MoxyWolfPlugin Field GuideOperating guide

Full operating guide · academic-pipeline

Academic Pipeline and SCAMPER

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A voice-first, source-grounded path from bibliography to critiqued scholarly manuscript, with optional SCAMPER defixation between theme analysis and thesis selection.

Entry paths

Choose your starting point

  1. An idea, thesis, or topic: first use research-pipeline or bibtex-builder to create a source-backed BibTeX bibliography.

  2. A BibTeX bibliography: start at Stage 0 when abstracts are thin, otherwise start at Stage 1.

  3. An existing paper needing critique or revision: enter at Stage 8 for critique or use the relevant back-half utility.

Before you begin

Prerequisites

  • A source-backed BibTeX bibliography
  • At least three entries with usable abstracts before Stage 1
  • Author participation at the human checkpoints

Setup to evidence

First successful run

  • Choose a source-backed bibliography or an existing paper as the entry point; an idea alone needs source discovery first.
  • Check for at least three usable abstracts and enrich the bibliography if needed.
  • Confirm the run folder, working title and author availability for the thesis, voice and structure checkpoints.
  • Choose SCAMPER only when defixation would help. Confirm a human-selected thesis and distinguish real model output from built-in mock candidates.

Execution sequence

Pipeline stages

  1. Stage 0

    Stage 0 – Bibliography enrichment (optional)

    Add missing abstracts before theme analysis; skip this stage when the bibliography already has usable abstracts.

    Command
    /enrich-bibtex path/to/research.bib
    Inputs
    • BibTeX bibliography
    Outputs
    • pipeline/enriched.bib

  2. Stage 1

    Stage 1 – Theme analysis

    Read the bibliography, map the literature into a Mermaid theme tree, and propose two or three working titles.

    Command
    /academic-themes path/to/research.bib
    Inputs
    • BibTeX bibliography with at least three usable abstracts
    Outputs
    • theme_analysis.json
    • mermaid_diagram.md
    • Working title

  3. Stage 1.5

    Stage 1.5 – SCAMPER defixation (optional)

    Break fixation when the literature's consensus reading has become the assumption to challenge, after theme analysis and before perspective selection.

    Command
    /academic-pipeline path/to/research.bib --scamper
    Inputs
    • theme_analysis.json
    Outputs
    • scamper_baseline.json
    • scamper_results.json
    • scamper_outline.md (optional)
    How it works
    • Choose SCAMPER at the initial checkpoint or prescribe it with --scamper.
    • Distill theme_analysis.json into scamper_baseline.json fields: topic, consensus_claims, theoretical_frameworks, methodologies, and implicit_assumptions.
    • Score candidates from 0–10 against baseline texts using TF-IDF cosine distance. This measures distance from that baseline, not validated scholarly originality.
    • The highest novelty score is a proposal, not an automatic selection.
    • --topic alone uses a demo baseline. A genuine run derives its baseline from theme_analysis.json and generates and checks real candidates with a configured LLM client.
    Operators
    • Substitute
    • Combine
    • Adapt
    • Modify
    • Put to another use
    • Eliminate
    • Reverse

  4. Stage 2

    Stage 2 – Perspective

    Fix the paper's writing lens, specific target audience, and three to five emphasized sub-themes.

    Inputs
    • Working title
    • mermaid_diagram.md
    • Confirmed SCAMPER thesis when Stage 1.5 ran
    Outputs
    • pipeline/perspective.json

  5. Stage 3

    Stage 3 – Voice

    Capture the standing author voice and eight article-specific answers before drafting begins.

    Inputs
    • pipeline/perspective.json
    • Standing voice profile or author interview
    Outputs
    • pipeline/voice_context.json

  6. Stage 4

    Stage 4 – Formatting

    Distill Academia.edu structure and MoxyWolf anti-AI rules before any section is drafted.

    Inputs
    • pipeline/perspective.json
    • pipeline/voice_context.json
    Outputs
    • pipeline/formatting_requirements.json

  7. Stage 5

    Stage 5 – Research analysis and structure

    Analyze sources and design a section-by-section plan with word targets and mapped citations.

    Inputs
    • Bibliography
    • pipeline/perspective.json
    • pipeline/voice_context.json
    • pipeline/formatting_requirements.json
    Outputs
    • pipeline/handoff_for_writer.json
    • Approved section structure

  8. Stage 6

    Stage 6 – Iterative writing

    Draft the paper section by section from cited sources in the approved voice and format.

    Inputs
    • pipeline/handoff_for_writer.json
    • Approved section structure
    Outputs
    • pipeline/draft_document.md
    • Deduplicated citations used

  9. Stage 7

    Stage 7 – Bibliography and complete document

    Format every cited source, renumber Vancouver citations when applicable, and assemble the complete paper.

    Inputs
    • pipeline/draft_document.md
    • Deduplicated citations used
    • Source bibliography
    Outputs
    • complete_document.md

  10. Stage 8

    Stage 8 – Professor critique

    Run the ten-phase pre-submission review and produce a prioritized revision path.

    Command
    /academic-critique complete_document.md
    Inputs
    • complete_document.md
    Outputs
    • critique_report.md
    • improvement_plan.md

  11. Stage 9

    Stage 9 – Evidence-aware release gate

    Run the current seven checks before calling the manuscript complete, then read the examined counts and explicit skips.

    Inputs
    • Complete manuscript
    • References
    • Repository and archive records when applicable
    Outputs
    • Release report with PASS, FAIL and SKIP results
    How it works
    • Checks: em_dashes, forbidden_phrases, sections_present, duplicate_sources, citation_order, repository_references, archive_coverage.
    • A PASS over zero examined inputs becomes FAIL. Applicable failures block completion.
    • Non-Vancouver citation order, absent repository context or missing archival records may be explicit SKIP. Overall PASS can coexist with SKIPs; disclose them.
    • These checks do not establish that every citation supports its claim. Keep source verification and substantive critique separate.

Decisions and limits

Field notes

Reference

Outputs

  • complete_document.md – the finished, fully cited paper
  • critique_report.md – the professor's ten-phase review
  • improvement_plan.md – the prioritized revision path
  • mermaid_diagram.md – the literature theme tree
  • pipeline/ – intermediate state for auditing or restarting a stage

Handoffs

Relationships

TypePlugin or companionHow it connects
pluginresearch-pipelineDiscovers and verifies sources when the starting point is an idea or topic.
pluginbibtex-builderBuilds or enriches a standalone BibTeX bibliography from known URLs or DOIs.
pluginacademic-pipelineOwns the run folder, stages, checkpoints, manuscript, bibliography, and critique.
plugineditorial-forgeContinues author-owned editorial development after the scholarly pipeline when deeper editorial judgment is needed.

Stop conditions

Troubleshooting

  1. Stage 0

    Stage 0 cannot retrieve enough source material to leave at least three entries with usable abstracts.

  2. Stage 1

    Fewer than three entries have usable abstracts; return to Stage 0.

  3. Stage 1.5

    No human thesis confirmation is available, or built-in mock candidates are being mistaken for a completed LLM analysis.

  4. Stage 2

    The lens, audience, or sub-themes remain ambiguous.

  5. Stage 3

    The author's own position and language have not been captured.

  6. Stage 4

    The target venue or required format is unknown.

  7. Stage 5

    The evidence cannot support the thesis or the section structure is not approved.

  8. Stage 6

    A required claim lacks a supporting source or the draft departs from the approved structure.

  9. Stage 7

    In-text citations and reference entries do not reconcile.

  10. Stage 8

    The paper is incomplete or its references cannot be checked.

  11. Stage 9

    An applicable check fails or a skipped check is being described as completed verification.

Source verified October 25, 2026

Pinned source references

Source review verifies the documented workflow, not a successful run in your host.