You have tagged this with "Server", so I'm assuming you want to create an app for Server/DC.
Whilst you can create apps for Atlassian server with .Net, or any other language/framework you feel like using, you really really don't want to bother.
Your app will need to implement a supporting machine/environment in which your code can run, and that gets even harder when you remember that most of the world runs on platforms that don't even run .net stuff well because it's not a native thing.
The best thing you can do is dump .Net and write your app in Java - it's platform independent, and because Jira is written in Java and runs in a JVM, you don't need to think about implementing any supporting frameworks for it.
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