fix(filesystem): only apply MCP roots when no CLI directories are provided

[Will-hxw]

Summary

• Only call updateAllowedDirectoriesFromRoots when allowedDirectories.length === 0, so CLI arguments take precedence over MCP roots

Why

Issue #3929: When clientCapabilities.roots is true, the server unconditionally replaces CLI-specified directories with client roots, preventing the server from being limited to directories outside the client project root.

Validation

• Code review passed
• Branch pushed to fork

[Will-hxw]

CI Failure Analysis

The Test everything check is failing due to TypeScript strict mode type errors in src/everything/tools/get-env.ts.

Error Details

1. Line 33: Parameter 'args' implicitly has an 'any' type
2. Line 33: Argument of type '{ title: string; description: string; inputSchema: {...} }' is not assignable to parameter of type...

Root Cause

The new code uses args (via const { key } = args as { key: string }) but args lacks a proper type annotation. With tsconfig.json having strict: true, TypeScript requires explicit typing.

Suggested Fix

Add proper type annotation to the args parameter. Example fix pattern:

interface GetEnvArgs {
  key: string;
}

server.registerTool(name, config, async (args: GetEnvArgs): Promise<CallToolResult> => {
  const { key } = args;
  // ...
});