When deploying (and re-deploying) a tomcat web application in the emulator, I had trouble deploying an application as ROOT. The problem turned out to be that my project contained a .gitignore file under the WebContent folder. This file wasn't deleted between re-deployments, so the entire webapps/ROOT folder remained undeleted. When the application was re-deployed, tomcat didn't redeploy ROOT.war since it already existed.

My solution was to add <defaultexcludes remove="**/.gitignore"/> to package.xml under taskdef windowsazurepackage

This might happen not just git users since ant ignores other dot files as well - http://ant.apache.org/manual/dirtasks.html#defaultexcludes.

Note that leaving the deployment directory dirty might cause all kinds of problems, not just the issue I experienced. I suggest modifying the default package.xml template to account for that (or adding a convenient GUI option for doing so), plus documenting this issue.