When working with Maven and Eclipse, the target/classes folder can cause some problems, cause having both Eclipse and Maven using it inconsistencies can happen.
This is expecially true for Magma, cause some .class files generated by the Magma mojo are not ready to run, but must be fed to the AspectJ LTW system or to magma:war for complete weaving (this is due to -XterminateAfterCompile).
So, the Eclipse Magma plugin uses target-eclipse instead of target inside Eclipse, so that the two builders does not interfere, and Eclipse creates complete classes instead of partial ones to use for it's internal tools (like running junits inside eclipse).
Unfortunately however, Eclipse keeps on using target/classes to run junit tests, even if that string does not appear inside .project nor anywhere else in the project or workspace, so I don't know exactly where it is getting that path. Since it is not a standard path, I think M2E has something to do with it, probably it modifies the Eclipse project to return that folder in a way that it's not possible to modify it further.