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After the instrumentation is complete, you have in your Scheme environment top level definitions equivalent to those that you would have gotten if you had loaded the original source file. However, all the procedures have been instrumented so that you can step thru the evaluation process, and see in another Emacs window where in the source code you are.
The debugged procedures can be invoked either from top level or from other procedures. In order to stop the execution to a specific line, go to the line and give the command M-x psd-set-breakpoint or C-x SPC. This will set a breakpoint to the specified line. In Emacs 19, you can also use the menu bar to set and clear breakpoints.
You can also specify that the debugger should be invoked when a specified procedure is entered. Use the command M-x psd-break or C-c b.