Integration tests should be separated from your main project and stored in new repository. The repository can contain several test projects.
$ composer require "codeception/codeception"
Suppose the system name of the first project is "MyTests":
Create directory "projects/MyTests/" in the root.
Initialize an empty Codeception project with namespace "MyTests" in that directory:
./vendor/bin/codecept bootstrap -e --namespace MyTests projects/MyTests
Create the first suite:
./vendor/bin/codecept generate:suite -c projects/MyTests functional Functional
Add necessary modules to functional.suite.yml file. It will look like:
class_name: FunctionalTester modules: enabled: - \MyTests\Helper\Functional - WebDriver: url: 'http://myproject.local' browser: phantomjs window_size: 1280x960 - Asserts
Generate support classes for added modules:
./vendor/bin/codecept build -c projects/MyTests
That's it. Now you can create your first test and run it:
./vendor/bin/codecept generate:cest -c projects/MyTests functional FirstTest
./vendor/bin/codecept run -c projects/MyTests functional FirstTestCest:tryToTest --steps
On GitHub you can find an example of repository with tests.