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Drafts or audits a scientific paper’s introduction and framing — the real-world "why", an evidence audit, the funnel from theory to a falsifiable if-then with a named estimand, bridges across experiments, and a contribution list matched to the design. Use when the user asks to write, restructure, or critique an introduction, motivate or frame a paper, repair a gap-in-the-literature opening, sharpen or calibrate a contribution claim, or connect experiments into one argument. Sentence-level flow and wording are out of scope.

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Provides a pre-submission manuscript audit covering argument, numerical consistency, references and DOIs, writing, figures, CONSORT flow, pre-registration, and the replication archive. Use before paper submission or when a draft needs an adversarial, quote-grounded review with a journal-readiness checklist. Add `--codex` to run the specification independently on Claude and Codex, GPT-6 Astra, and cross-check findings.

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Writes or reviews a pre-analysis plan before data collection — registry choice (OSF, AEA RCT Registry, AsPredicted, registered reports), PAP structure, models and decision rules locked in advance, analysis code run on simulated data, contingencies for attrition, failed manipulations, and exclusions, deviation records, and timeline. Operationalizes the pre-data-collection side of DA-RT. Use when the user asks to draft or audit a pre-registration or PAP, choose a registry, decide what to lock versus leave exploratory, or handle a later deviation. Hypotheses and estimands come from hypothesis-building, post-hoc reporting from methods-reporting.

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Launches and configures the standalone presubmit CLI, an API-driven adversarial peer-review pipeline with 30-plus stages, including Red Team finders, Blue Team defence, verification cascade, legal pass, and copyedit, producing one consolidated report on disk. Verifies installation and API key, chooses the output location and smoke, standard, or custom mode, launches the run, and reports the result path. Use when the user asks to run presubmit, wants a deep unattended pre-submission audit, or needs a math or replication-code audit. Everyday self-audits go to paper-review-lite, and external refereeing to journal-review.

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Operates or audits a live Qualtrics survey through the v3 APIs without disrupting fielding. Covers publish gating, quotas, flow routing, embedded data, panel-vendor redirects, read-back verification, and a read-only pre-fielding audit. Use when publishing or patching a fielding instrument, when a quota counts without blocking, when configuring panel-vendor redirects or flow gates, or when auditing a survey before launch for consent gates, force-response completeness, quotas and redirects, anti-bot instrumentation, and language-arm symmetry.

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Organizes an author’s response to peer review. Extracts every referee and editor point, tags severity and type, orders the revision by dependency, flags defensible pushbacks as questions, and builds a numbered comment → response → location letter whose substantive answers the author writes. Use when the user has referee reports, a revise-and-resubmit decision, or an editor’s letter and wants to plan the revision, draft the response letter, or check that every point was addressed. The reviewer-side twin is journal-review.

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Scaffolds or audits a social-science replication package and evaluates the manuscript and archived research objects against FAIR principles. Scaffold mode writes the folder structure, README, master.R, figure-table crosswalk, codebook, LICENSE placeholder, and .gitignore; audit mode grades the package against a pre-release checklist and audits data, code, materials, identifiers, licenses, access restrictions, and availability statements. Use when setting up or repairing a package, checking one before submission, auditing FAIR compliance, or drafting availability statements. Adapted from Yusaku Horiuchi’s replication-package-guide.

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Plans a research project as a decision map that persists across sessions, resolving one ticket per session until the design is defensible and pre-registerable. The map lives as Markdown in the repository, literature sweeps run as parallel research tickets, and the resolved map compiles into a pre-analysis plan. Use at project start, when a design has more open decisions than one conversation can hold, or when planning restarts each session. Not for executing analyses or writing the paper.

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Designs survey instruments, covering question wording, scale construction and index reliability, flow and treatment placement, pretesting and soft launches, respondent burden with attention and speeding rules, sensitive questions and social-desirability bias, and treatment delivery. Use when the user writes or revises survey questions, chooses a scale, orders blocks, plans a pilot, or worries respondents will not answer honestly. Indirect measurement goes to list-experiment, multi-country instruments to cross-national-design, and live-survey operations to qualtrics-ops.

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Designs publication tables for social-science manuscripts. Covers whether a result belongs in a table at all, column order, row grouping and panels, decimal precision, standard-error and confidence-interval conventions, self-contained titles and notes, and code-generated output. Use when building or revising a regression, balance, descriptive, or robustness table, or when working with modelsummary, stargazer, gt, esttab, or booktabs. Finished tables go to figure-table-audit for end-stage QA.

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Advises on setting up and validating topic models for survey and experimental text. Covers the discovery-versus-measurement question, choosing STM, LDA, or BERTopic, preprocessing consequences, prevalence and content formulas, topic-count selection across coherence, exclusivity and FREX, held-out likelihood, and residuals, validation of topics against human judgment, robustness, and DA-RT-compliant reporting. Use when the user has open-ended responses or another corpus and asks what topics are present, how many topics to use, about STM, searchK, coherence, or FREX, or wants topic prevalence compared across treatment arms or countries. Fixed-codebook coding goes to text-classification.

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OCRs scanned or image-only corpora with vision-language models in four phases. Triage inventories the scans, identifies script and language, and shortlists models by script, hardware, and data constraints. Evaluate selects a system by measured CER or WER against ground truth, using born-digital twins, a second reader, and decision rules set in advance. Run builds the production pipeline. Clean removes model artifacts, audits what every cleaning rule deletes, corrects with rule-based and LLM passes, and records provenance. Use when choosing an OCR model for a corpus, measuring OCR accuracy, transcribing scans at scale, or correcting raw OCR. Born-digital documents with text layers go to doc-to-markdown; runs on Leiden's ALICE cluster add vlm-ocr-alice.

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Typesets a working paper or journal submission in house-style LaTeX from Markdown, Word (.docx), TeX, ODT, RTF, or HTML. Converts with pandoc, wraps the body in an EB Garamond template, builds the PDF with latexmk, and sets journal-specific spacing, page limits, anonymization, disclosures, and citation style. Use to format or convert a paper to LaTeX, make a working paper, or prepare a submission to a named journal.

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Advises on setting up LLM-based text classification as a validated measurement design. Covers codebook construction, learning-regime and model choice, prompt construction, validation against human coding with kappa and F1, hybrid human-LLM review, downstream measurement error, and reporting, plus a short resumable batch pattern with a rule-based baseline for repeated free text against a closed codebook. Use when the user wants to classify, code, or label text at scale. Category discovery goes to topic-modeling.

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Checks whether each claim in a manuscript is supported by the source it cites, reading the project's per-source Markdown knowledge base. Flags contradicted, unsupported, overclaimed, out-of-scope, and misattributed claims with verbatim source quotes. Runs citation-check first, and stops at a pre-flight gate when the knowledge base is missing, incomplete, or holds unconverted PDFs. Use to verify that a draft's claims match the sources it cites.

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Runs a multi-model orchestration workflow led by the session's Fable or Claude Opus model. Sends menial tool-calling work to Haiku subagents, judgment work to Opus subagents at an effort matched to each task, and high-stakes or fresh-perspective questions to a GPT-6 Astra Codex peer. Detects the lead from session context; `--lead fable` or `--lead opus` overrides. Use to orchestrate, delegate, fan out, get a decorrelated Codex opinion, run a blind Opus-Codex cross-check, or act as tech lead.

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Scaffolds or audits a research-project repository organized around its source library (original PDFs, tracked Markdown conversions, drop zone, bibliography, intake pipeline) plus the analysis, manuscript, and review folders the project type needs. Use when starting, structuring, or auditing a research repo or its sources folder. Single-PDF intake goes to process-source, replication packages to replication-package.

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Designs conjoint and factorial-vignette experiments, covering attribute architecture and randomization restrictions, effective-N power, treatment realism, the choice among AMCE, marginal-mean, and AMIE estimands, forced-choice versus rating designs, and PAP tiers. Use when the user is planning a conjoint, drafting or critiquing an attribute table, asking how many respondents or tasks are needed, whether to report AMCEs or marginal means, or how to test interactions. Reviewing an existing design goes to conjoint-diagnostics, cleaning the export to conjoint-cleaning.

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Reviews an existing conjoint study for threats to inference and returns severity-ranked findings on design integrity, estimation, measurement error, external validity, and interpretation, including the guardrail against reading an AMCE as majority preference. Use when the user asks whether a conjoint design or analysis holds up, has referee comments on a conjoint, or wants a second opinion on estimation or interpretation. New designs go to conjoint-design, reshaping to conjoint-cleaning.

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Designs multi-country survey experiments, covering case selection with a stated comparative logic, instrument localization and TRAPD translation, stimulus calibration, per-country power, and pooled versus per-country analysis with measurement-equivalence checks. Use when the user fields the same experiment in several countries, asks which countries to include, how to adapt an instrument without breaking comparability, whether to pool, or how large each country sample must be. Question wording goes to survey-design, reporting to methods-reporting, the study plan to pre-registration-writing.

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Generates 3-5 conceptually distinct approaches (Novel, Surprising, Diverse, Conventional) and holds for selection before implementing. Use before committing to an approach when a task has more than one non-obvious solution; --codex delegates the brainstorm to a fresh subagent.

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Opens a talk, module, paper, chapter, or referee report as a multi-session deliverable. Interviews the author, then scaffolds deliverable.yml, HANDOFF.md, the planning/ wiki, inbox/, and checks/. Use for deadline-driven work spanning sessions.

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Turns dictated captures in a deliverable's inbox/ into a proposed planning-wiki diff, classifying and tracing each statement; decisions need the author's assent. Use to intake notes or process the inbox.

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Generates 3-5 conceptually distinct approaches labeled Novel, Surprising, Diverse, or Conventional, and holds for the user's selection before implementing. The --codex mode runs the brainstorm on GPT-6 Astra via codex exec, then has Codex implement the selected approach. Use before committing to an approach when a creative, architectural, or analytical task has more than one non-obvious solution; use --codex when another model family should widen the range.

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