Apply suggestions from code review comments on docs and logging

Co-authored-by: Ola Hungerford <olahungerford@gmail.com>

Author: nandsha

src/filesystem/README.md

@@ -9,26 +9,26 @@ Node.js server implementing Model Context Protocol (MCP) for filesystem operatio
 - Move files/directories
 - Search files
 - Get file metadata
-- Dynamic directory access control via MCP roots protocol
+- Dynamic directory access control via [Roots](https://modelcontextprotocol.io/docs/concepts/roots)
 
 ## Directory Access Control
 
-The server uses a flexible directory access control system. Directories can be specified via command-line arguments or dynamically via the MCP roots protocol.
+The server uses a flexible directory access control system. Directories can be specified via command-line arguments or dynamically via [Roots](https://modelcontextprotocol.io/docs/concepts/roots).
 
 ### Method 1: Command-line Arguments
 Specify Allowed directories when starting the server:
 ```bash
 mcp-server-filesystem /path/to/dir1 /path/to/dir2
 ```
 
-### Method 2: MCP Roots Protocol (Recommended)
-MCP clients that support the roots protocol can dynamically update the Allowed directories. 
+### Method 2: MCP Roots (Recommended)
+MCP clients that support [Roots](https://modelcontextprotocol.io/docs/concepts/roots) can dynamically update the Allowed directories. 
 
 Roots notified by Client to Server, completely replace any server-side Allowed directories when provided.
 
 **Important**: If server starts without command-line arguments AND client doesn't support roots protocol (or provides empty roots), the server will throw an error during initialization.
 
-This is the recommended method, as MCP roots protocol for dynamic directory management. This enables runtime directory updates via `roots/list_changed` notifications without server restart, providing a more flexible and modern integration experience.
+This is the recommended method, as this enables runtime directory updates via `roots/list_changed` notifications without server restart, providing a more flexible and modern integration experience.
 
 ### How It Works
 

src/filesystem/index.ts

@@ -876,14 +876,14 @@ server.oninitialized = async () => {
       if (response && 'roots' in response) {
         await updateAllowedDirectoriesFromRoots(response.roots);
       } else {
-        console.log("Client returned no roots set, keeping current settings");
+        console.error("Client returned no roots set, keeping current settings");
       }
     } catch (error) {
       console.error("Failed to request initial roots from client:", error instanceof Error ? error.message : String(error));
     }
   } else {
     if (allowedDirectories.length > 0) {
-      console.log("Client does not support MCP Roots, using allowed directories set from server args:", allowedDirectories);
+      console.error("Client does not support MCP Roots, using allowed directories set from server args:", allowedDirectories);
     }else{
       throw new Error(`Server cannot operate: No allowed directories available. Server was started without command-line directories and client either does not support MCP roots protocol or provided empty roots. Please either: 1) Start server with directory arguments, or 2) Use a client that supports MCP roots protocol and provides valid root directories.`);
     }
@@ -896,7 +896,7 @@ async function runServer() {
   await server.connect(transport);
   console.error("Secure MCP Filesystem Server running on stdio");
   if (allowedDirectories.length === 0) {
-    console.log("Started without allowed directories - waiting for client to provide roots via MCP protocol");
+    console.error("Started without allowed directories - waiting for client to provide roots via MCP protocol");
   }
 }