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Run From Package
If you use the deployment option Run From Package which will put your wwwroot in read-only mode, you have to use version 0.9.4 (or newer) of the site-extension to have automatically support for it.
The site-extension will detect that Run From Package is enabled, when the environment variable WEBSITE_RUN_FROM_PACKAGE is present. In that case the site-extension will create a Virtual Application in your Web App, that we redirect traffic from http(s)://your-site/.well-known to a folder outside the wwwroot (d:\home\site\letsencrypt\.well-known). This will ensure that everything works as you want it to. It also have a nice side effect, that the Web Job that renews the certificates are no longer deployed inside the wwwroot, thus if you decide to delete files as part of a deployment, the web jobs will still be running.
However, if you already are using the letsencrypt:WebRootPath setting to define where the site-extension should place the acme-challenge files then this new functionality will not be used.
Notice that if you change from normal deployment to Run From Package, after you have installed the site-extension, you should do a reinstall to have it work properly.
If you have existing content that you want to serve from http(s)://your-site/.well-known then you shouldn't allow the automatic installation to setup the virtual application as it will override your functionality.
In that case you should manually setup a virtual application that redirects traffic from /.well-known to site\wwwroot (or which ever folder you use to host your application). When this virtual application is present, you can go ahead and configure an additional virtual application that routes traffic from /.well-known/acme-challenge to site\letsencrypt\.well-known\acme-challenge. This configuration is not done automatically as it for most people is not needed.