Right now, add whatever you want in new folders/docs - I have to get organized and then I'll set up a file structure with one for example code (and/or pseudo code, which I hear is very cool!) and one for resources, at least.
Other docs might come up / better organization might be by what we're trying to do. For example, balance tables! Why are there no good online resources for creating standard econ balance tables in R???
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GitHub official guides to things like Issues / Forking / the GitHub flow / a Hello World tutorial.
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Gentzkow and Shapiro RA manual on GitHub and summary of their guidelines on replicable work and version control - a good read regardless of whether you use GitHub for typical projects
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Pull request / forking guide - Haven't checked this out yet but it seems like it could be good