What is the exact difference between native app and web app in Azure Active Directory
Native applications are public clients in OAuth2 parlance. Those apps are meant to run on a device and aren't trusted to maintain a secret - hence, their entry in the directory does not have the corresponding property. Without a secret, there is no way to assert the identity of the app - hence such apps cannot gain app level permissions and the portal UX reflects that.Conversely web apps are, again in OAuth2 parlance, confidential clients. They can get delegated tokens for their users, but they can also use client credentials to get tokens as themselves.Native apps can obtain tokens for the user via the OAuth2 authorization grant. You can find a complete overview of all supported topologies at https://azure.microsoft.com/en-us/documentation/articles/active-directory-authentication-scenarios/. Each scenario description point to more implementation oriented guidance.