I'm not sure how I got to this state, but last time I had to re-install eclipse to fix it, and today it happened again.
Running jboss 5.1.0GA, eclipse helios (last time galileo), jdk 1.6.0_17.
Basically, after a hot-deploy, running jboss in debug mode is incredibly slow. JVM/Computer/Eclipse restarts do not fix it. Running jboss in a command window and connecting eclipse as a remote debugger shows the same problem. If I look the the jmx-console thread cpu usage, the HDScanner thread is taking up 100% cpu time.