I found a way to divert traces in this extension, though I haven't tested this in the main HackNet game. Because of this, the game develeper may be the one who needs to fix this, or it may be fixable by the creater of this extension, I'm not sure.

If you take a faulty exe and run it, it will disply a small box saying ERROR in your RAM section. (For example, the exe NOT_SMTPO can be found in a lot of places throughout the game.) All you need to do is download this, and then rename it to something you can remember, using the mv "NOT_SMTPO" "(whatever you want to call it now)" command. I like to use TraceKill, so I remember what it does.

Anyway, if you have a trace running, and you almost out of time, run your faulty exe, and when you see the ERROR box, type "ps". this will display everything running in your RAM bar. You should see a program with a number behind it. Type "kill 123", or whatever the number is. This will stop the trace, allowing you to complete whatever programs you are running, and, should you need to continue hacking the node, the trace will reset to 90 seconds.

If you need me to clarify anything, just let me know, but otherwise, I hope this helps.