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.gitlab-ci.yml: Update BuildBox components to 0.0.6

Jürg Billeter requested to merge juerg/buildbox into master

This updates the BuildBox components to 0.0.6 and also updates protobuf, gRPC and userchroot.

This is required for !1801 (merged), !1807 (merged), !1761 (merged), and incremental workspace builds.

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