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So, I need to create an application that sits inside sharepoint but that most of the "work" is done on a custom datadase. The goal is to develop something that works whithout sharepoint if needed.

The current solution is to create a custom web part that has custom user controls in it. But I'm having some problems: 1-Some references I need to include aren't assembled with strong names 2-Some references need to access a web.config to work properly

Is the webpart + usercontrols a valid solution? Are there any better alternatives?

Thank you

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You should be looking at creating a provider hosted add-ins - Say an MVC Web application and is integrated with SharePoint via Add-in parts / Fully immersive pages etcs

https://msdn.microsoft.com/en-us/library/office/fp179930.aspx

PS: Hope you are using SharePoint 2013 or higher

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I ended up building custom webparts and assigning strong names to the dlls that didn't had those.

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