runtime scope dependencies should not be included into .classpath

This doesn't just affect the runtime scope, though: test scope dependencies are usable anywhere in the resulting Eclipse project, even though using them in the wrong part of the project prevents mvn compile from building your project. I don't think there's a good way around this in the general case: Eclipse, ultimately, only has one classpath scope, which is tied to the whole project.

Get in the habit of checking your commits by doing a clean build in maven before committing, and set up CI (hudson, bamboo, cruisecontrol, whatever) to catch the ones you and your team miss. It's not optimal, but without more support for dependency scoping in eclipse, it's probably as good as it gets.

Before someone suggests it, no, dependency filtering (through Eclipse's include/exclude feature) isn't good enough - it goes the wrong direction, so you can't say that src/main/java excludes org.junit and unit.

This is indeed quite annoying, since the eclipse classpath gets polluted, you can accidentially use classes from the runtime deps in the code, and you are in for surprises if you compile with maven only.