@pikaa-ai/pikaa 0.3.1 → 0.3.4

package/skills/peer-review/references/ethical_review_practice.md

@@ -1,233 +0,0 @@
-# Ethical and Confidential Peer Review
-
-Verified on **2026-07-23** against COPE, ICMJE, and illustrative publisher policies listed in `assets/source_ledger.csv`.
-
-COPE identifies peer review as one of its 10 Core Practices and states that the process should be transparently described and well managed, with policies for conflicts, appeals, and disputes. The target journal’s published process controls the individual assignment.
-
-## Role boundary
-
-This skill supports an accountable human preparing a review draft or structured assessment. It must not:
-
-- Claim to be the assigned reviewer, editor, journal, funder, or decision-maker
-- Submit a review or contact authors, editors, institutions, or third parties without authorization
-- Invent manuscript content, experiments, analyses, citations, reviewer identity, or editorial outcomes
-- Present generated text as an independently completed review
-- Investigate authors or search unpublished content outside the authorized process
-
-The editor decides the editorial outcome. The reviewer provides evidence-bounded advice within the requested scope.
-
-## Before accepting or starting
-
-COPE’s Ethical Guidelines for Peer Reviewers and ICMJE recommendations require reviewers to consider:
-
-### Competence
-
-- Accept only work for which the reviewer can provide a useful assessment.
-- State material subject-matter, methods, statistics, ethics, language, or domain limits.
-- Ask the editor for a specialist reviewer when a central issue exceeds competence.
-- Do not conceal limits by producing confident generic criticism.
-
-### Conflicts
-
-Disclose actual, potential, or perceived conflicts before proceeding. They can be:
-
-- Financial or commercial
-- Personal or family
-- Institutional
-- Recent collaboration, supervision, mentorship, or competition
-- Intellectual commitments or directly competing work
-- Political, religious, advocacy, or legal interests
-
-The journal decides whether a disclosed conflict permits review. If unresolved, stop. Do not accept merely to gain access to unpublished work.
-
-### Capacity and timeliness
-
-Accept only if the review can be completed within the agreed time. Tell the editor promptly if scope or timing changes.
-
-### Journal policy
-
-Record:
-
-- Review model and anonymity expectations
-- Whether co-review is allowed and how contributors are named
-- Confidentiality and retention requirements
-- Required author-facing and editor-only fields
-- AI and tool policy
-- Citation, image-integrity, data, ethics, and reporting expectations
-
-Journal practices differ. A policy from another publisher is an example, not authority for the target venue.
-
-Use `scripts/validate_review_intake.py` before substantive review.
-
-## Confidentiality and data handling
-
-An unpublished manuscript, its supplements, review comments, and editorial correspondence are privileged confidential material.
-
-### Default rule
-
-Keep processing local. Do not send, paste, upload, transcribe, summarize, or expose unpublished manuscript or review text to:
-
-- Public or external generative-AI systems
-- Search engines or web research tools
-- Citation, plagiarism, grammar, translation, or image services
-- Unapproved collaborators
-- Cloud storage or telemetry outside the authorized environment
-
-unless the publisher or author has authorized that specific use, the target venue permits it, and applicable privacy, contract, intellectual-property, and data-governance requirements are satisfied.
-
-Authorization to review is not automatically authorization to disclose material to a service. A tool’s promise not to train on data is not, by itself, authorization.
-
-The bundled CLIs:
-
-- Use only Python’s standard library
-- Read bounded local JSON, CSV, or Markdown
-- Make no network, model, image, subprocess, environment-variable, or dynamic-code calls
-- Emit identifiers, counts, rule codes, and line numbers rather than raw manuscript or review text
-- Refuse symlink inputs and implicit output overwrite
-
-They do not make an external service safe and do not authorize its use.
-
-### Assistance and co-review
-
-Obtain journal permission before sharing with a trainee or colleague. Record the contributor and acknowledge the contribution to the editor as required. The invited reviewer remains responsible for confidentiality and the submitted report.
-
-### No reuse
-
-Do not:
-
-- Appropriate ideas, methods, code, data, or language before publication
-- Use the material for model training, benchmarking, product improvement, or unrelated research
-- Build a private corpus of manuscripts or reviews
-- Retain content for convenience beyond policy
-
-### Retention and deletion
-
-After submitting or ending the review:
-
-1. Follow the target venue’s retention rule.
-2. Delete local manuscript and review copies when required.
-3. Empty derivative exports and temporary files within the authorized workspace.
-4. Retain only what policy requires.
-5. Record deletion or authorized retention without copying confidential content into the record.
-
-ICMJE recommends that reviewers not retain manuscripts for personal use and delete copies after review. Local law, publisher policy, or a documented investigation may impose a different rule; follow the controlling requirement.
-
-## AI and automated assistance
-
-ICMJE says reviewers must follow the journal’s AI policy or request permission before using AI, maintain confidentiality, disclose use, and remain responsible for output that may be incorrect, incomplete, or biased.
-
-For any permitted assistance:
-
-- Identify the tool, version, purpose, and material exposed
-- Use only the minimum necessary content
-- Keep an accountable human in control
-- Verify every statement, citation, calculation, and proposed comment
-- Disclose use exactly as the journal requires
-- Do not let a model create an autonomous review or editorial outcome
-
-If permission is absent, the policy is unclear, or confidentiality cannot be assured, do not use AI on the material. Local deterministic checks may still be possible if policy and authorization permit local file processing.
-
-Illustrative policies, not universal rules:
-
-- [Nature Portfolio](https://www.nature.com/nature-portfolio/editorial-policies/peer-review) asks reviewers not to upload manuscripts to generative-AI tools and asks for transparent declaration when AI supported claim evaluation.
-- [BMJ](https://authors.bmj.com/policies/ai-use) requires declaration of AI used for review-language assistance and prohibits placing unpublished material into publicly available tools when confidentiality cannot be guaranteed.
-- [JAMA Network](https://jamanetwork.com/journals/jama/fullarticle/2807956) states that entering manuscript, abstract, or review text into a chatbot or language model violates its confidentiality agreement and requires disclosure of other AI resource use.
-
-Always check the current target-venue policy.
-
-## Preparing the report
-
-COPE and ICMJE emphasize constructive, honest, polite, fair, and timely comments.
-
-### Evidence and proportionality
-
-- Anchor every consequential criticism to a location and reason.
-- Distinguish missing reporting from demonstrated methodological error.
-- Explain why the issue changes validity, interpretation, reproducibility, ethics, or reader understanding.
-- Request the least burdensome adequate remedy.
-- Label optional suggestions as optional.
-- Do not expand the study beyond its stated scope merely to satisfy reviewer preference.
-- Do not request citations to benefit the reviewer or associates.
-
-### Tone
-
-Critique the work, not the people. Avoid:
-
-- Insults, sarcasm, ridicule, threats, or speculation about competence or motives
-- Language policing unrelated to scientific clarity
-- Bias based on identity, institution, location, seniority, language, or reputation
-- Accusations when the evidence supports only a question or discrepancy
-- Vague commands such as “redo the statistics” or “needs more work”
-
-Use direct language without hostility:
-
-> “The analysis appears to treat three observations per participant as independent. Please define the analysis unit and account for within-participant dependence, or explain why independence is justified.”
-
-### Requests for additional work
-
-Request a new experiment or analysis only when it is necessary and proportionate to evaluate or support a central claim. State:
-
-- Which claim depends on it
-- Why existing evidence is insufficient
-- Whether a narrower claim, correction, sensitivity analysis, or limitation would be an adequate alternative
-
-Do not turn review into an opportunity to redesign the authors’ research program.
-
-## Separate communication channels
-
-### Comments to authors
-
-Include:
-
-- Neutral summary of the work actually reviewed
-- Specific strengths
-- Major comments affecting validity, interpretation, reproducibility, ethics, or central claims
-- Minor comments affecting clarity, consistency, figures, tables, citations, or reporting
-- Review limitations and unavailable materials when useful
-
-Do not include:
-
-- Reviewer identity when policy requires anonymity
-- Unnecessary personal information
-- Editor-only conflict details
-- Accusations or investigative instructions
-- An editorial outcome presented as decided
-
-### Confidential comments to editor
-
-Use only for matters that require a separate channel:
-
-- Reviewer conflicts or competence limits
-- Permission, confidentiality, or AI-use disclosures
-- Credible ethics, integrity, duplicate-publication, image, or security concerns
-- Reasons an issue cannot safely be raised directly with authors
-- Requests for specialist review
-
-Ordinary scientific criticism should not appear only in the editor channel. Do not write a harsher private review that contradicts the author-facing report. The bundled scaffold keeps these channels visibly separate.
-
-## Suspected integrity problems
-
-Reviewers identify concerns; they do not adjudicate misconduct.
-
-1. Preserve confidentiality.
-2. Record the exact location and observable discrepancy.
-3. Describe uncertainty and plausible benign explanations.
-4. Notify the editor through the designated confidential route.
-5. Do not contact authors, institutions, journals, funders, or media independently.
-6. Do not run external similarity, face-recognition, image, or data-search services on confidential material without authorization.
-7. Follow editor instructions and retain or delete evidence according to policy.
-
-Use “Figure 3 appears similar to Figure 5 after rotation; please assess under the journal’s image-integrity process,” not “the authors fabricated the data.”
-
-## Final ethical check
-
-- Authorization and role are documented.
-- Conflicts are resolved or disclosed.
-- Competence limits and specialist needs are stated.
-- Target-venue policy and review model are known.
-- No unauthorized person or service received confidential material.
-- AI or other assistance is permitted and disclosed.
-- Author and editor channels are separate.
-- Every criticism is specific, evidence-backed, proportionate, and professional.
-- No invented citation, analysis, experiment, or editorial outcome appears.
-- Deletion or authorized retention is planned.

package/skills/peer-review/references/reporting_standards.md

@@ -1,249 +0,0 @@
-# Reporting Guidelines and Domain Metadata Standards
-
-Verified against primary or official sources on **2026-07-23**. The dated evidence record is `assets/source_ledger.csv`; the machine-readable selector catalog is `assets/reporting_guidelines.json`.
-
-## What reporting guidelines do—and do not do
-
-A reporting guideline identifies information that should be reported so readers can understand and appraise a study. It is not, by itself:
-
-- A method for designing or conducting the study
-- A risk-of-bias tool
-- A statistical reanalysis
-- A measure of truth, importance, novelty, or manuscript merit
-- A publication recommendation
-
-Checklist completion must never be converted automatically into a quality score. A fully reported study can have serious design problems; an incompletely reported study may be impossible to assess. Record missing information as a reporting gap, then separately assess any design, conduct, analysis, reproducibility, or ethics concern using appropriate evidence and expertise.
-
-Use the guideline’s current statement together with its explanation and elaboration. Check applicable extensions and the target venue’s instructions. Do not copy checklist wording into a review when a specific, contextual comment is more useful.
-
-## Selection workflow
-
-1. Identify the **report kind**: results, protocol, abstract, or data release.
-2. Identify the **study design**, not merely the topic or journal section.
-3. Add cross-cutting features: AI intervention, diagnostic AI, routinely collected data, clustered design, qualitative interviews, and so on.
-4. Select the current base guideline and applicable extensions.
-5. Use the official checklist to record `reported`, `partly_reported`, `not_reported`, `not_applicable`, or `not_assessed`.
-6. Explain `not_applicable`; do not treat it as a defect.
-7. Keep reporting coverage separate from methodological appraisal.
-
-Run:
-
-```bash
-python3 scripts/select_reporting_guidelines.py \
-  assets/study_profile_template.json \
-  --coverage assets/reporting_checklist_template.csv
-```
-
-The bundled catalog is a dated aid, not a live registry. Consult the [EQUATOR Network](https://www.equator-network.org/) and official guideline site when the study type is unclear or a newer extension may apply.
-
-## Major current health-research guidelines
-
-### Randomized trial results — CONSORT 2025
-
-- Current statement: **CONSORT 2025**, published 14 April 2025
-- Structure: 30 main checklist items and a participant flow diagram
-- Supersedes: CONSORT 2010
-- Use for: reports of randomized trials
-- Review with: explanation and elaboration plus design/intervention extensions
-- Important boundary: the statement explicitly says it is not a quality assessment instrument
-
-Check registration, protocol and statistical analysis plan consistency, allocation, participant flow, outcomes and harms, effect estimates and uncertainty, protocol changes, data sharing, conflicts, and patient/public involvement where applicable.
-
-Official sources: [CONSORT–SPIRIT](https://www.consort-spirit.org/) and the [CONSORT 2025 statement](https://www.bmj.com/content/389/bmj-2024-081123).
-
-### Randomized trial protocols — SPIRIT 2025
-
-- Current statement: **SPIRIT 2025**, published 28 April 2025
-- Structure: 34 main checklist items and a participant timeline
-- Supersedes: SPIRIT 2013
-- Use for: randomized trial protocols
-
-Compare the protocol with registration, statistical analysis plan, ethics records, amendments, and any completed-trial report. Explicitly stated non-applicability with rationale is not missing reporting.
-
-Official sources: [CONSORT–SPIRIT](https://www.consort-spirit.org/) and the [SPIRIT 2025 statement](https://www.bmj.com/content/389/bmj-2024-081477).
-
-### Systematic reviews — PRISMA 2020
-
-- Current statement: **PRISMA 2020** (named 2020; published 2021)
-- Structure: 27 main items, expanded checklist, abstract checklist, and flow diagrams
-- Use for: completed systematic reviews, primarily reviews of intervention effects
-- Protocols: use PRISMA-P
-- Extensions: use the appropriate extension for scoping, diagnostic, individual-participant-data, network, equity, harms, or other specialized reviews
-
-PRISMA explicitly does not assess review conduct or methodological quality. Use appropriate methods and risk-of-bias tools separately.
-
-Official sources: [PRISMA 2020 resources](https://www.prisma-statement.org/prisma-2020) and the [primary statement](https://www.bmj.com/content/372/bmj.n71).
-
-### Observational studies — STROBE
-
-- Current base statement: **STROBE 2007**
-- Structure: 22 main items with cohort, case-control, cross-sectional, and combined checklists
-- Use for: reports of observational epidemiologic studies
-- Extensions: examples include RECORD for routinely collected health data, STREGA for genetic association studies, STROBE-MR, and domain-specific extensions
-
-STROBE helps identify whether selection, measurement, bias, confounding, missing data, sensitivity analyses, and generalizability are reported. It does not establish that those methods were adequate.
-
-Official source: [STROBE](https://www.strobe-statement.org/).
-
-### Diagnostic accuracy — STARD 2015
-
-- Current base statement: **STARD 2015**
-- Structure: 30 main items and a flow diagram
-- Use for: studies estimating diagnostic accuracy against a reference standard
-
-Separately assess risk of bias and applicability with a suitable tool such as the current QUADAS family when relevant. STARD’s official implementation guidance explicitly says not to use the reporting checklist as a design-quality tool.
-
-Official source: [STARD 2015](https://www.equator-network.org/reporting-guidelines/stard/).
-
-### AI-centered diagnostic accuracy — STARD-AI
-
-- Current statement: **STARD-AI 2025**
-- Published: 15 September 2025; an author correction was published 13 July 2026
-- Structure: 40 items, including 18 new or modified items relative to STARD 2015
-- Use for: AI-centered diagnostic accuracy studies, including suitable diagnostic classification tasks
-
-Check dataset practices, index-test specification, evaluation, algorithmic bias and fairness, applicability, and generalizability. If the primary aim is development or evaluation of a multivariable prediction model, use TRIPOD+AI instead.
-
-Official source: [STARD-AI](https://www.nature.com/articles/s41591-025-03953-8).
-
-### Clinical prediction models — TRIPOD+AI
-
-- Current statement: **TRIPOD+AI 2024**
-- Structure: 27 main items plus a 13-item abstract checklist
-- Replaces: TRIPOD 2015
-- Use for: development, evaluation, or updating of diagnostic or prognostic prediction models using regression or machine-learning methods
-
-Do not select it solely because software called “AI” appears in a paper. Select it when the study’s primary object is a prediction model. Relevant extensions include TRIPOD-Cluster, TRIPOD-SRMA, and TRIPOD-LLM.
-
-Official sources: [TRIPOD](https://www.tripod-statement.org/) and the [TRIPOD+AI statement](https://www.bmj.com/content/385/bmj-2023-078378).
-
-### Case reports — CARE
-
-- Current base checklist: **CARE 2013**
-- Explanation and elaboration/manual: 2017
-- Structure: 13 main items
-- Use for: clinical case reports
-
-Check timeline, diagnostic reasoning, interventions, outcomes, adverse events, patient perspective where available, informed consent, privacy, and venue requirements.
-
-Official source: [CARE checklist](https://www.care-statement.org/checklist).
-
-### In vivo animal research — ARRIVE 2.0
-
-- Current statement: **ARRIVE 2.0**, published July 2020
-- Structure: Essential 10 plus 11 Recommended Set items
-- Use for: research involving live animals across bioscience disciplines
-
-The Essential 10 are a minimum reporting set, not a ranking. Review study design, sample size, inclusion/exclusion, randomization, blinding, outcome measures, statistics, animal details, procedures, and results; also assess ethics, welfare, humane endpoints, adverse events, protocol registration, data access, and interests.
-
-Official source: [ARRIVE 2.0](https://arriveguidelines.org/arrive-guidelines).
-
-### Quality improvement — SQUIRE 2.0
-
-- Current statement: **SQUIRE 2.0**, published 2015
-- Structure: 18 main items
-- Use for: system-level work intended to improve healthcare quality, safety, value, or equity where methods seek to relate outcomes to the intervention
-
-SQUIRE states that every item should be considered, but not every element belongs in every manuscript. Attend to local context, rationale, intervention evolution, measures, analysis, ethics, unintended consequences, and sustainability.
-
-Official source: [SQUIRE 2.0](https://www.squire-statement.org/index.cfm?fuseaction=page.viewPage&pageID=471&nodeID=1).
-
-### Health economic evaluations — CHEERS 2022
-
-- Current statement: **CHEERS 2022**
-- Structure: 28 main items
-- Replaces: CHEERS 2013
-- Use for: economic evaluations of health interventions
-
-Assess perspective, comparators, time horizon, discounting, outcome and cost measurement, model assumptions, heterogeneity, distributional effects where applicable, uncertainty, engagement, funding, and conflicts. Use a separate critical-appraisal framework for methodological quality.
-
-Official source: [ISPOR CHEERS](https://www.ispor.org/heor-resources/good-practices/cheers).
-
-### Qualitative research — SRQR and COREQ
-
-- **SRQR**: broad qualitative research reporting standard
-- **COREQ**: 32-item checklist specifically for interviews and focus groups
-
-Select by methods, not by the presence of quotations. Review researcher reflexivity, sampling, context, data collection, analytic process, credibility, participant voice, ethics, and limitations without imposing one epistemology on all qualitative traditions.
-
-Official registry records: [SRQR](https://www.equator-network.org/reporting-guidelines/srqr) and [COREQ](https://www.equator-network.org/reporting-guidelines/coreq/).
-
-## AI extensions and overlap
-
-Use the guideline that matches the study’s primary design and claim:
-
-- Randomized trial of an AI intervention: CONSORT 2025 plus current CONSORT-AI guidance
-- Protocol for such a trial: SPIRIT 2025 plus current SPIRIT-AI guidance
-- AI diagnostic accuracy: STARD-AI
-- Prediction model development or performance evaluation: TRIPOD+AI
-- Biomedical large-language-model prediction or evaluation: check TRIPOD-LLM and design-specific guidance
-- Medical imaging AI: consider current modality guidance in addition to the design-specific base
-
-Multiple guidelines can apply, but do not create redundant demands. State which base and extension address each concern.
-
-## Domain metadata standards: verified legacy status
-
-These standards describe minimum experiment or repository metadata. They complement, rather than replace, study-design reporting and methodological appraisal.
-
-### MIAME and MINSEQE
-
-**Retain with qualification.** NCBI GEO’s page was last modified 8 July 2026 and still states that GEO submission procedures implement:
-
-- MIAME for microarray experiments
-- MINSEQE for next-generation/high-throughput sequencing experiments
-
-ArrayExpress/Annotare also continues to reference these standards. Verify the current repository’s fields, file formats, raw/processed data expectations, and accession requirements; do not rely on an old static project page alone.
-
-Official implementation source: [GEO and MIAME/MINSEQE](https://www.ncbi.nlm.nih.gov/geo/info/MIAME.html).
-
-### MIAPE
-
-**Retain as a modular current-qualified standard.** The HUPO Proteomics Standards Initiative lists released components with separate versions, including mass spectrometry, mass-spectrometry informatics, quantification, gel electrophoresis, gel informatics, chromatography, and capillary electrophoresis.
-
-Select only components relevant to the actual workflow and verify current repository expectations. Do not present “MIAPE” as one unversioned universal checklist.
-
-Official source: [HUPO-PSI MIAPE](https://www.psidev.info/miape).
-
-### MIFlowCyt
-
-**Retain with qualification.** ISAC continues to identify MIFlowCyt 1.0 as an ISAC recommendation for experiment overview, samples, instrumentation, and data analysis. Also check current FCS, gating, panel, controls, and FlowRepository requirements.
-
-Official source: [ISAC MIFlowCyt](https://isac-net.org/miflowcyt-2/).
-
-### MIAPPE
-
-**Use MIAPPE 1.2**, released October 2024, for plant phenotyping metadata. It remains compatible with 1.1; version 2.0 was still in early development on the verification date.
-
-Official source: [MIAPPE releases](https://www.miappe.org/releases).
-
-### MIGS and MIMS
-
-**Do not present standalone MIGS/MIMS as the current umbrella.** The Genomic Standards Consortium now organizes these legacy checklists within **MIxS** (Minimum Information about any Sequence), alongside newer checklists and environmental packages. Select the current MIxS release and applicable checklist/package.
-
-Official source: [GSC standards](https://www.gensc.org/pages/standards-intro.html).
-
-## Other study types
-
-The EQUATOR database contains hundreds of guidelines. Common additional choices include:
-
-- Protocols: design-specific protocol guidance
-- Routinely collected health data: RECORD
-- Clinical practice guidelines: RIGHT and AGREE reporting guidance
-- Surveys: design-appropriate survey reporting guidance
-- Implementation studies: current implementation-reporting guidance
-- Mixed methods: current mixed-methods guidance
-- Laboratory and omics studies: study-design reporting plus current repository metadata standards
-
-If no suitable guideline exists, say so. Do not force the nearest checklist or invent one.
-
-## Coverage language for reviews
-
-Use:
-
-> “Item 12 is not reported clearly enough to determine the analysis population. Please identify the included participants and reconcile this denominator with Figure 1.”
-
-Avoid:
-
-> “The manuscript scores 18/30 on CONSORT and is therefore low quality.”
-
-Report counts or item identifiers only as navigation aids. The local selector deliberately emits no percentage or merit score.

package/skills/peer-review/references/security_validation.md

@@ -1,75 +0,0 @@
-# Security Validation Record
-
-Validation date: **2026-07-23** (local project date).
-
-## Baseline
-
-The repository `SECURITY.md` entry recorded **10 findings** with maximum severity **CRITICAL**:
-
-- Cross-file environment-variable and network exfiltration
-- A multi-file collection/transmission chain
-- Environment harvesting in both schematic scripts
-- API-key transmission to an external model service
-- Full environment propagation to a subprocess
-- Repeated costly model/image operations
-- Mandatory external schematic/cross-skill behavior
-
-The affected files were:
-
-- Deleted: scripts/generate_schematic.py
-- Deleted: scripts/generate_schematic_ai.py
-- The former `SKILL.md`
-
-## Remediation
-
-- Deleted both external schematic scripts.
-- Removed credentials, environment access, `.env` loading, subprocess chaining, network requests, model calls, image generation, mandatory figures, and cross-skill calls.
-- Replaced them with bounded deterministic local JSON/CSV/Markdown validators and generators.
-- Added strict schemas, duplicate-key/header detection, size/row/cell limits, symlink rejection, private atomic output, and no implicit overwrite.
-- Added report minimization: IDs, counts, rule codes, and line numbers instead of manuscript/review prose.
-- Added AST tests that reject network libraries, executable serialization, dynamic code execution, and environment credential access.
-- Added confidentiality, no-reuse, authorization, conflict, competence, AI-policy, disclosure, and deletion/retention gates.
-
-## Validation results
-
-- Agent Skills reference validator: **PASS**
-- Dependency-free CLI help checks: **PASS**
-- Synthetic standard-library tests: **26 passed**
-- Explicit AST parse with bytecode disabled: **8 scripts parsed**
-- Bytecode artifacts: **0**
-- IDE lints: **0**
-- Documented local-path link test: **PASS**
-- Markdown link check: **PASS** (access-controlled HTTP 403 treated as reachable)
-- Direct behavioral security scan: **SAFE, 0 findings**
-- Pull-request gate with `--fail-on HIGH`: **PASS**
-  - CRITICAL: 0
-  - HIGH: 0
-  - LOW: 3
-
-## Residual LOW findings
-
-The final LLM-assisted pull-request scan reported:
-
-1. **Missing `allowed-tools` declaration** — informational. This field is optional under the Agent Skills specification. The compatibility and body explicitly constrain bundled tools to local standard-library processing with no network, model, image, credential, or environment access.
-2. **Broad description** — accepted as a scoped capability description. The mandatory authorization and venue-policy gate applies before confidential content is read, and the body limits all functions to peer-review assessment.
-3. **Bounded CSV/JSON processing** — defensive observation with “no action required” in the scanner output. Inputs are already limited to 4 MiB, 5,000 CSV rows, 12,000 characters per cell, and finite list sizes; tests cover oversize rejection.
-
-None of the LOW findings permits data transmission or credential access. No CRITICAL or HIGH issue remains.
-
-## Reproduction
-
-```bash
-PYTHONDONTWRITEBYTECODE=1 python3 -m unittest discover \
-  -s tests/peer-review -p "test_*.py" -v
-
-uv run skills-ref validate skills/peer-review
-
-uv run skill-scanner scan skills/peer-review --use-behavioral
-
-uv run python scan_pr_skills.py \
-  --fail-on HIGH \
-  --output /tmp/peer-review-pr-scan.md \
-  skills/peer-review
-```
-
-The repository-level `SECURITY.md` was intentionally not edited in this scoped refresh; its generated snapshot will update through the repository’s normal scan process.