Parallel agent (subtree) submodule folder is empty

[henryz (Henry)]

Where does the bug appear (feature/product)?

Cursor IDE

Describe the Bug

I’m working on a repository with private submodules. When not using subtree, the agents work fine, and they are able to read and edit files inside the submodule folder without issue.

However, if I start a chat or parallel agent with git subtree, the agent cannot find any files referenced inside the submodule folder. And by opening the subtree folder in Finder, I can see the folder is completely empty.

This basically makes the parallel agent feature useless for repos with private submodules. Am I missing some configuration, or is this a limitation? Thanks!

Steps to Reproduce

Run agent in subtree mode against a repo with private submodules

Operating System

MacOS

Current Cursor Version (Menu → About Cursor → Copy)

Version: 2.0.69
VSCode Version: 1.99.3
Commit: 63fcac100bd5d5749f2a98aa47d65f6eca61db30
Date: 2025-11-07T18:21:29.650Z
Electron: 37.7.0
Chromium: 138.0.7204.251
Node.js: 22.20.0
V8: 13.8.258.32-electron.0
OS: Darwin arm64 25.1.0

Does this stop you from using Cursor

No - Cursor works, but with this issue

[deanrie]

Hey, thanks for the report. It looks like this is a real issue: in subtree mode the parallel agent is not correctly initializing git submodules when creating the workspace copy.

When agents run in subtree mode, they clone your repository to a separate location. It seems the clone process is not running git submodule update --init --recursive, which is required to pull in private submodule folders.

To help with further investigation, please share:

• The Request ID from a parallel agent session where this happened (Chat context menu → Copy Request ID)
• Any console errors (Help → Toggle Developer Tools → Console tab) when starting the parallel agent
• Which authentication method you use for git submodules

I’ll pass this on to the team.