@monoes/monomindcli 2.15.3 → 2.15.5

package/org-skills/scientific-writing/assets/REPORT_FORMATTING_GUIDE.md

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+# Fail-Closed Report Formatting Guide
+
+This asset replaces the former LaTeX package and example report. The former template
+contained plausible-looking placeholder findings that could compile into a polished but
+unverified document. Use the Markdown scaffold and structured registries instead.
+
+## Safe default
+
+1. Generate a workspace with `scripts/scaffold_manuscript.py`.
+2. Keep the `DRAFT — NOT FOR SUBMISSION` banner while any placeholder or verification
+   gate remains.
+3. Draft in plain Markdown. Apply publisher formatting only after content verification.
+4. Treat the target journal's current author instructions and supplied template as
+   controlling.
+5. Re-run every local audit after formatting because conversion can change citations,
+   symbols, tables, and references.
+
+## Hierarchy
+
+- Use one document title and a predictable heading hierarchy.
+- Do not encode scientific meaning only with typography or color.
+- Keep terminology, abbreviations, units, and statistical notation consistent.
+- Preserve machine-readable identifiers and evidence markers until final rendering.
+- Never replace a missing value with an aesthetically plausible value.
+
+## Tables
+
+- Every cell must derive from a named evidence record.
+- Include units, analysis population, numerator and denominator where relevant.
+- Distinguish missing, not measured, not applicable, and zero.
+- Keep exact values consistent with prose and the numeric registry.
+- Use editable tables unless the venue explicitly requires another format.
+
+## Figures
+
+Figures are optional. This skill does not generate images. A retained figure must have:
+
+- a provenance record linking it to data, code, or a licensed source;
+- a caption that identifies the analysis population, units, uncertainty, and panels;
+- alt text that communicates the figure's purpose and principal pattern without adding
+  unsupported interpretation;
+- labels or patterns in addition to color;
+- a manual check at the final display size;
+- documented permissions and transformations for reused or adapted material.
+
+Never invent a figure, image, diagram, graphical abstract, or missing visual result.
+
+## Conversion gate
+
+Before producing a submission format, confirm:
+
+- placeholders are absent;
+- factual and numeric claims map to verified evidence IDs;
+- citations and reference identifiers pass local checks;
+- methods, results, units, denominators, and sample sizes agree;
+- authorship, CRediT roles, declarations, and AI use are human-approved;
+- confidentiality and target-journal policy reviews are complete;
+- reporting-guideline coverage was reviewed without treating it as a quality score.
+
+Formatting quality cannot make incomplete evidence submission-ready.

package/org-skills/scientific-writing/assets/manuscript_scaffold.md

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+# DRAFT — NOT FOR SUBMISSION
+
+This scaffold is intentionally incomplete. Remove this banner only after every local
+validator passes and accountable human authors approve the final document.
+
+# [[TODO: verified title]]
+
+## Abstract
+
+[[TODO: draft from verified methods and results only; preserve uncertainty and append
+claim and evidence markers to every factual or numeric assertion]]
+
+## Introduction
+
+[[TODO: establish context from verified sources, state the gap without exaggeration,
+and distinguish prior evidence from the present study]]
+
+## Methods
+
+[[TODO: report what was actually done, including design, materials or participants,
+outcomes, analysis intent, deviations, ethics status, and provenance]]
+
+## Results
+
+[[TODO: report all prespecified, exploratory, negative, null, and adverse findings that
+are supported by the evidence registries; keep denominators, units, and sample sizes
+consistent]]
+
+## Discussion
+
+[[TODO: interpret only supported results, compare with verified evidence, preserve
+alternative explanations, and state concrete limitations]]
+
+## Author contributions
+
+[[TODO: insert only the human-approved statement generated from the validated CRediT
+record]]
+
+## Funding
+
+[[TODO: insert a verified funding statement or a verified not-applicable statement]]
+
+## Competing interests
+
+[[TODO: insert a verified disclosure or a verified not-applicable statement]]
+
+## Ethics and consent
+
+[[TODO: insert only verified approvals, identifiers, consent language, or a verified
+not-applicable statement]]
+
+## Data and code availability
+
+[[TODO: state actual access conditions, restrictions, repositories, persistent
+identifiers, and applicable consent or policy limits]]
+
+## AI-use disclosure
+
+[[TODO: follow the current target-journal policy; identify tools and purposes when
+required; AI is not an author and humans remain accountable]]
+
+## References
+
+[[TODO: render only entries whose metadata and identifiers were verified against the
+opened source]]

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

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+# Authorship, CRediT, AI, and Confidentiality
+
+## Human authorship and accountability
+
+Use the current target-journal authorship policy. For biomedical work, ICMJE's four
+criteria require substantial contribution, drafting or critical revision, final
+approval, and accountability for all aspects of the work [SW-S01].
+
+AI systems and other nonhuman tools are not authors. They cannot approve the work,
+accept accountability, disclose conflicts, or manage copyright and license agreements
+[SW-S01, SW-S03].
+
+Do not:
+
+- add or remove an author without all required human approvals;
+- infer contributions from author order, affiliations, or email;
+- generate an author-contribution statement from incomplete records;
+- use CRediT roles as a substitute for the venue's authorship criteria.
+
+## CRediT
+
+CRediT is the ANSI/NISO Z39.104-2022 taxonomy of 14 contributor roles. The standard
+explicitly describes contributions and does not define authorship [SW-S19].
+
+Record only roles confirmed by the contributor and accountable author team:
+
+- Conceptualization
+- Data curation
+- Formal analysis
+- Funding acquisition
+- Investigation
+- Methodology
+- Project administration
+- Resources
+- Software
+- Supervision
+- Validation
+- Visualization
+- Writing – original draft
+- Writing – review & editing
+
+One person may have multiple roles; a project need not use every role. Non-author
+contributors may also receive appropriate credit and acknowledgment subject to consent
+and journal policy.
+
+## AI-use disclosure
+
+The January 2026 ICMJE Recommendations require transparency about which AI tool was
+used and for what purpose, place writing assistance in acknowledgments, and place AI
+used for data collection, analysis, or figure generation in Methods as applicable
+[SW-S01, SW-S02]. COPE's formal position likewise requires disclosure and keeps full
+responsibility with human authors [SW-S03].
+
+Journal and publisher rules differ and evolve. Check them at the time of use and again
+before submission. Record:
+
+- tool, provider, and version or access date;
+- purpose and affected stage;
+- whether output entered text, code, analysis, tables, or figures;
+- human verification performed;
+- disclosure locations required by the venue;
+- what material, if any, was sent outside the approved environment;
+- authorization and policy review for any restricted transfer.
+
+Do not fabricate an AI-use statement or claim that no AI was used. Obtain confirmation
+from the human authors.
+
+## Confidentiality boundary
+
+Do not send any of the following to an external service without explicit authorization
+and a documented policy review:
+
+- unpublished manuscripts or drafts;
+- peer-review or editorial material;
+- sensitive or restricted data;
+- protected health information or other personal data;
+- proprietary or contract-restricted content;
+- source documents, including full articles, reports, protocols, and datasets.
+
+Authorization must come from a person or body empowered to grant it and must be
+consistent with journal policy, consent, ethics approval, contracts, law, institutional
+policy, and data-use terms. Removing obvious names does not by itself make content safe.
+
+When authorization is absent or unclear, keep processing local and use only minimal
+metadata. This skill's bundled tools make no network calls and do not read environment
+variables or `.env` files.
+
+ICMJE treats submitted manuscripts as privileged communications and warns editors and
+reviewers not to upload them to AI systems where confidentiality cannot be assured
+without author permission [SW-S01]. JAMA provides a journal-policy example with the same
+confidentiality concern [SW-S24].
+
+## COPE status as of the research date
+
+COPE's 2017 Core Practices are historical: COPE states they were retired in 2024. As of
+2026-07-24, its website stated that a replacement Code of Conduct would be published in
+2026; do not present the archived Core Practices as current membership standards
+[SW-S04, SW-S05]. Continue to use current topic-specific COPE guidance and distinguish
+formal positions from discussion documents, webinars, comments, and case advice.
+
+## Validation
+
+Populate `authorship.json`, then run:
+
+```bash
+python3 scripts/validate_authorship.py authorship.json
+```
+
+The validator checks human authorship gates, exact CRediT role names, guarantors, final
+approval, hashed declarations, AI disclosure, and restricted external-transfer gates.
+It cannot adjudicate contribution disputes or determine who deserves authorship.

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

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+# Citation Integrity and Reference Formatting
+
+## Verification before style
+
+Formatting cannot repair an unverified reference. For every cited source:
+
+1. Open the source or authoritative bibliographic record.
+2. Confirm the cited proposition at a precise locator.
+3. Confirm authors or organization, title, publication state, venue, year, and version.
+4. Copy identifiers exactly from the verified record.
+5. Record corrections, retractions, expressions of concern, updates, and preprint status.
+6. Assign an evidence ID and human verification record.
+
+Do not cite a source that was not read for the proposition. Do not copy a DOI, PMID,
+quotation, or reference from generated text, a search snippet, or another article
+without verification. ICMJE assigns authors responsibility for reference accuracy and
+rejects AI-generated material as a primary source [SW-S01].
+
+## Quotations and paraphrases
+
+- Verify every quotation character-for-character and record a stable locator.
+- Preserve context, qualifications, and negation.
+- Mark changes, omissions, or translations according to venue policy.
+- Paraphrase from understanding, not by superficial word substitution.
+- Obtain permissions where copyright or license terms require them.
+- For personal communications or unpublished information, obtain required permission
+  and follow current journal policy [SW-S01].
+
+## Source choice
+
+Prefer the original source for a reported method, dataset, result, policy, or guideline.
+Use a review for synthesis when it actually supports the synthesized claim. Clearly
+identify preprints and other non-peer-reviewed versions. Check that a later correction
+or published version does not supersede the cited record.
+
+Do not use citation counts, venue prestige, recency, or a target percentage of recent
+references as a substitute for relevance and evidentiary fit.
+
+## Identifiers
+
+The local checker validates syntax and duplicates only. It does not resolve identifiers
+and cannot establish that an identifier belongs to the recorded work.
+
+Supported local checks include:
+
+- DOI;
+- PMID;
+- PMCID;
+- ISBN checksum;
+- HTTP or HTTPS URL shape;
+- duplicate normalized titles and identifiers.
+
+After the local check, a human must compare each identifier with the opened source.
+
+## NLM and journal styles
+
+For biomedical references, use *Citing Medicine* and NLM's sample references for the
+relevant source type [SW-S20, SW-S21]. These cover articles, books, datasets, software,
+and online material. The current target journal's instructions override generic style
+examples.
+
+For APA, AMA, Chicago, IEEE, ACS, Vancouver-derived, or publisher-specific styles:
+
+- use the current official manual or journal style;
+- render from verified structured metadata;
+- check author truncation, title case, journal abbreviation, version, date, locator,
+  and identifier rules;
+- inspect the rendered list manually after conversion.
+
+Do not invent a complete-looking example reference. Templates should use explicit
+fields or evidence IDs until verified metadata exists.
+
+## Citation audit
+
+Before submission:
+
+- every factual or numeric claim maps to verified evidence IDs;
+- each in-text citation maps to a source-manifest record;
+- every reference-list entry is cited unless the venue explicitly permits a
+  bibliography;
+- citation ordering and repeated citation behavior match the target style;
+- reused figures, tables, datasets, software, protocols, and standards are attributed;
+- direct quotations have locators and permissions where needed;
+- duplicate and malformed identifiers are resolved;
+- no retracted or corrected status is concealed.
+
+Run:
+
+```bash
+python3 scripts/audit_claims.py manuscript.md claims.csv source_manifest.json
+python3 scripts/check_references.py source_manifest.json
+```

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

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+# Local CLI Reference
+
+All bundled commands use only the Python standard library. They:
+
+- accept explicit UTF-8 JSON, CSV, or Markdown files;
+- reject symbolic-link inputs;
+- cap file size, records, fields, JSON nodes, and nesting;
+- make no network calls;
+- read no environment variables or `.env` files;
+- perform no dynamic evaluation or pickle loading;
+- report issue codes, IDs, and line numbers without echoing manuscript or source text.
+
+Run from the skill directory with Python 3.11 or newer.
+
+## Scaffold
+
+```bash
+python3 scripts/scaffold_manuscript.py \
+  --output-dir ./draft-workspace \
+  --document-id local-draft \
+  --study-design randomized_trial \
+  --guideline consort-2025
+```
+
+The output directory must not exist. The command never overwrites files. Generated
+documents are explicitly incomplete and not submission-ready.
+
+## Manifest validation
+
+```bash
+python3 scripts/validate_manifest.py manuscript_manifest.json --kind manuscript
+python3 scripts/validate_manifest.py source_manifest.json --kind source
+python3 scripts/validate_manifest.py source_manifest.json --kind source --require-verified
+```
+
+The validator checks structure, IDs, verification gates, confidentiality status, and
+required-statement status. It does not read files named inside the manifest.
+
+## Reporting-guideline routing and coverage
+
+```bash
+python3 scripts/select_reporting_guidelines.py select --study-design systematic_review
+python3 scripts/select_reporting_guidelines.py check reporting_coverage.json
+```
+
+Selection and coverage are non-scoring. Open the official guideline after selection.
+
+## Claim and citation audit
+
+```bash
+python3 scripts/audit_claims.py manuscript.md claims.csv source_manifest.json
+```
+
+Required CSV headers:
+
+```text
+claim_id,section,claim_kind,claim_text_sha256,evidence_ids,verification_status,uncertainty,analysis_intent
+```
+
+Separate multiple evidence IDs with semicolons in CSV. Use inline Markdown markers:
+
+```text
+[claim:C001] [evidence:E001,E002]
+```
+
+The audit also flags numeric content without a claim marker.
+
+## Numeric and methods-results consistency
+
+```bash
+python3 scripts/check_consistency.py consistency_manifest.json
+```
+
+The command checks duplicate concepts across sections, units, percentages against
+numerators and denominators, sample sizes, evidence IDs, declared methods, outcome
+mappings, and confirmatory or exploratory status.
+
+## Reference identifiers and duplicates
+
+```bash
+python3 scripts/check_references.py source_manifest.json
+```
+
+The command checks local syntax and duplicates for DOI, PMID, PMCID, ISBN, URL, and
+normalized title. It never resolves an identifier; a human must compare each value with
+the opened source.
+
+## Authorship and disclosure
+
+```bash
+python3 scripts/validate_authorship.py authorship.json
+```
+
+The command checks human authorship criteria, exact CRediT role names, corresponding
+author and guarantor IDs, final approval, hashed declarations, AI disclosure, human
+verification, journal-policy review, and authorization gates for restricted material.
+
+## Language, placeholder, and confidentiality lint
+
+```bash
+python3 scripts/lint_manuscript.py manuscript.md \
+  --manifest manuscript_manifest.json
+```
+
+Possible sensitive-content findings are review prompts, not a de-identification
+certificate. The linter intentionally fails on unresolved placeholders.
+
+## Exit behavior
+
+- exit `0`: no error-level findings;
+- exit `1`: invalid input or one or more error-level findings.
+
+Warnings still require human review. JSON output is deterministic for the same inputs.

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

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+# Evidence and Provenance Workflow
+
+## Core separation
+
+Drafting and evidence verification are different activities.
+
+- **Drafting** organizes language from already recorded evidence IDs. A draft may remain
+  incomplete and uncertain.
+- **Verification** requires an accountable human to open the source, confirm the exact
+  support and locator, check bibliographic metadata, and record who verified it and
+  when.
+- A fluent sentence is not evidence. Search snippets, generated summaries, memory, and
+  another paper's reference list are discovery aids, not verified support.
+
+## Registries
+
+The scaffold creates five linked records:
+
+1. `source_manifest.json` assigns each source an `E` ID and records identifiers,
+   location, confidentiality class, and verification state.
+2. `claims.csv` assigns each claim a `C` ID, stores a hash rather than raw claim text,
+   and maps the claim to one or more verified `E` IDs.
+3. `consistency_manifest.json` binds numeric facts, methods, outcomes, analysis intent,
+   units, denominators, sample sizes, and result locations.
+4. `authorship.json` records human authorship criteria, CRediT roles, accountability,
+   declarations, and AI use.
+5. `reporting_coverage.json` records high-level coverage without scoring or certifying
+   the manuscript.
+
+These registries contain metadata, not full source documents. Do not paste unpublished
+manuscripts, peer-review files, PHI, sensitive datasets, proprietary content, or source
+documents into them.
+
+## Claim markers
+
+Append machine-readable markers to every factual or numeric assertion while drafting:
+
+```text
+[claim:C001] [evidence:E001,E002]
+```
+
+An alternative citation marker is `[@E001]`. Keep the claim and evidence markers on the
+same line until the audit passes. A final publisher conversion may replace evidence IDs
+with rendered citations only after preserving an auditable mapping.
+
+## Verification procedure
+
+For each source:
+
+1. Open the authoritative source or record.
+2. Confirm title, author or organization, publication state, year, and identifiers.
+3. Record the exact supporting location, such as section, page, table, figure, or
+   registry field.
+4. Confirm that the source supports the claim's direction, population, intervention or
+   exposure, outcome, time point, and uncertainty.
+5. Record caveats, retractions, corrections, expressions of concern, or version status.
+6. Mark the source verified only after a named human completes the check.
+
+For each claim:
+
+1. Classify it as factual, numeric, method, result, interpretive, or declaration.
+2. Hash the normalized claim text and store the hash in `claims.csv`.
+3. Map it to verified evidence IDs.
+4. Record uncertainty and whether the analysis was confirmatory, exploratory,
+   descriptive, or not applicable.
+5. Keep unsupported or conflicting claims out of submission-ready prose. If useful,
+   retain them in a clearly marked unresolved-issues log.
+
+## Drafting gates
+
+Do not infer or complete missing:
+
+- citations, identifiers, quotations, or source locators;
+- data values, denominators, units, sample sizes, or statistical results;
+- methods, protocol details, analysis decisions, or deviations;
+- approvals, consent, registrations, author contributions, conflicts, funding, or
+  availability statements.
+
+Use explicit missing states. Preserve negative, null, adverse, unexpected, and
+inconclusive findings. Never convert absence of evidence into evidence of no effect.
+
+## Final audit
+
+Run:
+
+```bash
+python3 scripts/validate_manifest.py source_manifest.json --kind source --require-verified
+python3 scripts/audit_claims.py manuscript.md claims.csv source_manifest.json
+python3 scripts/check_consistency.py consistency_manifest.json
+python3 scripts/check_references.py source_manifest.json
+```
+
+Tool output contains IDs and line numbers, not manuscript or source text. A passing
+machine audit supports review; it does not replace human scientific judgment.

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

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+# Optional Figures and Tables
+
+Figures and tables are optional. Include a display only when it communicates verified
+evidence more clearly than prose and the target venue permits it. This skill does not
+generate images, schematics, graphical abstracts, or synthetic scientific visuals.
+
+## Provenance gate
+
+Each display needs a record containing:
+
+- stable display ID and version;
+- source data or evidence IDs;
+- code, query, or manual transformation used;
+- accountable creator and reviewer;
+- date generated or revised;
+- analysis population, exclusions, and sample size;
+- units, scales, denominators, and uncertainty definitions;
+- license, attribution, and permission status for reused material;
+- documented adjustments, cropping, compositing, or preprocessing.
+
+Do not recreate missing source data from a screenshot or published graphic. Do not
+alter an image in a way that hides, removes, duplicates, or misrepresents information.
+Retain original files and an audit trail.
+
+## Choosing a form
+
+Use:
+
+- prose for a small number of directly relevant values;
+- a table when exact values and multidimensional comparison matter;
+- a figure when pattern, distribution, relationship, sequence, or spatial information
+  matters.
+
+Avoid duplicating the same information in prose, a table, and a figure. There is no
+universal minimum, maximum, or display-per-word rule.
+
+## Tables
+
+Check:
+
+- title and notes define population, time point, analysis set, units, and abbreviations;
+- rows and columns preserve denominators and distinguish missing from zero;
+- percentages can be recomputed from the recorded numerator and denominator;
+- precision is consistent with the measurement and analysis;
+- uncertainty and statistical quantities are named, not implied by symbols alone;
+- values match the abstract, prose, figures, supplements, and consistency registry;
+- cells remain accessible as text rather than an image when the venue allows.
+
+## Figures
+
+Check:
+
+- axes, scales, transformations, units, and reference lines are explicit;
+- truncated or nonlinear scales are visible and justified;
+- individual observations or distributions are shown when scientifically appropriate;
+- uncertainty is defined;
+- group sizes and exclusions are available;
+- legends identify all encodings;
+- colors, shapes, line styles, labels, or patterns provide redundant cues;
+- image panels include scale and orientation information where relevant;
+- the final exported file matches current journal format and size instructions.
+
+Do not add significance stars or trend lines unless they map to a verified analysis.
+
+## Captions and alt text
+
+A caption should state what is shown, define panels and encodings, identify the analysis
+population, units, uncertainty, and relevant methods, and link to evidence IDs during
+drafting.
+
+Alt text should:
+
+- identify the display type and purpose;
+- summarize the principal visible pattern without adding a new conclusion;
+- describe axes, groups, direction, and uncertainty needed to understand the display;
+- avoid repeating the full caption or listing every data point;
+- be reviewed manually with the final display.
+
+Automated accessibility checks do not verify scientific correctness. Inspect contrast,
+color independence, reading order, label size, keyboard or screen-reader behavior where
+applicable, and legibility at final size.
+
+## Flow diagrams
+
+Use the current official flow-diagram resource for the selected guideline, such as
+CONSORT 2025 or PRISMA 2020 [SW-S07, SW-S10]. Populate it only from verified counts.
+Reconcile every branch and denominator with the methods, results, and registry.
+
+## Final manual review
+
+An accountable human should compare each display against source data and analysis
+output, inspect permissions and confidentiality, verify captions and alt text, and
+confirm the rendered export. Passing a file-format or consistency check does not certify
+the display.