I'd make undo check each file before restoring it. File tools snapshot before a write and shell_exec changes aren't rolled back, so a turn that edits calc.go with file_edit and then runs gofmt -w . leaves undo holding a snapshot from before both. Restoring it quietly drops the formatter's change to calc.go, while every other file gofmt rewrote stays changed, and the tree ends up half undone. Recording a hash after each file-tool write, and refusing to restore or showing the diff when the current hash differs, turns that into a visible conflict instead of a silent loss.