Fix Table of Contents in README and markdown linter warnings.

[petervandenabeele]

The Table of Contents of the README was outdated => fixed
Also fixed Markdown linter warnings.

Motivation and Context

Small contribution to improve the documentation.

How Has This Been Tested?

[x] I visually inspected the updated Markdown in the Github site.
[x] I clicked the corrected ToC links, they all work.

Breaking Changes

None.

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 Documentation
• My code follows the repository's style guidelines
• New and existing tests pass locally
• I have added appropriate error handling
• I have added or updated documentation as needed

[ihrpr]

Thank you!