fix(index.ts): fix windows url encode

[stolen-programmer]

Description

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Motivation and Context

How Has This Been Tested?

Breaking Changes

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

[olaservo]

Hi @stolen-programmer, thanks for taking the time to investigate and fix this Windows URL encoding issue! 🙏

After reviewing this PR (with help from Claude Code), we found that this fix has been superseded by PR #3205, which was merged on Feb 19, 2026. That PR introduced a roots-utils.ts module with a parseRootUri() function that already handles fileURLToPath conversion for file:// URIs:

// roots-utils.ts - parseRootUri()
const rawPath = rootUri.startsWith('file://') ? fileURLToPath(rootUri) : rootUri;

The notification handler at index.ts:718 calls updateAllowedDirectoriesFromRoots() → getValidRootDirectories() → parseRootUri(), so the conversion now happens automatically for all root URIs — including the file:///d%3A/work/ case you identified.

Closing this as the underlying issue is resolved, but thank you for catching it — your report helped confirm the fix path!

[olaservo]

Closing as superseded by #3205 (merged). See comment above for details.