Review fixes

[iraiosub]

Summary

• Improved protocol style validation and fixing for edge cases:

  • avoids false positives for labels such as 25S rRNA, 3S RNA, Figure 2H, CHIP3, FISH3, and NGS2
  • normalizes ddH2O to ddH<sub>2</sub>O
  • clarifies Greek mu μ versus micro sign µ diagnostics for copy/pasteable fixes

• Improved generated PDFs:

  • renders HTML subscripts as proper PDF subscripts
  • improves PDF header layout for repository URL, commit hash, and actor metadata

• Improved README validation workflow:

  • content validation and style/unit validation now both run after validator tests pass
  • users can see structural and unit/style issues in the same CI run

• Improved legacy migration guidance:

  • harmonized docs/PROMPT.md, Copilot instructions, and protocol-migration skills
  • clarified allowed formatting normalization, migration notes, image/table handling, and output requirements
  • keeps the template attribution badge while avoiding template release-version badges in migrated protocol README files

• Improved user documentation:

  • expanded release guidance
  • added tips for issues, projects, pull requests, and Slack notifications
  • added maintainer/contributor notes for template maintainers
  • clarified that the required Materials section must be top-level and may be numbered, for example # Materials or # 7. Materials