Markdown file links to secondary workspace folders are not clickable (multi-root workspace)

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?

Title: Markdown file links to secondary workspace folders are not clickable (multi-root workspace)

Environment

• Claude Code VS Code extension
• Windows 11
• Multi-root VS Code workspace with three folders:
• Primary: c:\Git\msa\account-list\dev
• Additional: c:\Git\Customer Lifecycle\Customer Profile\customers-profile-system
• Additional: c:\Git\msa\CustomerMasterDataProvider

Description

When Claude references a file located in the primary workspace folder, the markdown link it outputs (e.g. [file.ts](src/path/file.ts#L10)) is clickable in the chat panel and correctly jumps to the file/line in the editor.

When Claude references a file located in one of the additional (non-primary) workspace folders, the equivalent markdown link is rendered as plain text instead of a clickable jump-link, regardless of the link format used.

Repro steps

1. Open a multi-root VS Code workspace where the primary folder is A, with two additional folders B and C added alongside it (not nested under A).
2. Ask Claude Code to reference a file that lives in folder B or C.
3. Observe that:

• A link relative to the additional folder's display name (e.g. [file.js](CustomerMasterDataProvider/data/queries/userPerson.js#L34)) does not become clickable.
• An absolute file:/// URI (e.g. [file.js](file:///c:/Git/msa/CustomerMasterDataProvider/data/queries/userPerson.js#L34)) does not become clickable.
• A vscode://file/ URI (e.g. [file.js](vscode://file/c:/Git/msa/CustomerMasterDataProvider/data/queries/userPerson.js:34)) does not become clickable either.

1. Meanwhile, the same style of link pointing to a file under the primary folder A works correctly.

Expected behavior

Markdown links to files in any workspace folder (primary or additional) should be clickable and jump to the correct file/line in the editor, since all three folders are part of the same open VS Code workspace.

Actual behavior

Only links to files under the primary workspace folder are clickable. Links to files in additional workspace folders render as plain, non-interactive text no matter which link format is used (relative-with-folder-prefix, file://, or vscode://file/).

Additional notes

Also worth checking: whether the model/extension is even reliably informed of all open workspace folders at session start — in this case, the "additional working directories" reported to the assistant only listed one of the two non-primary folders; the third (CustomerMasterDataProvider) was not mentioned in the environment context at all, and its existence had to be discovered manually via shell commands. This may be a related/underlying cause.

What Should Happen?

Markdown links to files in any workspace folder (primary or additional) should be clickable and jump to the correct file/line in the editor, since all three folders are part of the same open VS Code workspace.

Error Messages/Logs

Steps to Reproduce

Repro steps

1. Open a multi-root VS Code workspace where the primary folder is A, with two additional folders B and C added alongside it (not nested under A).
2. Ask Claude Code to reference a file that lives in folder B or C.
3. Observe that:

• A link relative to the additional folder's display name (e.g. [file.js](CustomerMasterDataProvider/data/queries/userPerson.js#L34)) does not become clickable.
• An absolute file:/// URI (e.g. [file.js](file:///c:/Git/msa/CustomerMasterDataProvider/data/queries/userPerson.js#L34)) does not become clickable.
• A vscode://file/ URI (e.g. [file.js](vscode://file/c:/Git/msa/CustomerMasterDataProvider/data/queries/userPerson.js:34)) does not become clickable either.

1. Meanwhile, the same style of link pointing to a file under the primary folder A works correctly.

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

Version 2.1.220

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_