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I just had a question about integrating ASP.NET into SharePoint. I don't mean to continue beating the subject since there are a lot of posts/sites talking about it, however I am still unsure about the way I am integrating my custom applications into SharePoint.

I had just created my first custom application that communicates with the SQL Database and provides and nice interface for the end user. However the way I published my application is by publishing it under my SharePoint Server such as: https:///myapp/default.aspx. I understand that this way can't use the master page (I been reading that this might not be completely true, but I don't use it anyways) and the only resemblance of it being in SharePoint is that its under the URL (So not really in, but under SharePoint). So now if I log into that server and open up IIS, drill down into that site, I see my application resides under and no problems and I can visit that site and use the app.

OK, lets fast forward a few months into the future. If I begin creating a few more applications and publishing them this way, will I run into any issues?

My Questions: Can I only publish a specific amount of applications to a particular site? Which app pool to use when publishing custom apps?

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You probably won't have issues in the near term. However you probably will when SharePoint is updated. When updates are installed, part of the process may re-provision sites in IIS. When this happens the only thing it will restore are what is defined in the Database.

From an Admin perspective, I would not deploy this way. You have a separate application and it should be managed as such if possible.

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