@monoes/monomindcli 2.15.3 → 2.15.4

package/org-skills/hypothesis-generation/references/source_ledger.md

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+# Dated Source Ledger
+
+Verification and research cutoff: **2026-07-23**.
+
+Machine-readable ledger: `assets/source_ledger.csv`.
+
+## Search boundary
+
+Research used `parallel-cli` search against official or primary domains with focused queries for:
+
+- NIH rigor, reproducibility, and the 2026 replication initiative;
+- Cochrane PICO and the original well-built clinical-question article;
+- FINER’s attributed historical source and current interpretation;
+- Platt’s original strong-inference essay;
+- COS/OSF preregistration and Registered Reports;
+- SPIRIT 2025 and CONSORT 2025;
+- causal questions, counterfactuals, estimands, and bias;
+- negative controls, HARKing, multiplicity, reproducibility, and replication;
+- NIST/UNESCO responsible AI and primary evidence on output homogenization;
+- human, animal, biosafety, biosecurity, dual-use, data, and regulatory gates.
+
+Searches prioritized official domains and primary publications. Full-text extraction or search excerpts were used to verify titles, dates, versions, and relevant passages. This was a targeted skill refresh, not a systematic review, patent search, or proof of scientific novelty.
+
+## Core methodology sources
+
+### Question formulation
+
+- `SRC-COCHRANE-PICO` — current Cochrane Handbook Chapter 2. PICO is used for intervention-effect review questions, with objectives defined in advance and stakeholder input where appropriate.
+- `SRC-PICO-ORIGINAL` — Richardson et al., 1995, *The well-built clinical question*. Foundational four-part clinical-question article.
+- `SRC-FINER-1988` — Hulley and Cummings, *Designing Clinical Research*, first edition metadata (1988). It is the earliest FINER-attributed source located in this refresh.
+- `SRC-FINER-CURRENT` — Werner and Willis, 2023, current FINER interpretation.
+
+**Historical limitation:** the available targeted search confirmed the 1988 book’s bibliographic metadata and later attribution but did not establish the exact first printed use or coinage of the FINER mnemonic. The skill therefore does not claim that provenance as proven.
+
+### Multiple hypotheses and falsification
+
+- `SRC-PLATT-1964` — John R. Platt, “Strong Inference,” *Science* 146:347–353, DOI `10.1126/science.146.3642.347`.
+- `SRC-NEG-CONTROL` — Lipsitch, Tchetgen Tchetgen, and Cohen, 2010, negative controls for confounding and bias, DOI `10.1097/EDE.0b013e3181d61eeb`.
+- `SRC-HARKING` — Kerr, 1998, HARKing, DOI `10.1207/s15327957pspr0203_4`.
+- `SRC-ASA-PVALUE` — ASA statement: thresholds alone do not support scientific conclusions; p-values do not measure hypothesis truth or effect importance; full reporting is required.
+
+### Rigor, reproducibility, and replication
+
+- `SRC-NIH-RIGOR` — NIH guidance on scientific premise, rigorous design, relevant biological variables, authentication, and transparency.
+- `SRC-NIH-REPLICATION` — NIH’s agency-wide replication and reproducibility initiative, page reviewed June 22, 2026.
+- `SRC-NASEM-RR` — National Academies 2019 consensus report defining computational reproducibility and replicability with new data.
+- `SRC-TOP` — Transparency and Openness Promotion guidelines.
+- `SRC-NIH-DMS` — NIH Data Management and Sharing Policy.
+
+Open practices remain subject to consent, privacy, community governance, intellectual property, export control, and security restrictions.
+
+## Preregistration and intervention trials
+
+- `SRC-COS-PREREG` — preregistration separates planned from unplanned work; transparent exploration remains valuable.
+- `SRC-OSF-REG` — current OSF registration/preregistration implementation guidance.
+- `SRC-COS-RR` — Registered Reports and results-blind protocol review.
+- `SRC-SPIRIT-2025` — current 34-item randomized-trial protocol guideline; supersedes SPIRIT 2013.
+- `SRC-CONSORT-2025` — current 30-item randomized-trial result-reporting guideline, including open science, harms, outcomes, intervention details, and important changes.
+
+SPIRIT and CONSORT are reporting guidelines, not design-quality, ethics, regulatory, or efficacy certifications.
+
+## Causal inference and estimands
+
+- `SRC-WHATIF` — Hernán and Robins, *Causal Inference: What If*. The author page linked the latest revision found during verification.
+- `SRC-ICH-E9R1` — ICH E9(R1), defining the estimand as the precise treatment-effect target and aligning planning, design, analysis, sensitivity analysis, and interpretation.
+
+These sources ground the distinctions among target causal contrast, estimator, and estimate, and the explicit treatment of confounding, selection, collider, measurement, and intervention-definition assumptions.
+
+## Responsible AI
+
+- `SRC-NIST-GENAI` — NIST AI 600-1, covering confabulation, privacy, harmful bias/homogenization, information integrity, dangerous recommendations, and human–AI configuration.
+- `SRC-UNESCO-AI` — human rights, privacy, accountability, transparency, diversity, and human oversight.
+- `SRC-DOSHI-HAUSER` — Doshi and Hauser, 2024, DOI `10.1126/sciadv.adn5290`. In the studied story-writing task, AI-assisted outputs were more similar to one another while some individual creativity measures improved.
+
+The primary homogenization result is task-specific. The skill treats idea homogenization as a plausible risk, not a universal measured effect across scientific domains.
+
+## Ethics and oversight
+
+### Humans
+
+- `SRC-HHS-COMMON-RULE` — U.S. Common Rule/45 CFR 46 portal.
+- `SRC-BELMONT` — respect for persons, beneficence, and justice.
+- `SRC-HELSINKI` — World Medical Association Declaration of Helsinki, revised October 2024.
+
+An authorized IRB/REC or equivalent must determine applicability; the skill does not self-declare exemption.
+
+### Animals
+
+- `SRC-OLAW-PHS` — PHS Policy and IACUC/Assurance requirements for covered work.
+- `SRC-ARRIVE` — ARRIVE 2.0 reporting guidance.
+
+### Biosafety and dual use
+
+- `SRC-NIH-RSNA` — NIH Guidelines for research involving recombinant or synthetic nucleic acid molecules.
+- `SRC-NIH-BIOSEC` — current NIH biosafety/biosecurity portal.
+- `SRC-BMBL` — CDC/NIH BMBL sixth edition.
+- `SRC-WHO-LIFE` — WHO Global Guidance Framework for the Responsible Use of the Life Sciences.
+
+### U.S. dual-use transition status
+
+At the verification date:
+
+- `SRC-EO-14292` directed revision/replacement of the 2024 DURC/PEPP policy and pause/termination actions for covered dangerous gain-of-function research.
+- `SRC-NIH-NOT-25-112` stated the Executive Order superseded NIH’s 2024 implementation and rescinded NOT-OD-25-061.
+- `SRC-ASPR-DURC` still described the 2024 policy as awaiting revision or replacement and promised an update when the revised policy became available.
+
+This status is time-sensitive. Recheck current federal, funder, award, institutional, and jurisdiction-specific rules before any related work. Do not use this ledger as clearance.
+
+## Source-use rules
+
+1. Verify each citation and identifier against the live primary source before publication or registration.
+2. Recheck time-sensitive policy after the cutoff date.
+3. Link every scientific claim to evidence in `assets/evidence_ledger_template.csv`.
+4. Include challenging, null, and limitation evidence, not only support.
+5. Do not infer novelty from this source ledger; it documents the skill refresh, not a user’s research topic.
+6. Do not expose a sensitive research question in an external search query without authorization.

package/org-skills/hypothesis-generation/references/tool_reference.md

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+# Local Tool Reference
+
+## Runtime and safety model
+
+All bundled CLIs:
+
+- require Python 3.11+ standard library only;
+- read explicit local JSON, CSV, or Markdown paths;
+- reject URL-like paths, symlinks, wrong suffixes, oversized inputs, invalid UTF-8, and NUL bytes;
+- cap inputs at 2 MiB, CSV data at 1,000 rows, cells/Markdown lines at 8,000 characters, and JSON collections at bounded sizes;
+- reject duplicate JSON keys and require exact ordered CSV headers;
+- make no network, model, image, subprocess, credential, or environment-variable calls;
+- write only to an explicit existing local directory;
+- refuse implicit overwrite unless `--force` is given;
+- use private mode (`0600`) and atomic replacement for generated output.
+
+Reports contain identifiers, counts, rule codes, and line numbers rather than copying scientific prose where practical.
+
+## Exit codes
+
+- `0`: input was structurally valid; warnings or human-review gaps may remain.
+- `1`: input was parsed, but consistency or required-control errors were found.
+- `2`: malformed, unsafe, missing, oversized, or wrong-type input.
+
+No exit code means a hypothesis is true, novel, ethical, safe, feasible, supported, or selected.
+
+## 1. Hypothesis schema validator
+
+Asset: `assets/hypothesis_record_template.json`
+
+```bash
+python3 scripts/validate_hypothesis_schema.py local-record.json
+python3 scripts/validate_hypothesis_schema.py \
+  local-record.json -o local-validation.json
+```
+
+The exact top-level objects are:
+
+- observation;
+- research question;
+- hypotheses;
+- causal estimands;
+- predictions;
+- alternative explanations;
+- null hypotheses;
+- negative controls;
+- operationalizations;
+- analysis plan;
+- evidence/search link;
+- causal-bias risk register;
+- ethics/feasibility gates;
+- AI-use record.
+
+All hypothesis statuses must be `candidate`. Causal questions require at least one estimand. Cross-links among candidate, prediction, rival, measurement, analysis, control, and source IDs are checked.
+
+The validator does not read the evidence ledger, test measurements, appraise sources, or interpret results.
+
+## 2. Operationalization and measurement checklist
+
+Asset: `assets/operationalization_template.json`
+
+```bash
+python3 scripts/check_operationalization.py local-operationalization.json
+```
+
+Each measurement item records:
+
+- construct, operational definition, population/system, unit/categories, timing, and method completion;
+- variable role;
+- validity source IDs and applicability review;
+- reliability/repeatability;
+- calibration/quality control;
+- invariance/comparability;
+- masking;
+- missingness;
+- threshold/cut-point status;
+- limitations and human review.
+
+`planned`, `unresolved`, and `pending` states are reported as gaps, not converted to scores. A checklist cannot establish measurement validity.
+
+## 3. Prediction/rival matrix validator
+
+Asset: `assets/prediction_rival_matrix_template.csv`
+
+Exact header:
+
+```text
+prediction_id,hypothesis_id,rival_hypothesis_ids,conditions,observable,expected_if_focal,expected_if_rivals,falsifier,indeterminate_result,boundary_conditions,measurement_ids,negative_control_ids,analysis_ids,uncertainty
+```
+
+Use semicolons inside ID-list cells:
+
+```bash
+python3 scripts/validate_prediction_matrix.py local-matrix.csv
+python3 scripts/validate_prediction_matrix.py \
+  local-matrix.csv --record local-record.json
+```
+
+Checks include:
+
+- unique prediction IDs;
+- focal candidate not listed as its own rival;
+- declared focal and rival expectations are not lexically identical;
+- required falsifier, indeterminate result, boundary, measurement, control, analysis, and uncertainty fields;
+- optional cross-links to the hypothesis record.
+
+The validator cannot determine whether two predictions are scientifically distinguishable.
+
+## 4. Causal-versus-associational Markdown lint
+
+```bash
+python3 scripts/lint_causal_claims.py local-draft.md
+```
+
+Use one claim per annotated line:
+
+```markdown
+[claim:associational] Exposure X was associated with outcome Y in the observed sample.
+
+[claim:causal][estimand:E1][identification:observational_assumption_dependent][confounding:unresolved][selection:assessed][collider:assessed][reverse-causation:assessed] Under the stated assumptions, intervention X would reduce outcome Y.
+```
+
+Claim types:
+
+- `causal`
+- `associational`
+- `descriptive`
+- `predictive`
+- `mechanistic`
+
+Identification values:
+
+- `randomized`
+- `quasi_experimental`
+- `observational_assumption_dependent`
+- `mechanistic_experiment`
+- `other_assumption_dependent`
+
+Risk values:
+
+- `assessed`
+- `unresolved`
+- `not_applicable`
+
+The linter flags a bounded causal lexicon and annotation consistency. It is not a semantic classifier and will have false positives and false negatives.
+
+## 5. Falsification and negative-control checklist
+
+Asset: `assets/falsification_controls_template.json`
+
+```bash
+python3 scripts/check_falsification_controls.py local-controls.json
+python3 scripts/check_falsification_controls.py \
+  local-controls.json --record local-record.json
+```
+
+For each candidate it requires:
+
+- assumptions and boundary conditions;
+- a prediction-linked falsifier and assumption-failure checks;
+- at least one discriminating test with focal, rival, and indeterminate outcomes;
+- a linked null and interpretation limit;
+- controls including at least one negative-control type;
+- outcome paths for consistency, challenge, and neither/mixed;
+- human-review status.
+
+The checker does not validate that a negative control is biologically or causally appropriate.
+
+## 6. Evidence ledger and search-boundary audit
+
+Assets:
+
+- `assets/evidence_ledger_template.csv`
+- `assets/search_boundary_template.json`
+
+Exact evidence-ledger header:
+
+```text
+source_id,claim_ids,title,authors_or_organization,publication_date,source_type,identifier,url,accessed_on,relation,study_design_or_document_type,limitations,notes
+```
+
+```bash
+python3 scripts/audit_evidence_ledger.py \
+  local-evidence.csv local-search-boundary.json
+
+python3 scripts/audit_evidence_ledger.py \
+  local-evidence.csv local-search-boundary.json \
+  --record local-record.json
+```
+
+The audit checks:
+
+- exact schema and date/HTTPS/identifier formats;
+- unique source IDs;
+- source-to-claim links;
+- source-type and relation declarations;
+- dated search boundary, queries, limits, stop rule, and novelty status;
+- optional source, claim, and boundary links to a hypothesis record.
+
+It deliberately performs no network access. It cannot verify that a URL exists, a source says what is claimed, evidence is complete, or an idea is novel.
+
+Allowed novelty states:
+
+- `not_assessed`
+- `requires_specialist_review`
+- `supported_by_documented_comprehensive_search`
+
+The final state still requires a qualified human and supports only a bounded statement.
+
+## 7. Preregistration scaffold generator
+
+Asset: `assets/preregistration_scaffold_template.md`
+
+```bash
+python3 scripts/generate_preregistration_scaffold.py \
+  local-record.json -o local-preregistration.md
+```
+
+The generator:
+
+- first runs record validation;
+- refuses unresolved ethics/safety/feasibility gates;
+- renders all candidates and rivals without ranking;
+- escapes inserted text for inert Markdown;
+- marks the output as an unregistered draft;
+- leaves repository-, design-, oversight-, and sign-off fields for humans.
+
+It never uploads, registers, timestamps externally, or submits the result.
+
+## Suggested local sequence
+
+```bash
+python3 scripts/validate_hypothesis_schema.py local-record.json
+python3 scripts/check_operationalization.py local-operationalization.json
+python3 scripts/validate_prediction_matrix.py \
+  local-predictions.csv --record local-record.json
+python3 scripts/check_falsification_controls.py \
+  local-controls.json --record local-record.json
+python3 scripts/audit_evidence_ledger.py \
+  local-evidence.csv local-search-boundary.json --record local-record.json
+python3 scripts/lint_causal_claims.py local-draft.md
+python3 scripts/generate_preregistration_scaffold.py \
+  local-record.json -o local-preregistration.md
+```
+
+Qualified human review remains mandatory after every command.

package/org-skills/incident-command-playbook/LICENSE.txt

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+MIT License
+
+Copyright (c) 2025 Alireza Rezvani
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.