fix(filesystem): preserve CLI directories when MCP roots are available

[Christian-Sidak]

Summary

• CLI-provided allowed directories now take precedence over MCP roots, fixing the issue where clients that support the roots protocol would unconditionally override explicitly configured directories
• MCP roots are still used as a fallback when no CLI directories are provided, preserving backward compatibility
• Both the oninitialized handler and the roots/list_changed notification handler respect this precedence

Problem

When configuring the filesystem server with an explicit directory (e.g., /path/to/external-project) and using it from a client that supports MCP roots (e.g., Claude Code with project root at /path/to/my-repo), the server would replace the CLI directory with the client's root on initialization. This made it impossible to scope the server to directories outside the client's project root.

Fix

A cliDirectoriesProvided flag tracks whether directories were explicitly provided via CLI arguments. When set, both the initialization and runtime roots update handlers skip root resolution and keep the CLI-provided directories.

Fixes #3929

Test plan

• All 146 existing tests pass
• Existing startup validation tests confirm the new "CLI directories provided, ignoring MCP roots" log path is hit when CLI args are present
• Manual: configure server with explicit directory, connect from roots-capable client, verify list_allowed_directories returns CLI directory
• Manual: start server without CLI args, connect from roots-capable client, verify roots are used as before