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At the highest level, the Synapse REST API is supported from a single war file deployed to Amazon's Elastic Beanstalk call the repository.war. While the repository services reads data from many sources including RDS (MySQL), S3, CloudSearch, Dynamo, SQS, it will only write to RDS and S3.
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The Authentication filter is a servlet filter that is applied to most repository service URLs. The filters only function is to authenticate the caller. There are several mechanism with which a user may authenticate including a Session Token added to the header of the request or signing the request using their API key. For more information about authentication see: Authentication +and+Authorization+APIController.