[BUG] VS Code extension, multi-root workspace: file links in chat unclickable outside primary folder (re-filed from #62718)

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?

This is a re-file of #62718 (itself a re-file of #50936). Both were closed automatically by the stale bot as "not planned" without the bug being fixed or triaged, and only maintainers can reopen them. The closing message asks to open a new issue if the problem is still relevant: it is.

When the agent emits a markdown link to a file located in any workspace folder OTHER than the primary one, no link format produces a clickable result. The system prompt instructs the agent to use markdown relative paths (e.g. [file.ts](src/file.ts#L42)), which only works for files under the primary workspace folder.

On every cross-folder file reference the user has to copy/paste the path into Quick Open. In codebases made of related repos opened side by side, that is most file references.

Related issues:

• #62718 (closed as stale, 5 👍)
• #50936 (original report, closed as stale)
• #83089 and #80126 (both marked as duplicates of #62718 by a maintainer)
• #87827 (same root cause: @-mention file picker only searches the first folder)
• #53919, #41112 (Windows absolute paths in links)

What Should Happen?

Any one of the following would fix it:

(A) The relative-path resolver searches across all workspace folders, not just the primary one.
(B) The renderer accepts absolute filesystem paths (forward- or backslash) and rewrites them to vscode://file/...:line URIs at render time.
(C) The agent's system prompt specifies a link format known to work in multi-root workspaces, and the extension supports it.

Error Messages/Logs

Steps to Reproduce

1. Open a multi-root workspace in VS Code where the primary folder is apps/server and an additional folder is packages/plugin.
2. Ask the agent to reference a file in packages/plugin/src/mcp.js.
3. The agent emits one of these formats; none of them is clickable:

• Relative: [mcp.js](src/mcp.js#L89) (resolved against the primary folder, file not found)
• Windows absolute: [mcp.js](e:\repo\packages\plugin\src\mcp.js) (invalid URL, backslashes)
• Forward-slash absolute: [mcp.js](e:/repo/packages/plugin/src/mcp.js) (non-standard, ignored)
• file:// URI: [mcp.js](file:///e:/repo/packages/plugin/src/mcp.js) (does not click)
• vscode:// URI: [mcp.js](vscode://file/e:/repo/packages/plugin/src/mcp.js:89) (does not click)

Workaround: the agent falls back to plain path:line text with no clickable link.

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.288 (VS Code extension anthropic.claude-code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_