Research Paper Mode¶

Research paper mode is the evidence-forward pipeline for traditional research manuscripts. It produces a LaTeX draft with a verified BibTeX bibliography, a figures and tables pipeline, and a structured finalize-and-package stage for venue submission.

When to use¶

Choose research paper mode when your materials include:

• Experimental results, benchmarks, ablation studies, or statistical analyses
• Datasets and code
• A target venue with specific LaTeX formatting requirements
• A hypothesis-driven narrative that requires traceable quantitative claims

route_mode.py recommends this mode when materials show strong empirical signals: experimental logs, datasets, notebooks, or benchmark output. If routing is ambiguous, override at the routing checkpoint.

Stage D2: Global Planning¶

Entry condition: Checkpoint 1 and routing approved; canonical inputs available.

Folio reads your canonical inputs and generates five planning artifacts:

Gate B — Plan completeness: - Outline includes standard sections for the venue type - Every claim has a support_level; every unsupported claim is explicitly flagged - Figure plan covers all outline-referenced figures - Literature plan covers all citation needs

Human Checkpoint 2: Folio presents the outline, narrative arc, claim ledger summary (highlighting weak/unsupported claims), figure plan, and literature plan. Explicit approval required before Stage D3.

Stage D3: Support Artifact Generation¶

Three substages run in parallel (all must complete before drafting):

3A — Evidence accounting¶

Folio re-reads experimental_log.md and results_inventory.json, verifies each claim in claim_ledger.json, and updates support_level and notes.

Gate C — Evidence integrity: Blocks if any claim remains unsupported without user acknowledgment, or if numerical claims lack traceable sources.

3B — Literature discovery and verification¶

Folio searches using literature_plan.json queries (Semantic Scholar, Google Scholar, arXiv, PubMed as available), verifies each candidate via DOI or search, deduplicates, and produces:

• citations/citation_pool.json — Verified metadata with relevance scores
• citations/refs.bib — BibTeX bibliography built from verified citations only

Gate D — Citation integrity: Blocks on unverified pool entries or duplicate BibTeX keys. No fabricated citations enter the manuscript.

3C — Figure and table pipeline¶

Folio processes each figure_plan.json entry:

• existing — Verifies file; copies to figures/supplied/
• generate — Produces asset under figures/generated/
• collect — Flags for user provision

Produces: - figures/captions.json — Figure id, path, caption, existence flag - tables/generated/ — LaTeX table snippets as needed

Gate E — Artifact integrity: Blocks if any outline-referenced figure or table is missing and not explicitly deferred; blocks if required captions are missing.

Stage D4: Draft Composition¶

Entry condition: Stage D3 complete; Gates C, D, E pass.

Folio composes drafts/paper.tex section by section:

• Uses \cite{key} only for keys in refs.bib
• \ref{} labels consistent with captions.json and figure plan
• Quantitative claims grounded in claim ledger; weak support claims use softened language
• Uses inputs/template.tex as skeleton if present; otherwise standard article class

Gate F — Structural integrity:

cd plugins/folio && python scripts/check_artifacts.py workspace/

Broken cites and refs must be resolved before proceeding.

Stage D5: Review and Repair¶

IP scan (required):

cd plugins/folio && python scripts/scan_redlines.py workspace/

IP Gate: Violations block completion of review until addressed.

Folio runs a review pass writing reviews/review_round_1.md (argument flow, claim support, citations, figures/tables, clarity, venue fit, line-level suggestions) and reviews/scorecard.json with six numeric dimensions:

• argument_coherence
• evidence_support
• citation_quality
• writing_clarity
• venue_fit
• overall

Gate G — Non-regression: If overall drops after a repair round, Folio reverts to the pre-revision draft. Maximum 3 rounds; best-scoring draft is retained.

Stage D6: Finalize¶

Human Checkpoint 3: Folio presents the final scorecard, deferred issues, and softened claims. Explicit approval required.

After approval:

1. Accepted draft copied to final/paper.tex; final/refs.bib; figures to final/figures/; tables to final/tables/

2. Compile:

cd plugins/folio && bash scripts/compile_package.sh workspace/

1. On compile failure: Folio reports errors, attempts minimal fixes, re-runs. If still failing, delivers the source bundle without PDF and documents why.

2. logs/run_log.md updated.

Exit: Submission-ready package in final/ or documented partial export.

Artifacts produced¶

See Artifacts for the complete cross-mode artifact list.