Fix: requirements.txt and build errors

[KhushamBansal]

Description of Changes

This PR fixes several issues preventing the book from building successfully in a local environment, as well as some content structure warnings:

Dependency Updates: Added missing dependencies to requirements.txt and environment.yml (including sphinx-multitoc-numbering, linkify-it-py, and several core Sphinx extensions) that were required by conf.py but missing from the installation lists.

TOC Fix: Corrected a typo in DISCOVER/_toc.yml where the file 15_QA_Protocols.md was incorrectly referenced as 15_OA_Protocols.md.

Content Structure: Fixed the heading hierarchy in DISCOVER/15_QA_Protocols.md. The file started with an H2 (##) instead of an H1 (#), and subsequent headers were H3 (###), causing "Non-consecutive header level increase" warnings during the build.

Related Issue

Closes issue #438

Type of Change

Please check the appropriate box that describes your PR:

• 🐛 Bug Fix — Fixes a documented issue or incorrect behavior
• ✨ Content Enhancement — Updates or improves existing content
• ✍️ New Content — Adds new chapters, examples, or significant sections
• 🛠️ Other — Please describe in the Description of Changes section

Checklist

• I have searched open pull requests to avoid duplicates.
• I have built the book locally using the build instructions and verified my changes work as expected.
• I have written clear, conventional commit messages, as per the Pull Request Guidelines.

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