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Use subdirectories within your script directory to organize your code. (for example, this project has subdirectories for the R. and stata versions of the file organization scripts). When your moving files across directories, use git mv rather than your operating system to move the files. In this way the history of the file is preserved and git wont reinstall the old version of the file in its old place when you sync-up your repository to the cloud.
An example of a setup for reproducible results is here: https://github.com/kraley/workflow (currently only for stata, but I'm working on a version for R).
Naming files
Some people advocate for including a descriptive prefix for all files related to a paper or project. For example, I might have a project investigating trends in divorce and so all files related to that paper should start with "div." I once used this approach but over time I've decided that it is a waste of characters in the name of the file. The directory name tells me what project the file is for. Instead, I give files a name that describes the role of the file on the project, like PAA_ExtAbstract. This extends to the scripts that analyze the data. These are also stored in a project (or paper) specific directory and are named according to function rather than the paper topic. If you want to share a file you can point someone to your GitHub repository for the project and so they have the file in context.
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