fix(filesystem): preserve root aliases from MCP roots

[nnish16]

Summary

Preserve both the original root path and its resolved target when filesystem roots come from the MCP roots protocol. This keeps runtime allow-list checks symmetric with startup args, so mapped-drive or symlink-style paths keep working even when realpath() rewrites them.

Changes

• return both original and resolved root paths from getValidRootDirectories() when they differ
• dedupe validated root entries while preserving order
• add a regression test covering roots that resolve through an alias/symlink

Testing

• cd src/filesystem && npx vitest run
• npm run build --workspace @modelcontextprotocol/server-filesystem

Fixes #4129

[Copilot]

Pull request overview

This PR updates the filesystem server’s MCP-roots handling to preserve both the original root path and its realpath()-resolved target when they differ, aligning runtime allow-list checks with startup CLI behavior so alias/symlink/mapped-drive paths continue to validate correctly.

Changes:

• Update root URI parsing to return both normalized original and normalized resolved paths when they differ.
• Dedupe validated root directory entries while preserving insertion order.
• Add a regression test covering a root directory that resolves through a symlink/alias.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
src/filesystem/roots-utils.ts	Return both original and resolved root paths (when different) and dedupe validated directories.
src/filesystem/__tests__/roots-utils.test.ts	Add regression coverage for symlink/alias roots returned via MCP roots.

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[nnish16]

Quick update: I rebased this PR onto the current main and force-pushed the refreshed branch head: a5ce2d6c9ef907781c82c41bd2e7d27746383369.

Locally re-ran the touched package gates before pushing:

• npm run test --workspace @modelcontextprotocol/server-filesystem
• npm run build --workspace @modelcontextprotocol/server-filesystem

GitHub CI is now re-running on the rebased head. If there’s any maintainer preference on shape/scope, I can adjust it quickly.