docs: Fix markdown formatting and file references #4096

[0xnithin-ai]

Description

This pull request addresses several formatting and referential bugs found within the Everything MCP server documentation.

These documentation errors were breaking the rendering of the README.md on GitHub/NPM and providing confusing or mislabeled file references to developers.

Changes Made

1. Broken Markdown Rendering in README.md

   • Fix: Fixed a markdown syntax error in src/everything/README.md where an installation code block was closed with 4 backticks (````) instead of 3 (```), which was breaking the remainder of the markdown rendering on the page.

2. Incorrect Tool Filename in features.md

   • Fix: Corrected the typo for the long-running operation tool in src/everything/docs/features.md. Changed tools/trigger-trigger-long-running-operation.ts to tools/trigger-long-running-operation.ts.

3. Mislabeled Instructions File (startup.md & structure.md)

   • Fix: Updated references in src/everything/docs/startup.md and src/everything/docs/structure.md from server-instructions.md to instructions.md to match the actual file name.

4. Self-Referential Errors in structure.md

   • Fix: Cleaned up the docs/ folder outline in src/everything/docs/structure.md:
     • Labeled architecture.md properly as "Architectural overview."
     • Added structure.md to the tree and correctly labeled it as "This document."
     • Updated the instructions document reference to instructions.md.

Related Issues

Fixes #4096

Testing

• Verified that markdown renders correctly in IDE previews.
• Verified all mentioned file paths accurately reflect the repository's file structure.