feat(filesystem): ignore dot directories by default to reduce token usage

- Add environment variable MCP_FILESYSTEM_INCLUDE_HIDDEN (default: false)
- Filter dot-prefixed files/directories in list_directory, directory_tree, search_files
- Reduces token usage from large directories like .git, .terraform, etc.
- Enhances security by avoiding exposure of potentially sensitive hidden files
- Includes comprehensive tests for the new filtering functionality
- Update documentation to explain the new behavior and environment variable

Fixes #2219

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Co-Authored-By: Ola Hungerford <olaservo@users.noreply.github.com>

src/filesystem/README.md

@@ -15,6 +15,20 @@ Node.js server implementing Model Context Protocol (MCP) for filesystem operatio
 
 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/learn/client-concepts#roots).
 
+### Hidden Files and Directories
+
+By default, the filesystem server **ignores dot-prefixed files and directories** (like `.git`, `.env`, `.terraform`, etc.) to:
+- Reduce token usage (especially from large directories like `.git`)
+- Enhance security by avoiding exposure of potentially sensitive hidden files
+- Follow the convention that dot-prefixed items are typically "hidden" for good reason
+
+To include hidden files and directories, set the environment variable:
+```bash
+export MCP_FILESYSTEM_INCLUDE_HIDDEN=true
+```
+
+This affects the following operations: `list_directory`, `list_directory_with_sizes`, `directory_tree`, and `search_files`.
+
 ### Method 1: Command-line Arguments
 Specify Allowed directories when starting the server:
 ```bash