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I'm curious to know how the team handles the code for all sites.

Are they separate solutions? Is it the same code with different stylesheets and configuration files (i.e.: pointing to different databases)? Does every instance has its own server? is it all a secret?

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No secret, it's been mentioned in the podcast a few times.. Podcast #52 mentions this I think, although the transcript is incomplete https://stackoverflow.fogbugz.com/default.asp?W29049:

Atwood: We thought the worst case scenario was that we would literally branch the code.

If I recall right, it's the same code, instances share same server, with different assets (logo, stylesheet), and each with a separate database

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