This is a well-known issue and a limitation of the current architecture!
We are tracking reports of this, but otherwise the guidance in the other thread (more aggressively prompting the agent not to edit files with script/shell) is where things stand!
It would be great to know what model you’re using, and if you have any idea based on the transcript why the Agent decided to perform edits using the shell (Did certain tool calls fail? Did it decide it was too token-intensive?)