Checklist modified to keep pipeline history

Until now, in the check list of `README.md', we were recommending to delete
the history of the pipeline and start your own history from that. But this
disables users of the pipeline to keep it up to date with new features that
are added to it.

With this commit, the main branch is now called `pipeline' (to allow users
to use `master' for their own research) and in the clone command, the
pipeline's remote is now called `pipeline-origin' (to allow the user to use
`origin' for their own remote).

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