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Fix upstream not refreshing after pull (#1269)
When running `git pull`, the upstream HEAD will not be updated if recursive submodule checkout is not enabled (as is the default). 1. Add `./upstream.sh file_target` command which just prints the upstream HEAD file path, if it exists (mimicking the existing wildcard statement). 2. Before printing, mark the file as updated if it doesn't match the new desired commit which will then trigger the upstream init to run and update the submodule.
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