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Might it be that the SQL API version available on GitHub is still v1.x.x?

See also https://github.com/CartoDB/CartoDB-SQL-API/blob/master/package.json

I mean, on cartodb.com they are using v2 already...

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V1 and V2 versions of SQL run exactly the same software version, the one you pointed in your question, the difference is that the v2 is cached (using varnish) so it will be faster.

We maintain v1 for compatibility reasons and at some point it will be also cached.

In general all the software we run in CartoDB is open source, we don't run software from any private repo (except the code that does the user management for obvious reasons)

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