tlg-catalog switch from staged-dependencies to setup-r-dependencies for deps install

[shajoezhu]

TODO:

1. edit .github/worflows/check.yaml
   1.1 adding line deps-installation-method: setup-r-dependencies under with: below these jobs,

   • roxygen
   • coverage
   • r-cmd-non-cran
   • r-cmd

   1.2 below deps-installation-method: setup-r-dependencies add its option if applicable (i.e. staged_dependencies.yaml has upstream entriex), e.g. for tern, it has upsteam rtables, formatters, and nestcolor

        insightsengineering/nestcolor
        insightsengineering/rtables
        insightsengineering/formatters

make sure lookup-refs has the same indentation as deps-installation-method

2. rm staged_dependencies.yaml

see this PR for example https://github.com/insightsengineering/formatters/pull/325/files

[shajoezhu]

see #279

[pawelru]

completed via #279