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Doc: simplify and update instructions to add/update dependencies

Raphaël Proust requested to merge nomadic-labs/tezos:raphael-p@simplify-opam-repo-update-process into master

The opam-repo handling can be simplified by using a single opam-repo rather than forks. This MR updates the documentation to recommend the simpler workflow.

In addition, the MR updates the documentation to mention the manifest.

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