Finalize manuscript render workflow

[Tuminha]

Summary

• allow make manuscript to render with either xelatex or tectonic
• remove duplicate Pandoc section numbering from the manuscript PDF render
• ignore generated local HTML review reports under reports/

Verification

• brew install pandoc tectonic
• make manuscript
• make verify-submission
• git diff --check
• HTML parser smoke check for reports/publication_readiness_review.html

Summary by CodeRabbit

• Chores
  • Refined build output configuration to ignore HTML report files
  • Enhanced PDF manuscript generation with automatic PDF engine detection and fallback support

[coderabbitai]

Caution

Review failed

Pull request was closed or merged during review

📝 Walkthrough

Walkthrough

This PR makes two small updates to development and build infrastructure. The .gitignore file adds a pattern to exclude HTML reports and adjusts its file structure. The Makefile refactors the manuscript target to dynamically select a Pandoc PDF engine (xelatex or tectonic) at runtime instead of assuming a fixed engine, and removes the --number-sections flag.

Changes

Build Configuration and Ignore Patterns

Layer / File(s)	Summary
Git ignore for generated reports .gitignore	reports/*.html outputs are now ignored, and the file tail is adjusted after README_OLD.md.
Dynamic manuscript PDF engine detection Makefile	The manuscript target checks for xelatex or tectonic at runtime, exits with an error if neither exists, passes the detected engine to Pandoc via --pdf-engine=$$ENGINE, and removes --number-sections from the invocation.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Poem

📜 A rabbit hops through build scripts bright,
Ignoring HTML, left and right!
Pandoc's engine now picks its own way,
No more fixed paths—let engines play! 🐰

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'Finalize manuscript render workflow' accurately summarizes the main change: enhancing the manuscript rendering process with dynamic PDF engine selection and workflow improvements.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch finalize/manuscript-render-report

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