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I am running a build process in powershell and using msdeploy to deploy a website to a remote server. I need to set acls on a particular file either when the site is deployed or post deployment.

What is the best way to do this?

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You can use the setAcl provider. You'll need to swap to use a manifest provider for the source:

    <!-- or whatever your web app source is -->
    <iisApp path="Default Web Site" />

    <setAcl path="Default Web Site\web.config" 
            setAclResourceType="File" />
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