@monoes/monomindcli 2.15.3 → 2.15.4

package/org-skills/scientific-writing/references/imrad_structure.md

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+# Manuscript Structure and Consistency
+
+IMRAD is a useful default for many original-research reports, but the study design,
+reporting guideline, article type, and current journal instructions control the final
+structure [SW-S01, SW-S06].
+
+## Title and abstract
+
+The title should identify the work accurately without adding novelty, causality, design,
+or population claims that the manuscript does not support.
+
+Draft the abstract after the main text. Mirror, do not reinterpret:
+
+- objective or question;
+- design, setting, population or material, and key methods;
+- analysis population and prespecified primary result;
+- estimate, uncertainty, denominator, and harms where relevant;
+- conclusion limited to the reported evidence.
+
+Structured versus unstructured format is a venue decision. Do not apply a universal
+format. Any number in the abstract must match the same concept and analysis set in the
+main text and consistency registry.
+
+## Introduction
+
+Build a short evidence chain:
+
+1. verified context;
+2. what is known and uncertain;
+3. the specific gap;
+4. the objective, question, or prespecified hypothesis.
+
+Do not claim that no prior work exists unless a suitable search verifies that claim.
+Avoid previewing unsupported results or inflating significance.
+
+## Methods
+
+Methods should permit evaluation and, where feasible, reproduction. Cover the elements
+applicable to the design:
+
+- design, setting, dates, and protocol or registration;
+- participants, specimens, datasets, or source population;
+- eligibility, selection, sampling, exclusions, and analysis populations;
+- interventions, exposures, comparators, materials, instruments, and versions;
+- outcomes, predictors, thresholds, time points, and measurement methods;
+- bias controls, randomization, allocation, and masking where applicable;
+- sample-size rationale;
+- missing data, transformations, covariates, multiplicity, sensitivity analyses, and
+  statistical or computational methods;
+- confirmatory, exploratory, and descriptive status;
+- ethics, consent, privacy, data governance, and approvals only when verified;
+- data, code, materials, and protocol access conditions.
+
+Record deviations and timing. Never reconstruct a method from a result merely to make
+the paper appear consistent.
+
+## Results
+
+Follow the declared objectives and outcomes. Report:
+
+- participant, sample, or record flow;
+- exclusions, missingness, attrition, and analysis populations;
+- descriptive information needed for interpretation;
+- prespecified primary and secondary results;
+- estimates with units, denominators, sample sizes, and uncertainty;
+- exploratory, sensitivity, subgroup, negative, null, adverse, unexpected, and
+  inconclusive findings with correct labels;
+- protocol or analysis deviations that affect interpretation.
+
+Describe results before interpretation unless the venue combines Results and
+Discussion. Do not equate a threshold crossing with scientific or practical importance.
+
+## Discussion
+
+Start from the verified findings, then:
+
+- answer the objective at the supported level of certainty;
+- compare with verified prior evidence;
+- consider alternative explanations;
+- distinguish statistical, scientific, clinical, and practical interpretation;
+- explain limitations and likely consequences;
+- bound generalizability to the studied population, material, setting, and period;
+- identify implications without prescribing action beyond the evidence.
+
+Do not introduce new results, methods, approvals, or citations that bypass verification.
+
+## Declarations and end matter
+
+Treat each statement as data, not boilerplate:
+
+- author contributions and accountability;
+- acknowledgments and permissions;
+- funding and the funder's role;
+- competing interests;
+- ethics, consent, and registration;
+- data, code, materials, and protocol availability;
+- AI-use disclosure;
+- references, figure legends, tables, and supplements.
+
+Use verified or explicit not-applicable states. Never generate an approval identifier,
+grant number, registration, author role, conflict declaration, or availability promise.
+
+## Cross-section audit
+
+Before submission, compare:
+
+- objective ↔ outcome ↔ result ↔ conclusion;
+- methods ↔ results;
+- abstract ↔ main text ↔ tables ↔ figures ↔ supplement;
+- units, denominators, sample sizes, labels, and time points;
+- registration and protocol ↔ manuscript;
+- in-text citations ↔ source manifest ↔ reference list.
+
+Run `scripts/check_consistency.py` and complete a manual scientific review.

package/org-skills/scientific-writing/references/journal_policies.md

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+# Journal and Publisher Policy Review
+
+Generic guidance never overrides the target journal's current instructions.
+
+## Capture a dated policy record
+
+Before drafting and again before submission, record:
+
+- journal, article type, and policy URL;
+- date accessed;
+- word, abstract, reference, table, figure, and supplement limits;
+- required structure and reporting guideline;
+- registration, protocol, and analysis-plan requirements;
+- ethics, consent, participant privacy, and image requirements;
+- authorship, contributor, acknowledgment, and change-of-authorship rules;
+- funding, conflicts, and sponsor-role disclosures;
+- data, code, materials, and repository policies;
+- preprint, prior dissemination, duplicate submission, and copyright policies;
+- AI use by authors and any restrictions on external tools;
+- peer-review model and confidentiality;
+- file, accessibility, and submission-system requirements.
+
+Do not guess an absent policy. Ask the journal or leave the decision unresolved.
+
+## Official examples
+
+- JAMA's current Instructions for Authors illustrate article-type-specific requirements
+  and should be consulted directly for a JAMA submission [SW-S25].
+- JAMA's AI guidance illustrates author disclosure, human responsibility, and
+  confidentiality limits for peer review [SW-S24].
+- Nature Portfolio's reporting and availability policy illustrates venue requirements
+  for data, materials, code, protocols, restrictions, and access [SW-S22].
+- Nature Portfolio's authorship policy illustrates publisher-specific accountability
+  and contribution statements [SW-S23].
+- PLOS Biology's data policy illustrates how sharing expectations interact with
+  consent, privacy, legal, ethical, and sensitive-data restrictions [SW-S26].
+
+These are examples, not defaults for other journals. Publisher-level policy and
+journal-level instructions may both apply.
+
+## Submission review
+
+Perform a manual comparison against the live instructions:
+
+1. Select the exact article type.
+2. Confirm the latest reporting guideline and extensions.
+3. Verify every required statement from source records.
+4. Confirm whether checklists or flow diagrams must be uploaded.
+5. Confirm data, code, and materials deposits actually exist and are accessible as
+   stated.
+6. Confirm author order, corresponding author, CRediT roles, and approvals.
+7. Confirm AI-use disclosure wording and location with the human authors.
+8. Verify files, anonymization, accessibility, permissions, and metadata.
+9. Save the access date and policy URLs in the submission record.
+
+Passing local tools does not establish venue compliance.

package/org-skills/scientific-writing/references/professional_report_formatting.md

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+# Safe Formatting for Reports and Manuscripts
+
+## Content before presentation
+
+The former LaTeX style and demonstration report were removed. They could turn
+plausible-looking placeholder findings into a polished PDF. This version uses
+format-neutral Markdown and JSON/CSV registries so incompleteness remains visible.
+
+Do not format a draft as submission-ready while any verification gate is incomplete.
+Visual polish is not evidence.
+
+## Workflow
+
+1. Create a local scaffold.
+2. Draft and verify content in Markdown.
+3. Run manifest, claim, reference, consistency, authorship, coverage, and lint checks.
+4. Obtain accountable human approval.
+5. Copy the verified content into the current venue template.
+6. Re-run checks that remain applicable and inspect the rendered output manually.
+
+For a journal or conference, use its current author instructions and official template.
+For an institutional report or thesis, use the institution's controlled template.
+
+## Fail-closed placeholder policy
+
+Permitted draft markers are intentionally conspicuous, such as `[[TODO:...]]`. The
+language linter treats them as errors. Never replace an unresolved marker with generic
+boilerplate, a guessed number, a fabricated statement, or an invented citation.
+
+Keep:
+
+- `submission_ready` false;
+- the draft banner visible;
+- missing declaration statuses explicit;
+- human and confidentiality gates incomplete;
+
+until the underlying records are verified.
+
+## Headings and navigation
+
+- Use a single title and logical heading levels.
+- Preserve heading order when converting formats.
+- Include lists of tables or figures only when useful or required.
+- Use stable internal labels for tables, figures, appendices, and supplements.
+- Ensure generated bookmarks and reading order match the visible structure.
+
+## Typography and layout
+
+- Use the venue's prescribed font, spacing, margins, page size, and line numbering.
+- Do not use color, weight, or position as the only carrier of meaning.
+- Keep equations, symbols, units, subscripts, and superscripts intact through
+  conversion.
+- Check widows, orphans, clipped content, broken links, and misplaced floats manually.
+
+## Tables, figures, and accessibility
+
+Follow `figures_tables.md`. Verify alt text, captions, provenance, permissions, color
+independence, reading order, label legibility, and final-size rendering. Do not create a
+decorative visual simply to make a report appear complete.
+
+## References and declarations
+
+References must render from verified metadata. After conversion, inspect identifier
+links, special characters, author order, and citation order.
+
+Declarations must come from validated records. A style template must never supply a
+default ethics approval, consent statement, funding source, conflict statement, author
+contribution, data or code promise, or AI disclosure.
+
+## Archival handoff
+
+Retain:
+
+- the verified Markdown source;
+- the structured registries;
+- the exact venue template version;
+- conversion instructions and software versions;
+- the final rendered file;
+- validator outputs and human approval record.
+
+Do not archive sensitive source documents alongside a public manuscript package unless
+authorization, consent, law, contracts, and policy permit it.

package/org-skills/scientific-writing/references/reporting_guidelines.md

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+# Reporting-Guideline Selection and Coverage
+
+## Purpose and limits
+
+Reporting guidelines help authors report study design, conduct, analysis, and findings
+completely enough for appraisal. They do not make a study rigorous, replace a protocol,
+repair missing methods, appraise risk of bias, certify compliance, or predict acceptance.
+The bundled selector and coverage checker are deliberately non-scoring [SW-S06, SW-S12].
+
+Always open the current official statement, checklist, explanation-and-elaboration
+document, relevant extensions, and target-journal instructions. The bundled registry is
+a dated routing aid, not a copy of any official checklist.
+
+## Current major guidance as researched
+
+- **Randomized-trial results:** CONSORT 2025. The joint official site provides the
+  statement, checklist, expanded checklist, flow diagram, and explanation and
+  elaboration [SW-S07, SW-S08].
+- **Randomized-trial protocols:** SPIRIT 2025 and its participant-timeline resources
+  [SW-S07, SW-S09].
+- **Systematic reviews and meta-analyses:** PRISMA 2020. Choose relevant extensions,
+  such as protocol, scoping-review, search, or diagnostic-accuracy guidance, from the
+  official PRISMA and EQUATOR sites [SW-S10, SW-S06].
+- **Cohort, case-control, and cross-sectional studies:** STROBE and the applicable
+  design-specific checklist [SW-S11].
+- **Diagnostic-accuracy studies:** STARD 2015; add STARD-AI for an AI-centered
+  diagnostic-accuracy study [SW-S12, SW-S13].
+- **Clinical prediction models:** TRIPOD+AI 2024 covers regression and machine-learning
+  prediction-model studies and replaces TRIPOD 2015; add TRIPOD-LLM for biomedical or
+  healthcare LLM studies within its scope [SW-S14].
+- **Case reports:** CARE 2013, including consent-sensitive reporting [SW-S15].
+- **In vivo animal research:** ARRIVE 2.0, using both the Essential 10 and Recommended
+  Set as appropriate [SW-S16].
+- **Healthcare quality improvement:** SQUIRE 2.0 [SW-S17].
+- **Health economic evaluations:** CHEERS 2022 [SW-S18].
+- **Qualitative research:** use SRQR generally and verify whether COREQ or another
+  design-specific guideline is more appropriate through EQUATOR [SW-S06].
+
+For AI intervention trials or protocols, check CONSORT-AI or SPIRIT-AI in addition to
+the current parent statement. For routinely collected data, harms, equity, patient-
+reported outcomes, clusters, noninferiority, pilot studies, and other special designs,
+search EQUATOR for a current extension [SW-S06].
+
+## Selector
+
+Use the offline registry:
+
+```bash
+python3 scripts/select_reporting_guidelines.py select --study-design randomized_trial
+python3 scripts/select_reporting_guidelines.py select --study-design randomized_trial --protocol
+python3 scripts/select_reporting_guidelines.py select --study-design diagnostic_accuracy --ai
+python3 scripts/select_reporting_guidelines.py select --study-design prediction_model --ai --llm
+```
+
+The result is a candidate set. A human must confirm:
+
+- the actual design and article type;
+- whether a protocol or results report is being written;
+- every relevant extension;
+- current version and corrections;
+- target-journal requirements.
+
+If no local match exists, search the official EQUATOR library rather than forcing the
+nearest guideline.
+
+## Coverage record
+
+The bundled `coverage_topics` are original high-level prompts. They do not reproduce
+official item wording or numbering.
+
+For each topic, record:
+
+- `addressed`, with manuscript locations;
+- `not_applicable`, with a rationale;
+- `missing`.
+
+Then run:
+
+```bash
+python3 scripts/select_reporting_guidelines.py check reporting_coverage.json
+```
+
+A pass means every bundled topic has an allowed status and location or rationale. It
+does not mean every official checklist item is satisfied or well reported.
+
+## Workflow
+
+1. Select candidate guidance during planning.
+2. Open the official statement and explanation document.
+3. Record prospective items in the protocol, registry, or analysis plan where
+   applicable.
+4. Draft the manuscript from evidence and methods records.
+5. Complete the official checklist with actual manuscript locations.
+6. Record missing items honestly; do not invent information to fill them.
+7. Submit the official checklist or flow diagram if the journal requires it.
+8. Re-check guideline and journal versions immediately before submission.
+
+## Frequent errors
+
+- treating a checklist as a design-quality score;
+- claiming adherence when only a subset was reviewed;
+- using an outdated parent statement while overlooking a current update;
+- omitting a relevant extension;
+- writing a missing method into the paper as though it occurred;
+- checking boxes without recording manuscript locations;
+- assuming a journal endorsement means submission requirements are identical across
+  article types.

package/org-skills/scientific-writing/references/research_integrity_open_science.md

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+# Research Integrity and Responsible Open Science
+
+## Integrity principles
+
+The ALLEA 2023 Code frames research integrity around reliability, honesty, respect, and
+accountability across disciplines and research settings [SW-S27]. Apply those principles
+throughout drafting, not only at submission.
+
+- Preserve the original record and an audit trail.
+- Report methods, deviations, uncertainty, and findings honestly.
+- Correct material errors promptly and transparently.
+- Respect participants, communities, collaborators, animals, the environment, and
+  legitimate rights in knowledge and data.
+- Assign credit fairly and accept accountability.
+- Do not fabricate, falsify, plagiarize, selectively omit, or conceal provenance.
+
+If potential misconduct or a material error appears, preserve records and follow the
+institutional, funder, journal, and legal process. Do not investigate by exposing
+sensitive material to unapproved systems.
+
+## Open science with safeguards
+
+UNESCO's Recommendation supports accessible, inclusive, equitable, and sustainable open
+science while recognizing legitimate restrictions for confidentiality, personal
+information, intellectual property, threatened resources, and protected knowledge
+[SW-S28].
+
+For every data, code, materials, and protocol statement:
+
+1. Confirm ownership, consent, ethics terms, contracts, law, and repository policy.
+2. Identify what underlies the reported claims.
+3. Choose an appropriate repository and access model.
+4. Record versions, persistent identifiers, licenses, metadata, and retention.
+5. State restrictions and an actual access process.
+6. Verify that the deposited files match the analysis and do not expose restricted
+   information.
+
+Do not promise public availability merely because a template asks for it. "Available on
+request" must describe a real, authorized, sustainable process if the venue permits that
+form.
+
+## Prospective transparency
+
+Where applicable, record:
+
+- study registration;
+- protocol and amendments;
+- analysis plan and timing;
+- outcome and model definitions;
+- data-management and sharing plan;
+- materials, software, environment, and versions;
+- departures from prespecification.
+
+The Center for Open Science's TOP 2025 framework provides practices for registration,
+protocols, analysis plans, materials, data, code, reporting transparency, and
+verification [SW-S30]. These practices are flexible policy components, not a universal
+score for an individual manuscript.
+
+NIH's Data Management and Sharing Policy applies to covered NIH research and expects
+planning, budgeting, submission of a plan, and compliance with the approved plan
+[SW-S29]. Check the specific funder, award, institute, and effective requirements.
+
+## Reproducibility package
+
+When policy and rights permit, preserve:
+
+- immutable raw-data references rather than uncontrolled copies;
+- cleaned or analysis-ready data with provenance;
+- executable analysis code and environment information;
+- software and model versions;
+- randomization or seed handling where relevant;
+- machine-readable tables behind reported displays;
+- a mapping from outputs to manuscript claims;
+- checksums, releases, and persistent identifiers.
+
+Never share secrets, credentials, direct identifiers, restricted variables, proprietary
+source code, or licensed source documents in a public package.
+
+## Corrections and versions
+
+Before submission, check for corrected, retracted, superseded, or updated sources. After
+dissemination:
+
+- preserve the original version where policy requires;
+- describe what changed and why;
+- link corrections to the affected record;
+- update downstream data, code, tables, and claims;
+- notify the appropriate journal, repository, collaborators, and oversight bodies.
+
+Do not silently edit a scientific record in a way that hides a material change.
+
+## Negative and null findings
+
+Open science includes an accurate record of outcomes that do not support the preferred
+narrative. Preserve negative, null, adverse, failed, and inconclusive results when they
+are part of the study record. Describe their uncertainty and limitations; do not
+reinterpret them as proof of absence.