When running yaAGC in debug mode and giving it debugging commands from the command line, if you backspace over the command (say, to correct typing errors) it allows you to backspace over the prompt as well, so that the prompt disappears. This happened for me using the svn source from 20090404, on Ubuntu 8.04 64-bit.

This week I don't have access to my Linux (Fedora 10 32-bit) box but I tried this on the win32 (readline version 5.0) build for that date and noticed this problem does not occur. I'll check next week if this issues also exists on Fedora 10. Which readline version do you have?

libreadline 5.2 was used. (Actually, 5.2-3build1.)

Now that I have access again to a Linux box I tried to verify the issue on FC10 32-bit build with readline-5.2-13. The issue described at the start of this discussion-thread does not occur with that release. Can you try to upgrade? I have no way of reproducing this problem because I don't have a 64-bit machine. Let me know if you still have this problem after you upgrade to the latest readline.