[BUG] VSCode extension: multi-root workspace closes and reopens as single folder when running a BMAD skill

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Description

Using a multi-root .code-workspace file (three folders: an API repo, a web repo, and a BMAD repo), running a BMAD agent skill (bmad-agent-dev, a plain markdown-instructions Claude Code skill with no shell or VSCode-API calls) causes VSCode to drop the multi-root workspace and reopen as a single-folder window scoped to just the BMAD folder — the other two folders disappear from the window entirely.

Related issues

• #36949 — extension only recognizes the first folder in a multi-root workspace as its working directory
• #71710 — switching the open folder hides/loses sessions tied to other folders
• #49082 — chat session lost when opening a folder in VS Code

This may be the same underlying mechanism as #49082/#71710, but the visible symptom (whole workspace replaced by a single folder) doesn't appear to be filed yet.

Environment

• OS: Linux (WSL2)
• Claude Code: VSCode native extension

What Should Happen?

The multi-root workspace should remain open; the extension should operate within its assigned working directory without altering the VSCode window/workspace scope.

Error Messages/Logs

Steps to Reproduce

1. Open a multi-root .code-workspace containing 3+ folders in VSCode with the Claude Code extension.
2. Point Claude Code's working directory at one of the non-first folders (or the first — needs confirmation) in that workspace.
3. Run a Claude Code skill/command (e.g. a custom skill under .claude/skills/) from that folder.
4. Observe: the VSCode window closes the multi-root workspace and reopens showing only that one folder.

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.221 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_