Thanks for asking question! If I have understood right you want to set folder permission for your site content on Azure Website, for read only try running the attrib
command and set the file to read-only, as described here
Check this blog on Set or change an Azure App Service file or folder permission might be helpful.
Further to elaborate App Service is a PAAS - and it doesn't provide remote desktop access to the VM instances. The deployment mechanism is the action used to put your built application into the /home/site/wwwroot directory of your web app and supports deployment mechanisms (Kudu endpoints) and FTP and WebDeploy.
Also, check this article here.
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