paper-memory-builder

paper-memory-builder

Bridge between research-hub and academic-writing-skills. Reads a manuscript draft (Word, LaTeX, Markdown, Obsidian paper folder) plus the figures it references, and writes structured .paper/claims.yml + .paper/figures.yml so the writing skill can reason about the paper without parsing the manuscript on every call.

This skill does not edit the manuscript itself. That's the writing skill's job. We just produce the memory layer it consumes.

When to use

Trigger phrases:

• "Build paper memory for this manuscript."
• "Extract claims, figures, and evidence from this paper folder."
• "Prepare reusable memory for writing and revision."
• "I'm starting a rebuttal — give me the claims layer first."

Not for:

• Writing the rebuttal itself — academic-writing-skills.
• Building the orientation memo — research-project-orienter.
• Comparing papers — literature-triage-matrix.
• Verifying a NotebookLM brief — notebooklm-brief-verifier.

Inputs

In priority order:

1. .paper/ existing files — if claims.yml already exists, parse it; this run should refresh, not replace human edits.
2. The manuscript file — usually one of:
   • paper/manuscript.docx / manuscript.tex / manuscript.md
   • Obsidian paper note under raw/<paper-cluster>/manuscript.md
   • Word/LaTeX in a sibling repo specified by the user
3. Figure files under figures/ or outputs/figures/ — read filenames + captions; don't OCR images.
4. .research/project_manifest.yml — for project context (research question, datasets, current_stage). Use to anchor claims in the project's overall question.
5. .research/literature_matrix.md — for citation key lookup if the manuscript references "Smith 2024" but you need to disambiguate.

Outputs

Write to <project-root>/.paper/:

• claims.yml — every paper-level claim, with evidence pointers + status.
• figures.yml — every figure inventory, with key numbers + supported claims.
• revision_history.yml — append-only log of revision rounds (when a claim or figure changed, in which round, why). See references/revision_history_schema.md for the schema and the append-vs-overwrite rules.

Do not touch journal_format.md, reviewer_comments.md, or style_overrides.md — those belong to academic-writing-skills.

.paper/claims.yml structure

claims:
  - id: C1
    text: "Coupled ABM-CAT reduces flood-impact RMSE by 22%."
    evidence_artifacts:
      - "outputs/E2/calibration.csv"
      - "outputs/E2/figure3.png"
    figure_or_table: ["Fig3"]
    status: "draft"          # draft | supported | rejected
    risk: "Reviewer R2 may push back on calibration window."
    sentence_in_manuscript: "...we observe a 22% reduction in RMSE..."

Required per claim: id, text, status. Numbering: C1, C2, ... contiguous; if you regenerate, preserve human-assigned IDs.

.paper/figures.yml structure

figures:
  - id: "Fig1"
    file: "outputs/figures/Fig1_study_area.png"
    panels: ["a) site map", "b) gauge locations"]
    key_numbers: ["12 gauges", "1985-2024 record length"]
    supports_claims: []
    caption_in_manuscript: "Figure 1. Study area..."

Required per figure: id, file, supports_claims (may be []).

.paper/revision_history.yml structure

revisions:
  - round: 1
    date: "2026-04-15"
    trigger: "Initial draft v1"
    changed_claims: []          # all claims new
    changed_figures: []
    summary: "First complete draft."
  - round: 2
    date: "2026-05-02"
    trigger: "Reviewer 2 round 1: doubt on calibration window"
    changed_claims: ["C1", "C4"]
    changed_figures: ["Fig3"]
    summary: "Tightened calibration window claim, added robustness check (Fig S3), softened C4 claim wording."

Required per revision: round, date, trigger, summary. changed_claims and changed_figures may be [] for fresh drafts.

Append, do not overwrite. Each new revision round appends a new list entry. Past rounds stay verbatim — they're the audit trail. The full schema is in references/revision_history_schema.md.

Token-saving behavior

• Read manuscript ONCE per session, extract claims + figures, then reference .paper/*.yml in subsequent writing turns.
• Pass-through claim text exactly as in the manuscript; do not rephrase. The writing skill will polish later.
• For figures, read just the caption + filename; don't OCR or describe visual content.
• After running, hand off cleanly: tell the user "claims.yml and figures.yml ready. Load academic-writing-skills next for any writing/revision/audit pass."

Output format for the user

[paper-memory-builder]
  Read manuscript: paper/manuscript.docx (8 pages, 12 figures)
  Wrote: .paper/claims.yml (9 claims; 2 marked at risk)
  Wrote: .paper/figures.yml (12 figures; 8 mapped to claims, 4 are context)
  Suggested next: load academic-writing-skills for revision/audit passes.

What NOT to do

• Don't edit the manuscript file. Read-only.
• Don't paraphrase claim text. Copy exactly from the manuscript.
• Don't fabricate figures or claims that aren't in the source.
• Don't write to .paper/journal_format.md, reviewer_comments.md, or style_overrides.md. Those are owned by academic-writing-skills.
• Don't write to .research/ — that's the workspace layer, not the paper layer.
• Don't extract claims from cited works — only from THIS paper.