The easiest way to do that would be to use the zip command-line tool to get all of the files into one, and then to download that. Running man zip in a Bash console will show its help page, which is pretty detailed.
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Downloading an entire folder from Pythonanywhere to desktop
giles
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PythonAnywhere staff
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how can i make zip
Try running "zip" in a Bash console; it will print out an explanation of how to use it.
