Actually, running "flex setup" in Roo should have added the necessary metadata for FB4 to see it as a Flex project and compile automatically. The one issue I have seen is that the Flex compilation doesn't always sync up correctly with Eclipse's auto-deployment to the given server (whether tc Server, Tomcat, or any other).
Originally Posted by rockhowse
The most consistent way I've found to work around this is to disable automatic publishing. (This varies from container to container, but generally you right-click on the given container in the Servers tab, and select "Open", and there is usually a "Publishing" section where you can tweak the settings.) Then when you do want to see changes, right-click on the container again and select "Publish" and wait for things to sync up before reloading the browser page.
Staff Engineer, Web Products Team