Agents Window - The file tree doesn't work with multi root folder workspaces

Where does the bug appear (feature/product)?

Cursor IDE

Describe the Bug

I can only browse the files of the last folder in the workspace, all other folders appear empty like they have no files. When I use cmd+p to open a specific file I can search the whole workspace without issue and open it but it doesn’t highlight it in the file tree since it’s not even there.

One detail that might be causing the issue I’m not sure is that the workspace file we use is a symlink to a file within one of the workspace folders.

Steps to Reproduce

  1. Setup a multi root folder workspace
  2. Open the agent window
  3. Open the file tree
  4. Click on the top most folders of that workspace, they show nothing
  5. The last one should show its content

Operating System

MacOS

Version Information

Version: 3.9.8
VS Code Extension API: 1.105.1
Commit: 4aa8ff1b7877ed7bd01bcba308698f71a6735380
Date: 2026-06-25T01:39:30.490Z
Layout: glass
Build Type: Stable
Release Track: Default
Electron: 40.10.3
Chromium: 144.0.7559.236
Node.js: 24.15.0
V8: 14.4.258.32-electron.0
xterm.js: 6.1.0-beta.256
OS: Darwin arm64 25.5.0

Does this stop you from using Cursor

No - Cursor works, but with this issue

Hi @raphael-yapla!

So far, I haven’t been able to reproduce this. Am I doing aything differently than you are?

Could you share what this workspace file looks like?

Sure thing, our workspace file looks like this. I had to anonymize everything for security reason but the hierarchy of folders and the name composition with the / remains the same.

{
	"folders": [
		{
			"name": "app / orchard",
			"path": "app/orchard"
		},
		{
			"name": "ai / skills",
			"path": "ai/skills"
		},
		{
			"name": "app / fjord",
			"path": "app/fjord"
		},
		{
			"name": "app / kite",
			"path": "app/kite"
		},
		{
			"name": "app / lumen",
			"path": "app/lumen"
		},
		{
			"name": "app / mosaic",
			"path": "app/mosaic"
		},
		{
			"name": "app / nova",
			"path": "app/nova"
		},
		{
			"name": "app / oasis",
			"path": "app/oasis"
		},
		{
			"name": "app / orchard / wiki",
			"path": "app/orchard.wiki"
		},
		{
			"name": "app / pixel",
			"path": "app/pixel"
		},
		{
			"name": "app / quill",
			"path": "app/quill"
		},
		{
			"name": "cloud / quill",
			"path": "cloud/quill"
		},
		{
			"name": "cloud / ridge",
			"path": "cloud/ridge"
		},
		{
			"name": "cloud / spire",
			"path": "cloud/spire"
		},
		{
			"name": "codex",
			"path": "codex"
		},
		{
			"name": "package / rune",
			"path": "package/rune"
		},
		{
			"name": "package / tide",
			"path": "package/tide"
		},
		{
			"name": "package / tide-laravel",
			"path": "package/tide-laravel"
		},
		{
			"name": "package / composer / patch-set / widget-kit",
			"path": "package/composer/patch-set/widget-kit"
		},
		{
			"name": "package / weave",
			"path": "package/weave"
		},
		{
			"name": "ops / workshop / cabin",
			"path": "ops/workshop/cabin"
		},
		{
			"name": "ops / workshop / grid",
			"path": "ops/workshop/grid"
		},
		{
			"name": "ops / workshop / grid / wiki",
			"path": "ops/workshop/grid.wiki"
		},
		{
			"name": "ops / workshop / bench",
			"path": "ops/workshop/bench"
		},
		{
			"name": "ops / workshop / bench / wiki",
			"path": "ops/workshop/bench.wiki"
		},
		{
			"name": "ops / workshop / trace",
			"path": "ops/workshop/trace"
		},
		{
			"name": "ops / workshop / ping",
			"path": "ops/workshop/ping"
		},
		{
			"name": "test / harness",
			"path": "test/harness"
		},
		{
			"name": "hub",
			"path": "hub"
		}
	]
}

Important detail I noticed while giving you these info, it’s not just the last folder in the list that I can browse but all the folders that sit at the root level with the workspace file. So in my case “hub” and “codex”. For everything else while I can see the root folders in the file tree, when I open them they appear empty. So it looks like it’s more that the Agent Windows file tree doesn’t support workspace entries that are targeting subfolders.

More details on our workspace setup, we use a symlink to the actual versioned workspace file that resides in ops/workshop/bench/subfolder. That symlink is set at the root level so the folder containing all of these workspace folders.