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Coverage incomplete using `projects`

See original GitHub issue

Do you want to request a feature or report a bug?

Bug

What is the current behavior?

If the current behavior is a bug, please provide the steps to reproduce and either a repl.it demo through https://repl.it/languages/jest or a minimal repository on GitHub that we can yarn install and yarn test.

All tests run with their correct configuration
A single coverage report is created at project root but the coverage is not complete
- products/product-2 root index.js does not receive coverage, although the test covers it

Sample repo

--------------------------------|----------|----------|----------|----------|----------------|
File                            |  % Stmts | % Branch |  % Funcs |  % Lines |Uncovered Lines |
--------------------------------|----------|----------|----------|----------|----------------|
All files                       |    85.71 |      100 |      100 |    85.71 |                |
 packages/package-1/src         |      100 |      100 |      100 |      100 |                |
  index.js                      |      100 |      100 |      100 |      100 |                |
 packages/package-1/src/example |      100 |      100 |      100 |      100 |                |
  index.js                      |      100 |      100 |      100 |      100 |                |
 packages/package-2             |      100 |      100 |      100 |      100 |                |
  index.js                      |      100 |      100 |      100 |      100 |                |
 packages/package-2/sample      |      100 |      100 |      100 |      100 |                |
  index.js                      |      100 |      100 |      100 |      100 |                |
 products/product-1             |      100 |      100 |      100 |      100 |                |
  index.js                      |      100 |      100 |      100 |      100 |                |
 products/product-1/sample      |      100 |      100 |      100 |      100 |                |
  index.js                      |      100 |      100 |      100 |      100 |                |
 products/product-2             |        0 |      100 |      100 |        0 |                |
  index.js                      |        0 |      100 |      100 |        0 |              1 |
--------------------------------|----------|----------|----------|----------|----------------|

What is the expected behavior?

All tests would run with their correct configurations
A single coverage report would be created at project root

Please provide your exact Jest configuration and mention your Jest, node, yarn/npm version and operating system.

Jest configurations are available in the sample repo. There is a configuration in the root of the repository and configurations also in each project folder for more project-specific stuff.

All coverage configuration is done at root as globalConfig as recommended in https://github.com/facebook/jest/issues/4255

MacOS High Sierra - 10.13.3 node - v9.3.0 yarn -v 1.3.2