[its-amann]

Description

Update the filesystem server README to recommend command-line allowed directories for new configurations. Mark MCP Roots as deprecated, while preserving accurate guidance for existing Roots integrations, including the fact that valid client Roots replace CLI directories rather than extending them.

Motivation and Context

Fixes #4844. The MCP 2026-07-28 specification deprecates Roots but keeps them functional during the migration period. The README previously called Roots the recommended method.

How Has This Been Tested?

• git diff --check passes.
• Verified the linked MCP deprecation documentation resolves.
• Documentation only; runtime behavior is unchanged, so no LLM-client testing was performed.

Breaking Changes

None.

Types of changes

• Documentation update

Checklist

• I have read the MCP Protocol Documentation
• My changes follow the repository's style guidelines
• I have updated the server's README accordingly
• I have tested this with an LLM client (documentation-only change)

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[changeset-bot]

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Latest commit: 468b556

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[cliffhall]

Thank you for this pull request, and apologies for the long wait for a response.

Since it was opened, the reference servers have been rebuilt for the 2026-07-28 MCP specification (#4857) and released as v2 (2.0.0 on npm for the TypeScript servers, 2026.10.19 on PyPI for the Python servers). The code this PR changes has been replaced, and the behavior it addresses has either been fixed in v2 or no longer exists in the same form.

This is not a judgment on the change or on you; it's a consequence of the code it targets having been replaced. If the problem still happens on v2, please open a fresh issue with the version you're running and steps to reproduce. Note that this repository now accepts contributions as issues rather than pull requests from anyone but its maintainers; see CONTRIBUTING.md.

This is part of the backlog triage in #4875.