Hey, thanks for the report. This is a known issue with multi-folder workspaces. The Agent treats files in the second folder as “external,” so it asks for confirmation even when External-File Protection is turned off.
The team is aware and is working on a fix.
Temporary workaround: open each folder separately instead of adding them to one workspace. Not ideal, but it’s the only way to avoid the issue for now.
Related thread: Agent Mode keeps asking approval for changes