docs: Fix duplicate directory_tree tool entry in README.md

[zkl2333]

Description

Removed the duplicate directory_tree tool entry from the API documentation section. The documentation now correctly shows only one entry for this tool, which matches the actual implementation that supports both path and excludePatterns parameters.

Server Details

• Server: filesystem
• Changes to: README.md

Motivation and Context

The API documentation contained two separate entries for the directory_tree tool, which was confusing and inconsistent. The first entry was incomplete (only describing the path parameter), while the second entry correctly described both path and excludePatterns parameters. This change ensures the documentation accurately reflects the implemented functionality.

How Has This Been Tested?

• Verified that the actual implementation in src/filesystem/index.js supports both parameters
• Reviewed the modified documentation for clarity and accuracy
• Confirmed that the remaining documentation entry matches the code implementation

Breaking Changes

No breaking changes. This is purely a documentation fix.

Types of changes

• Documentation update

Checklist

• I have read the MCP Protocol Documentation
• I have updated the server's README accordingly
• My changes follows MCP security best practices

Additional context

The duplicate entry appeared to be a copy-paste error during documentation writing. The fix ensures users see the correct and complete tool specification.

[olaservo]

Thanks!