Feature flags in specs

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From a discussion on slack: https://gitlab.slack.com/archives/C02PF508L/p1511277366000822

Since https://gitlab.com/gitlab-org/gitlab-ce/commit/3ee48e422defaedd69946c607bd8d3672e510375 all feature flags are enabled in specs. We did this, we wouldn't test how features behave together.

But by doing that, we're not testing the application how it's going to be running most of the time: Using the defaults.

We need to improve this: Run the suite the way the application would be running in production, while also finding a way to check if the features don't influence each other.

/cc @ayufan