docs: fix broken markdown syntax and anchor links in /tools

[campox747]

Summary

Fixed broken anchor links in index.md towards file-system.md and reference/commands.md. Fixed minor formatting inconsistencies in file-system.md.

Details

• Updated the anchor tags in index.md's File Management section to properly match the generated header hashes.
• Removed the stray "5." and "6." numbering from the grep_search and replace headers in file-system.md to ensure clean formatting.
• Fixed broken link in hooks/reference.md.

Related Issues

Closes #20901

How to Validate

Check ### File management section in docs/tools/index.md to ensure the links navigate to the correct headers in file-system.md.

Pre-Merge Checklist

• Updated relevant documentation and README (if needed)
• Added/updated tests (if needed)
• Noted breaking changes (if any)
• Validated on required platforms/methods:
  • MacOS
    • npm run
    • npx
    • Docker
    • Podman
    • Seatbelt
  • Windows
    • npm run
    • npx
    • Docker
  • Linux
    • npm run
    • npx
    • Docker

[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request focuses on enhancing the usability and accuracy of the documentation for developer tools. It resolves issues with broken internal links and minor markdown formatting, ensuring that users can navigate and reference tool descriptions more effectively.

Highlights

• Documentation Navigation: Corrected broken anchor links within docs/tools/index.md to ensure proper navigation to sections in file-system.md and reference/commands.md.
• Markdown Formatting: Addressed minor formatting inconsistencies in docs/tools/file-system.md by adjusting heading levels for grep_search and replace sections, which also resolved anchor generation issues.

Changelog

• docs/tools/file-system.md
  • Reduced heading level for grep_search from ## to ###.
  • Reduced heading level for replace from ## to ###.
• docs/tools/index.md
  • Updated the 'File access' link to point to the correct commands.md reference.
  • Adjusted anchor links for list_directory, read_file, write_file, glob, grep_search, and replace to match generated header IDs in file-system.md.

Activity

• The author marked the 'Updated relevant documentation and README' item as complete in the pre-merge checklist.

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[gemini-code-assist]

Code Review

This pull request addresses broken links and formatting in the documentation. The changes are generally good, fixing heading levels and anchor links. I've identified one minor inaccuracy in the description of the grep_search tool, which has been retained as it does not conflict with any provided rules.

[g-samroberts]

Hi @campox747 , thanks for your contribution. Looks like there are some conflicts that need to be resolved, since some of these files have changed.

[campox747]

I didn't realize the docs/tools/index.md file had been completely deleted. I've synced my branch with main to resolve the conflicts and dropped that file. The two minor formatting fixes in the other files are still applied though. Please let me know if there are any other problems!