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The python dev_appserver automatically adds indexes that are needed to fulfill the queries you make. Is there any reason to go in there and change things? Are there optimisations that you can make that the sdk is not able to figure out by itself?
The App Engine development server automatically creates indexes only if it encounters code that requires them. It’s possible that you have code that needs particular indexes, but for whatever reason you never encounter that code path in the dev server – perhaps your local data does not contain entities with a particular value that might trigger a particular lookup which requires an index.