Add capability to filesystem reference server

[jl-0]

Various improvements born out of attempting to use this MCP for tasks including searching code bases, etc.

Description

Added a search_in_files features and other changes to due issues seen during usage with a LangGraph workflow.

Server Details

• Server: filesystem
• Changes to:

• Added, search_in_files
• Added some fuzzy matching for search hints in applyFileEdits (model kept trying replacements that were failing)
• Augmented the description of list_allowed_directories as AWS Nova kept limiting the files to only the top-level folder

Motivation and Context

Encountered a few issues using the tool in an LangGraph workflow. Needed the ability to search for files of interest based on contents not just file name. Also encountered cases where the model thought it was only allowed to search the top-level allowed directories not any sub-directories.

How Has This Been Tested?

I have used the updated package in several workflows. Some testing in MCP Inspector. No specific unit tests

Breaking Changes

No

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation update

Checklist

• I have read the MCP Protocol Documentation
• My changes follows MCP security best practices
• I have updated the server's README accordingly
• I have tested this with an LLM client
• My code follows the repository's style guidelines
• New and existing tests pass locally
• I have added appropriate error handling
• I have documented all environment variables and configuration options

Additional context

Not groundbreaking enhancements but I found them useful and other may as well.