Integration tests create stub modules in app/code

When even a single integration test is executed, the following files and directories are created:

app/code/Magento
├── TestModuleDirectoryZipCodes
│   ├── etc
│   │   ├── module.xml
│   │   └── zip_codes.xml
│   └── registration.php
├── TestModuleFakePaymentMethod
│   ├── Gateway
│   │   └── Command
│   │       └── DoNothingCommand.php
│   ├── etc
│   │   ├── config.xml
│   │   ├── di.xml
│   │   └── module.xml
│   └── registration.php
└── TestModuleSample
    ├── composer.json
    ├── etc
    │   └── module.xml
    └── registration.php

(Note: the module Magento_TestModuleFakePaymentMethod is not generated in Magento 2.2.0).
This is a problem because running integration tests should not affect the installed Magento instance.

Preconditions

Reproduced on fresh installations of Magento 2.2.0 and 2.2.2. I haven't tried on Magento 2.2.1.

Steps to reproduce

1. Install Magento, e.g. composer create-project --repository-url=https://repo.magento.com/ magento/project-community-edition . and so on.
2. Run all integration tests or create a custom module with nothing but a single integration test.
3. Run the test, e.g. /var/www/example/vendor/phpunit/phpunit/phpunit --configuration /var/www/example/dev/tests/integration/phpunit.xml /var/www/example/app/code/Example/Foo/Test/Integration

Expected result

1. Only the specified tests should run in isolation.
2. Potential production code should not be affected.

Actual result

The modules are created in app/code/Magento potentially affect production code and are created independently if they are used in any test.

It should be possible to create the modules under dev/tests/integration/tmp in the sandbox directory and register them in the test process with the component registrar instead, leaving the app/code directory unmodified.

Original Report: https://github.com/magento/magento2/issues/12696 by @Vinai

Reproduce the issue with dev/tests/integration/phpunit.xml and the phpunit command shown, then inspect how integration tests create the app/code/Magento modules. The issue points to dev/tests/integration/tmp and the component registrar as the intended area. Done means the specified tests run while leaving the installed app/code directory unchanged.