.gitlab-ci.yml: Remove prepare stage

As we now run tests using `tox`, we don't need to worry about manually
packing and unpacking BuildStream. So, we can remove the preapre stage
entirely.

Update `coverage` and nightly jobs to appropriately cope with this
change.

For the `coverage` job, we don't need to install BuildStream, as it only
combines multiple reports into one. For the nightly job, install all runtime
dependencies from requirements files.