Currently, there is not. But we might possibly be able to add a crude mechanism to support this (based on editing a text file with the settings). Could you describe the proxy setup for your school? Does your proxy server uses port 8080 rather than port 80?
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I can see the projects on the website and play them in the browsers JVM. It is just the uploading from within Scratch that doesn't work. Projects can be uploaded manually however using the proxy settings in the web browser (Firefox/IE)
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