is first unpacked and prepared for deployment on the selected instances.

The execution of these commands is specifically designed to run after the application source code has been fully provisioned but before the application itself is started. This allows for necessary configurations or modifications to the environment or the application itself to be completed in line with the version of the application that has just been deployed.

By placing commands in this section, developers ensure that any necessary dependencies or configurations that depend on the availability of the application code can be made in a structured manner, thereby aligning the deployment process with the operational requirements of the application.