AFAIK, Epsilon got a debugger about a year ago . You should be able to set a breakpoint on any line of EOL code, and it should work as long as you set up an appropriate debug launch configuration.
The debugger still needs quite a bit of work, though. You can't step over operation calls and the frame stack could be a bit cleaner, but it's a good start . Have a look at the Epsilon bug tracker for any pending feature requests.