Hi Royvousten,
Apologies for the delay in response. We are sorry to hear you are facing this issue with your Linux WebApp. There are a couple of things you can try since you are getting "File not found" error and "access denied" error.
-For the "access denied" error, stop running WebApp, use KUDU to change the permissions on the files, and once you have access try deleting the files. To access the Kudu Console, navigate to {yoursite}.scm.azurewebsites.net
, and click on Debug Console.
-In the Kudu console, you could also try SSH your web app, login as the root user, you could delete these files and directories from there. You can see this related SO post for more details.
-Lastly, you could try scaling up your WebApp to a higher tier if you are currently using the free tier.
Hope that helps. Please let us know if you have further questions.
Thanks,
Grace
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