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Generates California-compliant privilege logs for withheld or redacted discovery materials under CCP 2031.240. Use when the user mentions privilege log drafting, California privilege log, CCP 2031.240, attorney-client privilege logging, work product designation, Evid. Code 952/954, CCP 2018.030, redaction logging, meet-and-confer privilege disputes, waiver analysis, common interest doctrine, or asks for help documenting withheld documents. Also trigger on references to Hernandez v. Superior Court, Costco Wholesale, or Wellpoint.

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加州消费者隐私法（CCPA）和加州隐私权法（CPRA）合规顾问——企业门槛分析、消费者权利履行（访问、删除、更正、退出出售/共享、限制 SPI、ADMT 退出）、隐私通知起草、服务提供商与承包商与第三方分类、敏感个人信息（SPI）处理、数据最小化、退出机制（包括 GPC）、网络安全审计和风险评估（自 2026 年 1 月 1 日生效）、ADMT 义务（2026 年生效，期限 2027 年 1 月 1 日）、CPPA 执法（迪士尼 275 万美元、PlayOn 110 万美元、福特 37.5 万美元）、罚款敞口、GDPR 比较，以及面向在加州运营或面向加州居民的企业的差距评估。

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Build and adopt production AI agent infrastructure in 2026. Covers framework selection (LangGraph, CrewAI, AutoGen, MCP), orchestration patterns, evaluation, observability, memory systems, and tool use. Also covers the SOCIAL dimension: how to sell agent infrastructure internally, change management, measuring ROI, building trust in autonomous systems, and scaling adoption across teams. Activate on: "agent infrastructure", "agent framework comparison", "which agent framework", "sell AI tools internally", "agent adoption", "agent observability", "agent evaluation", "MCP architecture", "agentic mesh", "enterprise AI agents", "AI change management", "agent ROI". NOT for: building specific agents (use ai-engineer), designing agent behavior patterns (use agentic-patterns), prompt tuning (use prompt-engineer).

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Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST. Encodes Ensembl version stripping with GENCODE _PAR_Y preservation, the Ziemann 2016 Excel autocorrect debacle and Bruford 2020 HGNC renames (SEPT*->SEPTIN*, MARCH*->MARCHF*, MARC*->MTARC*, DEC1->DELEC1), OCT4/POU5F1 alias resolution, biomaRt archive endpoints for release pinning, the `filters` (plural) gotcha, MANE Select for clinical reporting, cross-species orthology via Ensembl Compara / OMA / OrthoDB, and tx2gene construction for tximport. Use when converting gene IDs across systems, handling renamed symbols, building tx2gene, pinning to a specific Ensembl release for reproducibility, or mapping cross-species orthologs.

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Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.

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Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart 2017), Cas9 cut-toxicity diagnostics, copy-number amplicon detection (Aguirre 2016 / Munoz 2016), bottleneck propagation through plasmid pool, infection, selection, and endpoint stages, MOI verification, and DepMap-style screen-quality scoring. Use when assessing screen quality before hit calling, deciding whether to repeat or rescue a screen, diagnosing low-confidence hits, choosing between MAGeCK / BAGEL2 / Chronos based on quality grade, picking a normalization strategy from QC signatures, or evaluating whether an in-vivo screen retained adequate library complexity.

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Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefaction-extrapolation (Chao & Jost 2012), asymptotic richness via Chao1/ACE/jackknife as a lower bound, Baselga turnover/nestedness partition with the Podani alternative as sensitivity check, mandatory Hellinger transformation before ordination (Legendre & Gallagher 2001), Faith PD and SES_MPD/SES_MNTD with explicit null-model choice, and Maire 2015 functional-diversity dimensionality optimization. Use when comparing diversity across sites with unequal sampling effort, picking the right richness estimator for singleton-heavy amplicon data, partitioning beta diversity into turnover vs nestedness, reporting Hill-number effective species counts rather than raw entropies, computing SES_MPD with explicit null-model justification, or deciding whether to apply standard metrics to compositional amplicon data. Not for clinical 16S microbiome diversity (see microbiome/diversity-analysis).

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Analyzes species-environment relationships with constrained ordination (CCA, RDA, db-RDA), variance partitioning, indicator species (indicspecies IndVal.g group-equalized), PERMANOVA paired MANDATORILY with PERMDISP (Anderson & Walsh 2013; dispersion confounds centroid tests), Joint Species Distribution Models (HMSC, sjSDM, gjam) with explicit rejection of "residual covariance equals biotic interaction", phylogenetic community ecology (SES_MPD/MNTD), trait-environment via RLQ + fourth-corner with corrected modeltype=6 (Dray 2014), bipartite network metrics (NODF, modularity) with curveball null (Strona 2014), and Mantel-test replacements (dbRDA, GDM) for spatial data. Use when testing how environmental gradients structure communities, identifying habitat indicator taxa, partitioning variance among predictors, deciding whether PERMANOVA significance is location vs dispersion, picking among HMSC/sjSDM/gjam, or replacing Mantel tests for landscape data.

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Designs and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers. Covers bottleneck math (250x cells/sgRNA requires ~25M cells implanted; impossible for most syngeneic models, forcing focused libraries), focused library design (Manguso 2017 Nature 547:413 immune screen; Chen 2015 tumor screens), CRISPR-StAR intrinsic-control screening (Uijttewaal 2025 Nat Biotechnol 43:1848), clonal-dynamics-limited detection, tumor-explant DNA recovery, syngeneic vs xenograft vs PDX considerations, and the relationship to downstream MAGeCK / drugZ analysis. Use when designing in vivo CRISPR screens for tumor / immune / metastasis biology, choosing focused vs genome-wide for animal models, addressing bottleneck-induced clonal collapse, picking the syngeneic / xenograft / PDX model, integrating in vivo with in vitro results, or applying CRISPR-StAR for animal experiments.

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Analyzes base-editing screens for variant function. Covers library design (Hanna 2021 ClinVar-scale CBE screen benchmarked on BRCA1/2, Cuella-Martin 2021 DDR saturation), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end; 4-7 for ABE7.10), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.

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Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, applies the Patel et al 2024 *Nat Biotechnol* failure-mode framework, and validates that normalization is applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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Prepares statistical reports for clinical trials following CONSORT 2025, SPIRIT 2025, ICH E9(R1) estimands, and FDA 2023 covariate adjustment guidance. Covers Table 1 generation, analysis populations (ITT/FAS/PP/Safety), the 5 ICH E9(R1) intercurrent-event strategies, MMRM under MAR (mmrm), reference-based MI (rbmi J2R/CR/CIR), Permutt tipping-point sensitivity, and Rubin's-rules vs frequentist variance debate. Use when preparing regulatory submissions, defining estimands, or implementing missing-data sensitivity analyses.

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Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data borrowing, EXNEX for basket trials, hierarchical models for safety AE (Berry-Berry), Bayesian platform trials (I-SPY 2, GBM AGILE, REMAP-CAP), and posterior probability stopping rules. Covers FDA Bayesian Devices Guidance (2010), FDA Bayesian Methodology in Drugs Draft (January 2026), BOIN Fit-for-Purpose qualification (December 2021), and Project Optimus dose-optimisation. Use when designing dose-finding studies, platform trials, or sensitivity analyses with informative priors.

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Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Decide when to order coronary artery calcium (CAC) scoring in a primary-prevention patient and interpret the result per the 2026 ACC/AHA multisociety dyslipidaemia guideline. Covers the Class 1 indication (men ≥40 / women ≥45, borderline / intermediate PREVENT-ASCVD risk, uncertainty about LLT), CAC score interpretation (0, 1–99, 100–299, ≥300, ≥1000), how CAC modifies LDL and non-HDL goals, when to repeat CAC, and pitfalls (incidental CAC on non-cardiac CT, radiation, cost). Use when a clinician asks should I order a CAC score, CAC indications, what does CAC 150 mean, treatment goals with CAC score, repeat CAC frequency, CAC in a smoker, CAC vs CCTA, is CAC useful in intermediate risk. Grounded in the 2026 ACC/AHA multisociety dyslipidaemia guideline.

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Work a primary-prevention patient through the 2026 ACC/AHA multisociety dyslipidaemia guideline CPR framework — Calculate (10-year and 30-year PREVENT-ASCVD), Classify (low / borderline / intermediate / high), Personalize (demographic, clinical, biomarker, and reproductive risk enhancers), and Reclassify (coronary artery calcium scoring where appropriate). Use when a clinician asks how to assess ASCVD risk for primary prevention, who needs a statin, borderline risk patient what to do, intermediate risk should I start a statin, risk enhancers to look for, premature family history of ASCVD how does it change risk, pregnancy-related risk factors, PCOS and cardiovascular risk. Grounded in the 2026 ACC/AHA multisociety dyslipidaemia guideline.

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Set absolute LDL-C, non-HDL-C, and ApoB treatment goals, PLUS percent LDL-C reduction, for a primary-prevention patient on lipid-lowering therapy per the re-introduced treatment goals in the 2026 ACC/AHA multisociety dyslipidaemia guideline. Covers goals by PREVENT-ASCVD category (low / borderline / intermediate / high), by CAC score, in severe hypercholesterolaemia / FH, in diabetes with multiple ASCVD risk factors, and the ApoB targets once LDL-C and non-HDL-C goals are met. Use when a clinician asks what LDL goal to aim for, LDL target for intermediate risk, non-HDL goal, ApoB target, dual goals on statin, patient at goal or not, how low should LDL go, statin not enough what next. Grounded in the 2026 ACC/AHA multisociety dyslipidaemia guideline.

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Synthesized reference notes from three US Government vehicle-safety sources: NHTSA Cybersecurity Best Practices for the Safety of Modern Vehicles (updated 2022, final), NHTSA Automated Driving Systems 2.0: A Vision for Safety (2017), and a 16-section selection of 49 CFR Part 571 (FMVSS) pinned at eCFR versioner date 2025-01-01. Use for voluntary vehicle cybersecurity practices, the ADS 2.0 twelve priority safety design elements, and FMVSS occupant protection, brakes/stability/lighting, and fuel/EV integrity requirements. Not ISO 26262, not ASPICE, not ISO/SAE 21434, not UNECE R155/R156, not SAE J3016, and not the full Part 571; the FMVSS material is a selection of vehicle-level minimum performance standards, not a process standard.

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Knowledge base from the NASA Schedule Management Handbook (2024 edition, Revision 2). Use for program/project schedule management of aerospace and large engineering efforts: the five sub-functions (Planning, Development, Assessment & Analysis, Maintenance & Control, Documentation & Communication); the Integrated Master Schedule (IMS) and the WBS/OBS/CBS breakdown structures; the Schedule Management Plan (SMP) and Basis of Estimate (BoE); Critical Path Method, logic, durations, float and margin; tiered schedule assessment (Requirements/Health/Basis checks, the Shock Test) and the Dimensions of Schedule Reliability; Schedule Risk Analysis (SRA), Integrated Cost-Schedule Risk Analysis (ICSRA), Monte Carlo, correlation, merge bias, and the Joint Confidence Level (JCL); baselining, replan vs. rebaseline, EVM schedule metrics (SPI, BEI, CEI, HMI, Earned Schedule, CPLI), and status/progress/forecast reporting. This is NASA's scheduling doctrine grounded in NPR 7120.5 and the GAO Schedule Assessment Guide. Thin on the underlying mechanics of CPM, statistics, and EVM (it points to companion handbooks); aerospace/space-flight-centric; anchored to the 2024 second edition.

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Knowledge base from the GAO Technology Readiness Assessment Guide (GAO-20-48G, 2020). Use for evaluating technology maturity in acquisition programs and projects: Technology Readiness Levels (TRL 1–9) and related scales (MRL, IRL), identifying Critical Technology Elements (CTEs), the five-step process for a high-quality TRA, the four characteristics of a reliable TRA (comprehensive, well-documented, credible, defensible), Technology Maturation Plans (TMPs), and using TRA results in knowledge-based, milestone decisions. Assessment/maturity oriented: it measures readiness and frames risk — it is not a full SE process model, cost-estimating, or schedule guide (see sibling packs for those).

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Knowledge base from MIL-HDBK-61B, the DoD Configuration Management (CM) guidance handbook (7 April 2020, cataloged with Change 1, 2025). Use for defense CM across the acquisition and sustainment life cycle: the five CM functions (planning, identification, control/change management, status accounting, verification & audit), the three configuration baselines (FBL/ABL/PBL) and FCD→ACD→PCD documentation, configuration items (CIs/HWCI/CSCI), change instruments (ECP/NOR/RFV), the CCB and Class I/II classification, CDCA/AA authority, FCA/PCA audits, data management and data rights (CDRL/DID, DFARS rights ladder, master/authoritative source), and tailoring CM by phase (EIA-649-1 R/T/NR matrix, Appendix C templates), plus digital-era CM (digital twin, viewpoints, MOSA). NOTE: 61B is advisory guidance that adopts and points to the SAE EIA-649 / EIA-649-1 / GEIA-HB-649 suite for the authoritative CM requirements — this pack names and describes that suite but does not reproduce its copyrighted requirement text. Thin on: the EIA-649 requirement clauses themselves, form-level detail (DD-form field instructions, full DID content), and non-DoD/commercial CM frameworks.

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Knowledge base from the OUSD(R&E) guidebook Implementing a MOSA in DoD Programs (Feb 2025). Use for the Modular Open Systems Approach as a DoD acquisition + design discipline: the statutory/regulatory basis (10 U.S.C. 4401–4403, FY2017/FY2021 NDAA, DFARS), the five OUSD(R&E) pillars, the plan→modularize→identify→define→standardize interface lifecycle, technical levers (WBS/MIL-STD-881F taxonomy, standards profiling, API-first software, COTS/cybersecurity), MOSA assessment metrics and tools (PART/OAAT/KOSS/SEAM/MAUT), technology-change and DMSMS management, roadmaps, MOSA across the six AAF pathways, and contracting/IP/data-rights mechanics. SCOPE LIMITS: this is U.S. DoD weapon-system acquisition policy, not a general open-architecture or interface-standards reference — it names standards (FACE, OMS, DISR) without reproducing them, is light on detailed engineering of any specific standard, and does not cover the underlying SE processes (use dau-se-guidebook / nasa-npr-7123) or general systems-engineering theory (use sebok).

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End-to-end playbook for creating a new NV oOS Pro toolkit under addons/pro/includes/tools/<toolkit> — folder layout, service layer, tool class conventions (canonical envelope, two-gate sanitisation, capability flags), ALL seven registration surfaces (central registry, admin Tools section, settings status map, both WP-CLI commands, schedule presets, workflow presets, SA Toolkit Manager), fixture/oracle testing with a standalone smoke harness, and the phpcs gotcha checklist. Use when asked to build a new Pro toolkit, add a toolkit to the plugin, scaffold toolkit tools, register toolkit presets/toggles, or debug why a new toolkit's tools or presets don't appear. First case study: food-beverage (F&B Management, 21 tools, 2026-10-08, 20/20 Check-totals oracle verified). Complements mcp-ai-wpoos-toolkit-audit (hardening existing toolkits) and mcp-ai-wpoos-test-suite (repair).

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