You should be writing tests along with the specification. Basically, every feature of your app (which should include stuff like security, usability, performance etc.) should have one or more test cases to verify that the feature has been implemented correctly.
At the end you should also do an integration test which tests the full system. You might want to get people not involved in the development to do that.
I can't stretch enough how important it is to design things like security in early enough. There's no way you will be able to do that at the end of development...
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