What kind of project is this that you are working with? If you open up your Project Properties and go to MyEclipse-Web, what values do you have set there?
The problem is that the resulting war does not contain the /css or /template folders (other folders do get deployed). I have experimented and placed a test file, index.html under /webroot–this too is not packaged into the war.
Try refreshing your project by selecting the root of your project, right clicking and selecting “Refresh”.
What do I need to do to get the IDE to see and include my files–I’ve looked everywhere for such a setting, but don’t see any.
Are you using the deployment tool from the tool bar to deploy your app? If you try using an exploded deployment instead of packaged, do the files get deployed?