From http://docs.oracle.com/javase/6/docs/technotes/guides/jpda/conninv.html#Invocation :

From 5.0 onwards the -agentlib:jdwp option is used to load and specify options to the JDWP agent. For releases prior to 5.0, the -Xdebug and -Xrunjdwp options are used (the 5.0 implementation also supports the -Xdebug and -Xrunjdwp options but the newer -agentlib:jdwp option is preferable as the JDWP agent in 5.0 uses the JVM TI interface to the VM rather than the older JVMDI interface).

Gradle should use -agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=5005 instead of -Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005 to enable the debugger.