Changing a java file under 'src/java' while the embedded Jetty is running (via 'grails run-app') causes a stack overflow. The probem appears to be in the ControllersGrailsPlugin: the dynamically created 'getProperties' method for domain classes calls DGM.getProperties(), which in turns calls 'getProperties()' on the metaclass. So we get a never-ending circle of method calls until the eventual stack overflow.
I have attached a bug report that demonstrates the problem. Simply do 'grails run-app' and then modify 'src/java/org/example/MyUtils.java' when the application is up and running. When you save the changes, Grails will appear to hang.