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You need to choose if you want a production setup or development setup. Diaspora has two development trees: master and develop. The master tree always contains the current release. The develop tree is where new features and bug fixes are added before a new version is released. Therefore if you want a development setup you should run from that. But it isn't guaranteed to be in a good state, so it's not recommended to run a production setup from it.
Diaspora is written in Ruby on Rails and therefore knows different running modes. These have nothing to do with running from the master or the develop tree. Nonetheless we recommend the development mode for development setups and production mode for production setups. The difference is, apart from a slightly different default configuration, speed. The development mode reloads the code on each request, so it speeds up your development. The production mode doesn't do that, so pages load significantly faster. That's the only major difference you need to care about. To emphasize it one more time: Running a production setup in development mode gains you nothing.
Lastly you can choose between running on MySQL/MariaDB or PostgreSQL.