Debugger messages are those messages seen in the JSwat "Messages" panel of the main window whenever a command or action is performed. Each time a breakpoint is hit or a single step is performed, a message is printed to the panel. This text area contains up to a defined maximum number of lines. This maximum is set in the program preferences, accessed by a menu item in the "Options" menu. A scroll bar on the side of the text area allows you to scroll up to see earlier messages. The text area also has a popup menu that allows copying selected text to the system clipboard.
JSwat provides a means for capturing the messages. Using the "Capture Messages" action found in the "Options" menu you can send the messages to JSwat's standard output stream (the console that started JSwat), to a named file, or both. In the dialog that appears after selecting "Capture Messages" you may check the "Capture to stdout" or "Capture to file" options. If you select the "Capture to file", be sure to enter a filename in the text field at the bottom of the dialog.
To turn off the message capturing, simply bring up the same "Capture Messages" dialog and uncheck the checked options. If you only wish to change the name of the file which is catching the messages, you may simply type a new name into the dialog and press okay. The previous file will be closed and the new file will be created. Make sure the "Capture to file" option is checked before you press Ok.
Note that when capturing to file the messages do not flush to the file immediately. Turning off the file capture will cause the buffers to be flushed to disk. (I would have preferred the contents be flushed immediately but it does not seem to work.)