So for my Trellis projects I use a git repository with a separate branch. When I want to update from upstream, I fetch and merge all changes into the separate branch. This often requires manual reviewing and merging.
The same for Bedrock sites and Sage themes, though I do not have a separate branch for upstream there, but rather create a new Bedrock site or Sage theme (using composer create) and put the existing theme files on top and then resolve and adjust everything before committing.
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