Add table of contents and missing pages

[xylar]

This pull request enhances the E3SM-Unified documentation by adding new sections, reorganizing content, and providing detailed information about tools and packages included in the environment. The changes improve clarity, accessibility, and usability for users and contributors.

Documentation Enhancements

• Added Table of Contents: Introduced a hidden, structured table of contents in docs/index.md to improve navigation across documentation pages.

• Reorganized Content: Removed redundant links and streamlined the "Contents" section in docs/index.md for better readability.

New Tool Documentation

• Detailed Tool Summaries: Added a comprehensive guide in docs/using-tools.md for tools like E3SM Diags, MOAB, MPAS-Analysis, NCO, zppy, and zstash, including usage examples, quickstart guides, and links to further documentation.

Package Information

• Package Catalog: Created a new section in docs/packages.md listing all packages included in the E3SM-Unified environment (1.11.1), along with version constraints and dependencies. This serves as a reference for users and developers.