Organize repository and publish AMOS papers

[EltonChang1]

Summary

• consolidate the two canonical AMOS papers and LaTeX sources under papers/
• add a startup-oriented system design proposal and retain the complete research manuscript
• move evaluation guidance under docs/evaluation/
• remove duplicate PDFs and generated publication output
• update repository documentation, citation metadata, build instructions, and ignore rules

Why

The repository had duplicate manuscripts, compiled output in multiple locations, and generated artifacts mixed with durable source. This change establishes a compact, reproducible layout with exactly two canonical single-column PDFs.

Validation

• pytest -q — 85 tests passed
• both LaTeX papers compile without warnings
• all 37 rendered pages visually inspected
• exactly two PDFs confirmed repository-wide

[Copilot]

Pull request overview

This PR reorganizes the repository’s paper and evaluation-document layout to remove duplicates and keep a compact, reproducible structure centered around two canonical PDFs under papers/.

Changes:

• Consolidates paper PDFs and LaTeX sources under papers/ and streamlines the top-level README to link to the two canonical PDFs.
• Moves evaluation guidance into docs/evaluation/ and updates cross-references accordingly.
• Updates ignore rules to drop generated artifacts while explicitly retaining only the two canonical paper PDFs.

Reviewed changes

Copilot reviewed 8 out of 12 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
README.md	Replaces long-form README with links to the two canonical PDFs.
papers/research_paper.tex	Updates PDF metadata/title to reflect the new paper naming.
papers/design_proposal.tex	Adds a new design proposal LaTeX source under papers/.
external_studies/HANDOFF.md	Updates protocol path references after moving evaluation docs.
docs/evaluation/independent_evaluation_protocol.md	Updates intake-doc reference to the new docs/evaluation/ location.
docs/evaluation/evidence_intake.md	Updates the intake document heading/title.
docs/evaluation/artifact_evaluation.md	Updates submission finalization command to point at papers/ and moved docs.
CITATION.cff	Updates citation title to match the new naming.
.gitignore	Ignores generated document outputs broadly while allowlisting the two canonical paper PDFs.

Comments suppressed due to low confidence (2)

papers/research_paper.tex:25

• The PDF metadata title includes a duplicated prefix ("AMOS: AMOS:"), which is likely a typo and will propagate to the rendered PDF’s document properties.
  papers/research_paper.tex:47
• The paper title includes a duplicated prefix ("AMOS: AMOS:"), which is likely unintended and will appear in the rendered manuscript title.

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