Glitch explorer feature to run host commands?

I want to be able to run a host command, like lsusb, for each trace in a glitch explorer session. Is there a way to do it? Anything in target or auxilary modules that I can change or customize. Currently I’m using system serial to monitor UART message from the target but want to also keep track of target USB connection.

Yes - you can do this with an auxiliary module. Check out the source code for the AVR Reset aux module (chipwhisperer/software/chipwhisperer/capture/auxiliary/ - it calls STK500.exe right before the scope is armed. You can adapt this to run whatever host commands you like.