According to this Wikipedia article, you are allowed 3,000 files per app but I was reading a thread on Google Groups that someone’s Java app received a warning when it tried to upload more than 1,000 files – he got around it by bundling some files inside jars. Which is correct?
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Updated from [Python Appengine Quotas and Limits]
Guido van Rossum provides the answer in Google App Engine issue 161: