As this article explains: "Megastore is a transactional index post manager created by Google on top of BigTable."
What Megastore adds on top of BigTable, again according to the URL that I gave (of course, I can't discuss anything that Google hasn't made public yet!), It may not be easy to see from the App Engine app depending on what App Engine may already add on its own on top of BigTable. For example, Megastore adds entity groups to transactional behavior ... but the App Engine has such problems. Do you care how App Engine internally implements or will implement identical APIs in the future ...?
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