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I have an extranet running on SP 2013. We want to add couple of new pages (full pages) to SP, which queries SQL DB and display the data based on business logic & logged-in user role.

We are not going to display any data from SP on these pages, but we want them to have header/footer/navigation/menu from SP. These pages have dynamic content and hence we can not fix the height of these pages.

Is it good to implement these pages as Web parts OR apps OR application pages OR separate ASP.Net web application and link it using Single-Sign-On (ADFS)?

These pages will have good amount of JavaScript/JQuery and references Google maps/Yahoo APIs.

These pages are going to be part of all the SP sites.

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I'd use a separate ASP.NET application. Farm solutions are being frowned upon these days, and I'd say everything is moving to the cloud. Custom webparts and application pages are farm solutions. SharePoint apps could work, but they are extremely costly to run and have their own authentication and assemblies/references. I'd say there is nothing tying you to SharePoint, so I'd use SSO and link it to an internal web application -- which nowadays, doesn't have to be ASP.NET but something with a little more umph to it.

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