Filesystem README recommends deprecated MCP Roots protocol for restricting directory access #4844

Summary

The README.md contains a section recommending the use of the MCP Roots protocol as the mechanism for restricting which directories the filesystem server can access. However, according to the current official MCP specification, Roots is deprecated as of protocol version 2026-07-28 and scheduled for removal.

Source: MCP Specification — Deprecated features

Why this matters

• New users following the README will adopt a deprecated mechanism that is scheduled for removal from the protocol.
• Roots-based access restriction may not work with newer MCP clients, so the documented guidance will break over time.
• The project's documented access-control story should stay aligned with the current specification.

Suggested changes

• Update the README section to stop recommending Roots as the primary way to restrict directory access
• Document the alternatives recommended by the spec:
  • passing directories/files via tool parameters
  • resource URIs
  • server configuration (e.g., allowed directories passed via CLI arguments, which the server already supports)
• If any Roots-related guidance or behavior is kept, mark it explicitly as legacy/deprecated with a pointer to the migration guidance
• Check whether the server implementation itself relies on Roots (e.g., ListRootsRequest) and, if so, open a follow-up issue for migrating away from it

References

• MCP Specification — Deprecated features (2026-07-28)
• README.md — section on restricting filesystem access via Roots