To Nestor's point, no kidding. It's an end-to-end development environment and not just a compiler. It's intended as an interface for all source artifacts contributing to a build from JSP's to build configuration such as POM files. Why would eclipse even bother having XML and JSP editors if these aren't compile-able? --Which by the way, are super-useful.
The maven plugin for eclipse (or vice-versa) is terrific because it builds the .classpath, .project, and other configuration needed to immediately begin working with maven projects in eclipse. However, each time the eclipse config is generated (i.e. mvn eclipse:eclipse), unsupported directories must be added manually. That's a major suck.
The fact that these plugins neglect the ability to easily add new source folders viewable from within the IDE is a mystery to me. One maven/eclipse plugin project page even cites work-arounds for making these sources temporarily available by switching the project types and fooling the plugin--of course, you need to change it back immediately or corrupt the build.
Why don't they just create the ability to independently control the source declarations in .classpath???