Hey thanks for the detailed report. Let me break it down. This isn’t a regression. It’s an intentional layout change. In Show Panel in Agents Window the file tree and panels are now always on the right with code on the left. It’s the same as in Diff / PR / Terminal / Browser panels. There’s no setting to choose the side right now. The old option with the tree on the left has been removed from the code so you can’t bring it back through settings.
If you need the classic IDE layout with Explorer on the left open the regular Editor Window. Use File > Open Editor Window or Cmd+Shift+N. It keeps the familiar layout and full panel customization like in VS Code.
I’ve logged your request about a toggle for the file tree position in Show Panel as a feature request. This topic has come up before. There’s a similar thread Agents view: cannot swap editor and file tree order at Agents view: cannot swap editor and file tree order ([Code][Files] stuck; no UI to get [Files][Code]). You can add your vote and details there. I can’t give an ETA on such an option right now.
Let me know if Editor Window works as a temporary solution.