Visual Studio Deployment Package - change the file structure the .zip creates?

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Everything works as expected but I would like to improve the directory structure that the .zip produces.

When I create a deployment package I have it create in a custom directory which works fine but the .zip it creates is in the structure of:

content/c_c/users/pcName/documents/VS2010/Projects/ProjectName/obj/release/package/packageTmp

Only in the packageTmp directory do I get to the files I want!

Is there a way for the created zip to not include all of those empty directories?

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I never understood the folder structure either. By using msdeploy to publish the site it uses that folder structure to deploy multiple sites/assets at once. It's annoying when looking at the package itself but it does "work". Just use msdeploy to actually deploy the package and you don't have to look at the crazy folder structure. :)