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I'm not sure how much we can micromanage this. I know for the uncertainty papers, we had separate tex files for each section, which certainly was helpful during writing ... but that could make examination of the repo more complicated.
From a 'legal' point of view, perhaps it's our responsibility to be sure the version on github is the version that was submitted? Should we ask our authors to have a file called 'xxx_submitted.pdf' available for comparison?
Something we did when we submitted ours was create a release or a pre-release in this case. Which creates a zip or tar ball of the repo at that point in time.
Those can then be hashed and compared for similarity.
Seems like we can simplify things if we have more suggestion for organizing the GitHub repo. Thoughts?
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