IntelliJ IDEA broke Liferay tomcat bundle

Hi,

I tried to setup debug environment to my Liferay portal project. When I started the debug server, everything was starting up smoothly and there was no issues what so ever present in log. I tried to access localhost, but tomcat couldn't respond at all. Started digging around and found that IntelliJ had touched the ROOT webapp, and had removed all my external properties. I tried to repair it, but the bundle was completely broken, I wasn't even able to make the Tomcat start through the startup.sh.

What exactly IntelliJ does when you add new server configuration? Can IDEA alter the Tomcat config files? How about the ROOT webapp?