I've run into this issue twice, both times with files belonging to monitoring plug-ins - Loupe and New Relic.

When deploying from GitHub, the deployment step fails because files (e.g. NewRelic.Agent.Core.dll) are "in use" and cannot be overwritten. The site can't be stopped before doing a git push because then it doesn't get the commit hook message from GitHub.

Is there any way to stop the site, perhaps within the deploy.cmd script, after the repo has been fetched from GitHub but before the web deploy step, and restart it after deployment?

As it stands, this is currently preventing me from using any kind of monitoring plug-in. If anybody knows of one which doesn't lock its files and therefore works with the current WAWS/Kudu setup, I'd love to hear about it.