ARS Pipeline Architecture (v3.21.2)

Full pipeline view across stages × skills × artifacts × gates. Every completed stage requires a user-confirmation checkpoint (per academic-pipeline/SKILL.md and pipeline_state_machine.md); the diagrams below surface the decision-heavy checkpoints visually so they are easy to locate. The post-stage confirmation checkpoints at 2.5 and 4.5 are machine-verified first, then confirmed by the user — they are not skipped.

How to read

Flow diagram (§2): macro view — which stage follows which, where loops exist, where gates block. Every rectangle ends in a post-stage user confirmation (elided for readability); 🧑 markers call out the decision-heavy moments where the user chooses a branch.
Matrix (§3): the only place where (stage × skill × mode × data_level × artifacts × agents × gate) all co-exist. Use this when asking "what happens at Stage X?" The Gate column lists both machine checks and the user-confirmation checkpoint that closes the stage.
Data access flow (§4) and skill graph (§6): orthogonal views answering "who sees what" and "who depends on what" respectively.
Literature corpus flow (§5): producer/consumer view of the optional Material Passport literature_corpus[] input port (v3.6.4) and Phase 1 consumer integration (v3.6.5).
Quality gates (§7): zoom on the blocking checks — both machine-enforced and human-enforced. §7.1 classifies the repo's CI workflows by enforcement strength (blocking / advisory / administrative / post-push detection).
Timeline (§8): why the architecture looks the way it does — each release added one honesty primitive or a new contract.
Modes (§9): reference when composing a pipeline invocation.

The matrix alone is insufficient: it hides data-access hierarchy and skill dependency. The diagrams alone are insufficient: they hide artifact flow and per-stage agent detail. Together they are the full architecture.

1. Checkpoints (at-a-glance)

The pipeline has two classes of user checkpoint. Both require the user to confirm before the pipeline advances; they differ in what the user is actually deciding.

Decision-heavy checkpoints — the user chooses a branch or accepts a material decision:

#	Stage	What the user decides
🧑 1	1. RESEARCH	RQ Brief + Methodology Blueprint
🧑 2	2. WRITE	Outline approval before drafting
🧑 3	3. REVIEW	Editorial decision (Accept / Minor / Major / Reject)
🧑 4	3 → 4 Revision Coaching	Revision strategy (up to 8 Socratic rounds; user can skip)
🧑 5	4. REVISE	Revision changes confirmed
🧑 6	3'. RE-REVIEW	Verification-review decision
🧑 7	3' → 4' Residual Coaching	Residual-issue trade-offs (up to 5 Socratic rounds; user can skip)
🧑 8	4'. RE-REVISE	Content frozen — no further review loop
🧑 9	5. FINALIZE	Output format selection (MD / DOCX / LaTeX / PDF)
🧑 10	6. PROCESS SUMMARY	Language confirmation + collaboration quality review

Post-stage confirmation checkpoints — machine verification runs first; the user then acknowledges the integrity report before proceeding. These are also user-gated (per pipeline_state_machine.md — every stage ends in [checkpoint]), but the decision is "acknowledge the automated report" rather than "choose a branch":

#	Stage	What runs	What the user acknowledges
✓ 1	2.5 INTEGRITY	7-mode failure checklist (see §3 for exact taxonomy)	Integrity Report PASS/FAIL + any SUSPECTED flags
✓ 2	4.5 FINAL INTEGRITY	Deep Mode 2 check, zero-tolerance	Final Integrity Report PASS + populated Material Passport

2. Pipeline Flow

flowchart TD
    Start([User input])
    S1[1. RESEARCH<br/>🧑 deep-research<br/>👁 observer]
    S2[2. WRITE<br/>🧑 academic-paper<br/>👁 observer]
    G25{{2.5 INTEGRITY<br/>✓ 7-mode checklist<br/>then user ack<br/>— observer SKIPPED}}
    S3[3. REVIEW<br/>🧑 academic-paper-reviewer<br/>👁 observer]
    D3{Decision}
    RC[🧑 3→4 Revision<br/>Coaching<br/>max 8 rounds]
    S4[4. REVISE<br/>🧑 academic-paper<br/>👁 observer]
    S3p[3'. RE-REVIEW<br/>🧑<br/>👁 observer]
    D3p{Decision}
    RS[🧑 3'→4' Residual<br/>Coaching<br/>max 5 rounds]
    S4p[4'. RE-REVISE<br/>🧑 content frozen<br/>👁 observer]
    G45{{4.5 FINAL INTEGRITY<br/>✓ Mode 2 deep check<br/>then user ack<br/>— observer SKIPPED}}
    S5[5. FINALIZE<br/>🧑 format selection]
    S6[6. PROCESS SUMMARY<br/>🧑<br/>👁 observer<br/>pipeline-completion dispatch]
    End([Done])

    Start --> S1 --> S2 --> G25
    G25 -- PASS --> S3
    G25 -- FAIL, max 3 retries --> S2
    S3 --> D3
    D3 -- Accept --> G45
    D3 -- Minor / Major --> RC --> S4
    D3 -- Reject --> End
    S4 --> S3p --> D3p
    D3p -- Accept / Minor --> G45
    D3p -- Major --> RS --> S4p
    S4p --> G45
    G45 -- PASS --> S5
    G45 -- FAIL --> S4p
    S5 --> S6 --> End

    classDef humanGate fill:#fff1f0,stroke:#cf1322,stroke-width:3px
    classDef integrityGate fill:#fff4e6,stroke:#d48806,stroke-width:2px
    classDef coaching fill:#fcffe6,stroke:#7cb305,stroke-width:2px
    classDef decision fill:#f9f0ff,stroke:#9254de
    class S1,S2,S3,S4,S3p,S4p,S5,S6 humanGate
    class G25,G45 integrityGate
    class RC,RS coaching
    class D3,D3p decision

Legend:

Solid red (🧑) = decision-heavy human gate — the user chooses a branch or approves a material decision.
Solid orange (✓) = integrity gate — machine verification runs first, user then acknowledges the report. Not skipped.
Green = Socratic coaching sub-stage. User may engage or say "just fix it" to skip the dialogue.
👁 observer (v3.5.0) = collaboration_depth_agent dispatches at every FULL/SLIM checkpoint + pipeline completion. Never blocks. Advisory only. MANDATORY integrity gates (2.5 / 4.5) explicitly skip the observer so compliance checks are not diluted.
Data level (§3 column) = the data layer of that stage's output artifacts (a postcondition), not the owning skill's declared data_access_level (see §4 — e.g. academic-pipeline declares raw, while its gate stages consume unverified drafts and produce the verified artifacts their rows are labeled by).

3. Stage × Dimension Matrix

Stage	Skill / Mode	Data level	Artifact produced	Core agents	Gate / Checkpoint
1. RESEARCH	`deep-research` v2.12.1 (full / socratic / lit-review / three-way-scan / systematic-review / fact-check / review / quick)	RAW	RQ Brief; Methodology Blueprint; Annotated Bibliography (S2-verified); Synthesis Report; INSIGHT Collection. Search Strategy report includes PRE-SCREENED block (v3.6.5) when Material Passport carries `literature_corpus[]`	research_question_agent; research_architect_agent; 📚 bibliography_agent (v3.6.5+ corpus reader — corpus-first / search-fills-gap flow); source_verification_agent; synthesis_agent; meta_analysis_agent; editor_in_chief_agent; devils_advocate_agent; risk_of_bias_agent; ethics_review_agent; 🟦 socratic_mentor_agent (v3.5.1 reading-check probe layer, opt-in); report_compiler_agent; monitoring_agent (13 agents); 👁 collaboration_depth_agent (v3.5.0, advisory)	🧑 Decision-heavy checkpoint: user confirms RQ brief + methodology. Machine checks: S2 API Tier-0 verification (Levenshtein ≥ 0.70); evidence hierarchy graded; anti-sycophancy on DA (score 1-5, concede only ≥ 4); corpus-first flow with 4 Iron Rules + F3/F4 provenance reporting (v3.6.5) when corpus present. 👁 Observer runs post-checkpoint; never blocks
2. WRITE	`academic-paper` v3.3.1 (full / plan / outline-only / lit-review / revision-coach / abstract-only / citation-check / disclosure / format-convert / revision)	REDACTED	Paper Configuration Record; Outline; Argument Map; Draft Text; Bilingual Abstract; Figures + Captions; Citation List. Literature Search Report includes PRE-SCREENED block (v3.6.5) when Material Passport carries `literature_corpus[]`; merged `final_included` set feeds the Literature Matrix and Research Gap Identification	12-agent pipeline: intake_agent; 📚 literature_strategist_agent (v3.6.5+ corpus reader — corpus-first / search-fills-gap flow); structure_architect_agent; argument_builder_agent; draft_writer_agent; citation_compliance_agent; abstract_bilingual_agent; peer_reviewer_agent; formatter_agent; socratic_mentor_agent; visualization_agent; revision_coach_agent; 👁 collaboration_depth_agent (v3.5.0, advisory)	🧑 Decision-heavy checkpoint: outline approved before drafting. Machine checks: anti-leakage protocol (unsupported fill → `[MATERIAL GAP]`); VLM figure verification (10-pt APA checklist, max 2 refinements); style calibration vs user voice; Stage 2 parallelization (Phase 1 + visualization after outline); corpus-first flow with 4 Iron Rules + F3/F4 provenance reporting (v3.6.5) when corpus present. 👁 Observer runs post-checkpoint; never blocks
2.5 INTEGRITY	`academic-pipeline` v3.21.2 (gate)	VERIFIED_ONLY	Material Passport (Schema 9, required) + `repro_lock` (v3.3.5, declared — populated or `null`); Claim Verification Report (pre-review sampling: #549 risk-stratified — 100% HIGH-IMPACT + 10% random sentinel, min(10, total) — per `claim_verification_protocol.md`); Data Provenance Audit	integrity_verification_agent; state_tracker_agent; pipeline_orchestrator_agent. 👁 collaboration_depth_agent: SKIPPED (MANDATORY gate — observer dilution explicitly prevented)	✓ Integrity gate + user ack. 7-mode AI failure checklist (Lu 2026, canonical order per `ai_research_failure_modes.md`): M1 implementation bug passing AI self-review; M2 hallucinated citation; M3 hallucinated experimental result; M4 shortcut reliance; M5 implementation bug reframed as novel insight; M6 methodology fabrication; M7 frame-lock at early pipeline stage. Pre-review claim sampling mode. FAIL → fix + re-verify (max 3 rounds)
3. REVIEW	`academic-paper-reviewer` v1.11.1 (full / guided / quick / methodology-focus / calibration)	VERIFIED_ONLY	First-round review package (per `academic-paper-reviewer/SKILL.md`): 5 review reports (Journal-Fit Reviewer + R1 methodology + R2 domain + R3 interdisciplinary + Devil's Advocate) + Editorial Decision (Accept / Minor / Major / Reject) + Revision Roadmap. Schema 13.2 Sprint Contract (`shared/sprint_contract.schema.json`) is required for `full` and `methodology-focus` modes (other modes reserved with pre-v3.6.2 behaviour).	field_analyst_agent (auto-detects domain, configures 3 field-adaptive reviewers); eic_agent; methodology_reviewer_agent; domain_reviewer_agent; perspective_reviewer_agent; devils_advocate_reviewer_agent; 🔒 editorial_synthesizer_agent (role-scoped three-step mechanical protocol + forbidden-ops list) (7 agents); 👁 collaboration_depth_agent (v3.5.0, advisory)	🧑 Decision-heavy checkpoint: user reviews editorial decision. Machine checks: concession threshold protocol (DA rebuttal scored 1-5, no concede below 4); attack intensity preserved through revisions; cross-model DA critique (optional, `ARS_CROSS_MODEL` env); read-only constraint (no new claims). Sprint Contract two-phase protocol: each reviewer runs paper-content-blind Phase 1 (eligible-dimension trigger commitments) then paper-visible Phase 2 via `<phase1_output>`; `check_phase_conformance.py` validates the boundary and the synthesizer applies two-stage eligible-seat arithmetic. 👁 Observer runs post-checkpoint; never blocks
3 → 4 Revision Coaching	`academic-paper-reviewer` (Journal-Fit Reviewer Socratic sub-stage)	VERIFIED_ONLY	Revision strategy dialogue (not an artifact handed forward; feeds Stage 4 revision plan)	eic_agent	🧑 Decision-heavy checkpoint: Socratic dialogue with the Journal-Fit Reviewer (max 8 rounds). User may say "just fix it for me" to skip. Source: `two_stage_review_protocol.md`
4. REVISE	`academic-paper` v3.3.1 (revision / revision-coach)	REDACTED	Point-by-Point Response; Revised Draft; Delta Report (what changed + why)	revision_coach_agent (v3.3 Socratic mode); draft_writer_agent (re-entry); argument_builder_agent (if structural); 👁 collaboration_depth_agent (v3.5.0, advisory)	🧑 Decision-heavy checkpoint: user confirms changes. The orchestrator performs a narrative, evidence-anchored comparison per named criterion; unresolved decision-bearing regressions trigger review and changed criteria become `NOT_COMPARABLE`. No numerical delta or typed machine trajectory is currently emitted. 👁 Observer runs post-checkpoint; never blocks
3'. RE-REVIEW	`academic-paper-reviewer` v1.11.1 (re-review — the default; a user-requested fresh full review at 3' dispatches full mode instead)	VERIFIED_ONLY	Verification package (re-review mode, per the spec in `academic-paper-reviewer/SKILL.md`): Revision response checklist + residual issues list + new Decision (Accept / Minor / Major) + R&R Traceability Matrix (Schema 11) with Author's Claim + Verified? columns. Fresh full review at 3' emits the normal full-review package instead (no R&R matrix)	Contract-governed re-review dispatch: orchestrating layer + three sequential fenced calls (Phase 1/2A use frozen-card routed personas; Phase 2B is one dedicated integration call; neither loads the first-round `eic_agent` / `editorial_synthesizer_agent` files), followed by the mandatory synthesis checker. Round-1 cards are reused and field_analyst_agent is NOT re-run except the protocol's visible regeneration fallback; a user-requested fresh full review at 3' runs full mode instead. 👁 collaboration_depth_agent (v3.5.0, advisory)	🧑 Decision-heavy checkpoint: user reviews verification decision. Hard cap: max 1 RE-REVISE round; 2 revision loops total across Stages 4 + 4'. Major outcome at 3' → Residual Coaching → Stage 4'. 👁 Observer runs post-checkpoint; never blocks
3' → 4' Residual Coaching	`academic-paper-reviewer` (Journal-Fit Reviewer Socratic sub-stage)	VERIFIED_ONLY	Residual-issue dialogue	eic_agent	🧑 Decision-heavy checkpoint: Socratic dialogue on trade-offs for residual issues (max 5 rounds). User may skip. Source: `two_stage_review_protocol.md`
4'. RE-REVISE	`academic-paper` v3.3.1 (revision)	REDACTED	Final Revised Draft (terminal; advances to 4.5)	draft_writer_agent; revision_coach_agent; 👁 collaboration_depth_agent (v3.5.0, advisory)	🧑 Decision-heavy checkpoint: user confirms content frozen. No further review loop permitted. 👁 Observer runs post-checkpoint; never blocks
4.5 FINAL INTEGRITY	`academic-pipeline` v3.21.2 (gate)	VERIFIED_ONLY	Updated Material Passport (`verification_status: VERIFIED`) + `repro_lock` declared — populated or explicit `null` (honest opt-out); Claim Verification Report (final-check mode: 100% of E1 registered claims; semantic extraction completeness unknown per `claim_verification_protocol.md`)	integrity_verification_agent (deeper re-run of 7 modes); state_tracker_agent. 👁 collaboration_depth_agent: SKIPPED (MANDATORY gate — observer dilution explicitly prevented)	✓ Integrity gate + user ack. Zero named gate defects within the registered/sampled populations; no skip permitted. Any mode SUSPECTED at 2.5 must be CLEAR or user-Overridden by 4.5. `repro_lock` is not read by the integrity gate at runtime (per `artifact_reproducibility_pattern.md`); if populated, `stochasticity_declaration` must be verbatim and is validated by the standalone `check_repro_lock.py` — this is post-hoc documentation, not a runtime block or global correctness certificate
4→5 CLAIM-AUDIT (v3.8, opt-in via `ARS_CLAIM_AUDIT=1`)	`academic-pipeline` v3.21.2 (gate)	VERIFIED_ONLY	`claim_audit_results[]` + `claim_drifts[]` + `uncited_assertions[]` + `constraint_violations[]` + `audit_sampling_summaries[]` aggregates; reads `claim_intent_manifests[]` (writer-side pre-commitment baseline). Emits 5 HIGH-WARN annotation classes consumed by Stage 5 formatter REFUSE rules 6-10	claim_ref_alignment_audit_agent (Stage 4→5 dispatch slot, after v3.7.1 cite finalizer, before formatter hard gate)	✓ Audit gate (default OFF for v3.8.0). Per-citation LLM-as-judge against retrieved excerpt; 8-row finalizer matrix discriminates paywall (LOW-WARN) / fabricated (HIGH-WARN) / anchorless (HIGH-WARN) / audit_tool_failure (MED-WARN) via `ref_retrieval_method`. Calibration runner (`scripts/test_claim_audit_calibration.py`) gates with FNR<0.15 + FPR<0.10 on the shipped 20-tuple gold set. Spec: `docs/design/2026-05-15-issue-103-claim-alignment-audit-spec.md`
5. FINALIZE	`academic-paper` v3.3.1 (format-convert / disclosure)	VERIFIED_ONLY	Publication-ready MD; DOCX (Pandoc, if available); LaTeX (user confirms); PDF (tectonic); default venue AI applicability/status bundle (`REQUIRED` / `ACTION_ONLY` / `NOT_REQUIRED` / `UNKNOWN` plus typed halt) or policy-anchor-specific render	formatter_agent	🧑 Decision-heavy checkpoint: user selects format before render. The disclosure output must match the selected venue or policy anchor (15-entry venue database: ICLR / NeurIPS / Nature / Science / ACL / EMNLP + medical-publishing targets incl. ICMJE, NEJM, The Lancet, JAMA, BMJ, PLOS, Frontiers, and two Chinese-language policy targets — one publisher-wide and one journal; see `venue_disclosure_policies.md`). v3.8 terminal hard gate (formatter_agent REFUSE rules 6-10) refuses output on any unresolved `[HIGH-WARN-CLAIM-NOT-SUPPORTED]` / `[HIGH-WARN-NEGATIVE-CONSTRAINT-VIOLATION]` / `[HIGH-WARN-FABRICATED-REFERENCE]` / `[HIGH-WARN-CLAIM-AUDIT-ANCHORLESS]` / `[HIGH-WARN-CONSTRAINT-VIOLATION-UNCITED]` annotation when `ARS_CLAIM_AUDIT=1` was set upstream. v3.10 rule 11 refuses on any `severity=HIGH-BLOCK` terminal-policy token (generic; co-emitted by the finalizer under a strict `terminal_policies` mode). v3.11 rule 12 (#182) refuses on a `lookup_verified == false` citation-existence row ONLY under `terminal_policies.citation_existence == strict` — default advisory passes (`/ars-mark-read`-ack-able); the narrowed ID-keyed `false` never fires on a title-only-unmatched `unresolvable` citation
6. PROCESS SUMMARY	`academic-pipeline` v3.21.2	VERIFIED_ONLY	Paper Creation Process Record (MD + PDF); AI Self-Reflection Report (concession rate, sycophancy risk, health alerts, Failure Mode Audit Log); narrative criterion-regression notes when recorded; Collaboration Depth Chapter (v3.5.0) summarising the per-checkpoint observer reports from `collaboration_depth_history[]`	state_tracker_agent; pipeline_orchestrator_agent; 👁 collaboration_depth_agent (v3.5.0, pipeline-completion dispatch — final advisory report)	🧑 Decision-heavy checkpoint: language confirmed with user. Collaboration quality evaluated. No typed criterion-trajectory visualization is claimed until its producer/validator is implemented. Post-publication audit report (if peer-review published). 👁 Observer runs final pipeline-completion dispatch; never blocks

4. Data Access Level Flow (v3.3.2+)

flowchart LR
    User[User input<br/>web / PDFs / queries / pasted drafts]
    Raw[deep-research<br/>data_access_level: raw]
    Red[academic-paper<br/>data_access_level: raw]
    Ver1[academic-paper-reviewer<br/>data_access_level: raw]
    Orch[academic-pipeline<br/>data_access_level: raw]

    User --> Raw
    User -- standalone modes: ungated drafts,<br/>reviewer comments, search-fills-gap --> Red
    User -- standalone /ars-reviewer:<br/>ungated pasted manuscript --> Ver1
    User -- Stage 1 request / mid-entry paper --> Orch
    Raw -- source_verification elevates artifacts --> Red
    Red -- Gate 2.5: 7-mode integrity --> Ver1
    Orch -. orchestrates .-> Raw
    Orch -. orchestrates .-> Red
    Orch -. orchestrates .-> Ver1

    classDef raw fill:#fff1f0,stroke:#cf1322
    class Raw,Red,Ver1,Orch raw

Rules (per shared/ground_truth_isolation_pattern.md):

data_access_level is a declarative annotation, not a runtime-enforced permission system. The CI lint scripts/check_data_access_level.py pins each skill's value and confirms the vocabulary; it does not inspect context windows at runtime.
raw skills consume layer-1 data (arbitrary, possibly adversarial).
redacted (sanitized material, no new raw ingestion) and verified_only (runs only after upstream integrity gates) remain in the legal vocabulary, but since #773 no top-level skill qualifies for either: the annotation takes the dirtiest input across all modes and entry paths, and every skill has at least one legitimate Layer-1 entry. Artifact-level elevation is tracked per stage output in the §3 Data-level column, not per skill.
academic-pipeline is raw (#756) because Stage 1 accepts raw user requests and mid-entry accepts raw existing papers — the integrity gates run inside the pipeline, downstream of its intake.
academic-paper is raw (#773) because its standalone modes ingest ungated user drafts and third-party reviewer comments, and literature_strategist_agent's search-fills-gap flow ingests external-index search results inside the skill. The former redacted described the orchestrated pipeline path, where Stage 2 inputs arrive as Stage-1 sanitized artifacts (Gate 2.5 runs after Stage 2, not before it).
academic-paper-reviewer is raw (#773) because the standalone /ars-reviewer entry legitimately consumes an ungated pasted manuscript — the former verified_only was at best true for the pipeline's initial Stage 3 dispatch (post-Gate-2.5; Stage 3' re-review consumes a freshly revised manuscript before Stage 4.5). That Stage 3 sequencing is unchanged.
The reviewer side may hold a rubric privately — the key guarantee is that rubric / gold-label content must not be present in the candidate-generating agent's context. Calibration gold sets are runtime-supplied by the human researcher, not bundled into the repository.
Stage 2.5 and Stage 4.5 (plus the user's review at each gate) are the actual enforcement points. This pattern document explains the data-flow structure that makes those gates meaningful; it is not itself a runtime lock.

5. Material Passport `literature_corpus[]` Flow (v3.6.4 input port + v3.6.5 consumers)

The Material Passport's literature_corpus[] is an optional Schema 9 input port for user-curated literature. Producers (out-of-band, before an ARS session) and consumers (Phase 1 literature agents at runtime) sit on opposite sides of the passport.

flowchart LR
    subgraph Producer["Out-of-band (user-owned)"]
        Source[User corpus<br/>Zotero / Obsidian /<br/>folder of PDFs / etc.]
        Adapter["Adapter<br/>(reference: scripts/adapters/<br/>folder_scan.py / zotero.py /<br/>obsidian.py — v3.6.4+)"]
        Source --> Adapter
    end
    Passport["Material Passport<br/>passport.yaml<br/>+ rejection_log.yaml<br/>(literature_corpus[]<br/>optional Schema 9 field)"]
    Adapter --> Passport
    subgraph Consumer["Phase 1 ARS runtime (v3.6.5)"]
        BA["📚 deep-research<br/>bibliography_agent<br/>(Phase 1)"]
        LS["📚 academic-paper<br/>literature_strategist_agent<br/>(Phase 1)"]
    end
    Passport -- presence-based<br/>auto-engage --> BA
    Passport -- presence-based<br/>auto-engage --> LS
    BA --> SR1[Search Strategy report<br/>+ PRE-SCREENED block<br/>final_included = pre_screened ∪ external]
    LS --> SR2[Literature Search Report<br/>+ PRE-SCREENED block<br/>+ corpus-aware Matrix / Gap]

    classDef producer fill:#fffbe6,stroke:#d48806
    classDef passport fill:#f0f5ff,stroke:#2f54eb,stroke-width:2px
    classDef consumer fill:#f6ffed,stroke:#52c41a
    classDef report fill:#f9f0ff,stroke:#9254de
    class Source,Adapter producer
    class Passport passport
    class BA,LS consumer
    class SR1,SR2 report

Producer side (v3.6.4 input port). Adapters run out-of-band — before an ARS session, not during. They read a user corpus source and emit passport.yaml with literature_corpus[] populated and a parallel rejection_log.yaml (always emitted; empty when no rejections). Three reference Python adapters ship at scripts/adapters/{folder_scan,zotero,obsidian}.py; users are expected to write their own adapters for non-reference sources following academic-pipeline/references/adapters/overview.md. Schema validated by scripts/check_literature_corpus_schema.py.

Consumer side (v3.6.5). Two Phase 1 literature agents read literature_corpus[] via the corpus-first, search-fills-gap flow — deep-research/agents/bibliography_agent.md and academic-paper/agents/literature_strategist_agent.md. The flow is presence-based: it auto-engages when the passport carries a non-empty literature_corpus[] and parses cleanly. When the corpus is absent, empty, or fails the minimal shape check, each consumer runs its existing external-DB-only flow unchanged (Iron Rule 4 graceful fallback for the failure cases).

Five-step shared flow. Step 0 minimal shape check → Step 1 pre-screen corpus against current RQ → Step 2 search-fills-gap (4-case dispatch on uncovered_topics × user_corpus_only) → Step 3 merge into final_included → Step 4 emit Search Strategy report with PRE-SCREENED block. final_included stays neutral — no provenance tags on bibliography entries, no provenance column in the Literature Matrix.

Four Iron Rules govern every consumer:

Same criteria. Apply the same Inclusion / Exclusion criteria to corpus entries and external database results. No exceptions.
No silent skip. Any skipped corpus entry is recorded in the PRE-SCREENED block's skipped sub-section with a reason. Silently dropping an entry is a prompt-layer violation.
No corpus mutation. Consumer agents never modify, backfill, or derive new content into literature_corpus[]. Read only.
Graceful fallback on parse failure. Consumer agents do NOT re-validate schema, do NOT parse JSON Schema at runtime, and do NOT dereference source_pointer URIs. When the corpus cannot be parsed, emit [CORPUS PARSE FAILURE: <cause>] and fall back to external-DB-only flow.

PRE-SCREENED reproducibility block. Lives inside the Search Strategy section of each consumer's report, immediately before the existing Databases line. Enumerates included / excluded / skipped citation_keys with reasons; carries F3 zero-hit note when corpus is non-empty but 0 entries survived screening; carries F4a–F4f provenance reporting for obtained_via (adapter origin) and obtained_at (snapshot date) covering full / partial / undeclared / wide-spread sub-cases. CI lint scripts/check_corpus_consumer_protocol.py enforces nine invariants L1-L9 with manifest-driven consumer list (scripts/corpus_consumer_manifest.json) and tuple-matched closed-set state machine.

Out of v3.6.5 scope. citation_compliance_agent corpus reading is deferred (target version TBD post-v3.8). source_pointer URI dereferencing and source verification remain a future source_verification_agent concern. Schema is unchanged from v3.6.4 — existing user adapters work without modification.

Authoritative references: academic-pipeline/references/literature_corpus_consumers.md (consumer protocol) + academic-pipeline/references/adapters/overview.md (adapter contract) + docs/design/2026-04-26-ars-v3.6.5-consumer-integration-design.md (consumer design).

6. Skill Dependency Graph

graph TD
    Pipeline[academic-pipeline<br/>orchestrator<br/>v3.21.2<br/>Agent Team: 5]
    Observer[collaboration_depth_agent<br/>observer · advisory only<br/>blocking: false]
    DR[deep-research<br/>13 agents<br/>v2.12.1<br/>+ corpus reader]
    AP[academic-paper<br/>12 agents<br/>v3.3.1<br/>+ corpus reader]
    APR[academic-paper-reviewer<br/>7 agents<br/>v1.11.1]
    Shared[shared/<br/>handoff_schemas.md<br/>ground_truth_isolation<br/>benchmark_report<br/>artifact_reproducibility<br/>cross_model_verification<br/>mode_spectrum<br/>style_calibration<br/>collaboration_depth_rubric<br/>sprint_contract.schema<br/>contracts/passport/reset_ledger_entry<br/>contracts/passport/literature_corpus_entry<br/>contracts/passport/rejection_log<br/>contracts/reviewer/full + methodology_focus]

    Pipeline --> DR
    Pipeline --> AP
    Pipeline --> APR
    Pipeline -. "FULL/SLIM ckpt + pipeline completion<br/>MANDATORY gates skip" .-> Observer
    DR -. "RQ Brief + Bibliography + Synthesis" .-> AP
    AP -. "Complete manuscript" .-> APR
    APR -. "Revision Roadmap" .-> AP
    DR --- Shared
    AP --- Shared
    APR --- Shared
    Pipeline --- Shared
    Observer --- Shared

    classDef orch fill:#f0f5ff,stroke:#2f54eb,stroke-width:2px
    classDef skill fill:#e6f4ff,stroke:#1677ff
    classDef shared fill:#f5f5f5,stroke:#595959,stroke-dasharray:5 5
    classDef observer fill:#f6ffed,stroke:#52c41a,stroke-dasharray:3 3
    class Pipeline orch
    class DR,AP,APR skill
    class Shared shared
    class Observer observer

7. Quality Gates

Two classes of gate: 🧑 decision-heavy (user chooses a branch or approves material) and ✓ integrity (machine verification + user ack). Pure machine-enforced 🤖 lint checks run in CI.

Gate	Class	Stage	What blocks advancement	Failure handling
RQ + methodology confirmation	🧑	1	User hasn't approved RQ Brief and Methodology Blueprint	Revise and re-present
S2 API verification	🤖	1	Citation not in Semantic Scholar; title Levenshtein < 0.70	Flag; user decides to drop or re-cite
Outline approval	🧑	2	User hasn't approved outline	Revise and re-present
Anti-leakage (v3.3)	🤖	2	Draft contains parametric fill not grounded in session materials	`[MATERIAL GAP]` tag; user provides material or accepts gap
VLM figure verify (v3.3)	🤖	2	Rendered figure fails 10-pt APA 7.0 checklist	Max 2 refinement iterations
Stage 2.5 integrity + ack	✓	2.5	Any mode SUSPECTED on 7-mode checklist, or Modes 1/3/5/6 INSUFFICIENT EVIDENCE, or user hasn't acknowledged report	Fix + re-verify (max 3 rounds); or user override with reasoning (logged)
Editorial decision review	🧑	3	User hasn't reviewed decision letter	Present decision; await user
Concession threshold	🤖	3	DA rebuttal scored < 4/5 by responder	No concession; frame-lock detector runs
Revision Coaching	🧑	3→4	User hasn't engaged or explicitly skipped (max 8 rounds)	User may say "just fix it" to skip
Revision confirmation	🧑	4	User hasn't confirmed changes	Revise; re-present
Revision loop cap	🤖	4 / 3' / 4'	2 revision loops already consumed	Forced advance to Stage 4.5
Residual Coaching	🧑	3'→4'	User hasn't engaged or explicitly skipped (max 5 rounds)	User may say "just fix it" to skip
Content-frozen confirmation	🧑	4'	User hasn't confirmed freeze	Await user; no further review loop permitted
Stage 4.5 final integrity + ack	✓	4.5	ANY issue on deeper 7-mode re-run; mode still SUSPECTED since 2.5 and unresolved	ZERO-tolerance; no skip; fix + re-verify
Format selection	🧑	5	User hasn't chosen output format	Await user format choice
Disclosure check	🤖	5	Venue-specific AI disclosure absent or wrong form	Block render until fixed
`repro_lock` (v3.3.5)	🤖 (standalone)	—	`repro_lock` key required in Material Passport v3.3.5+; value must be either a populated block or explicit `null` (honest opt-out). Populated blocks validated by `check_repro_lock.py`. Per `artifact_reproducibility_pattern.md`: not wired into the CI lint suite by default and not read by the Stage 2.5 / 4.5 integrity gate at runtime — this is post-hoc documentation, not a pipeline block	Run `check_repro_lock.py <passport>` on demand
Language + collaboration review	🧑	6	User hasn't confirmed output language / reviewed self-reflection	Await user
`benchmark_report` (v3.3.5, external)	🤖	—	Publishing a benchmark without honest disclosure	Users run `check_benchmark_report.py` before publishing
Collaboration Depth Observer (v3.5.0)	🤖 observer	Every FULL/SLIM checkpoint + pipeline completion	Never blocks. Advisory only. Scores user-AI collaboration pattern on 4 dimensions (Delegation Intensity / Cognitive Vigilance / Cognitive Reallocation / Zone Classification) per `shared/collaboration_depth_rubric.md`. Injects a named section into checkpoint presentation and a chapter in the Process Record. MANDATORY integrity gates (2.5 / 4.5) do NOT invoke the observer.	n/a — output is advisory; user `Ready to proceed?` prompt unchanged
Reading-check probe (v3.5.1, opt-in)	🤖 (Mentor sub-layer)	Stage 1 (Socratic mentor session)	Opt-in via `ARS_SOCRATIC_READING_PROBE=1`. Goal-oriented intent only; fires at most once per session when user has cited a specific paper. Decline logged without penalty. Outcome inline in Research Plan Summary; carried into Stage 6 AI Self-Reflection Report.	n/a — non-blocking; flag OFF preserves pre-v3.5.1 behaviour byte-for-byte
Sprint Contract hard gate (Schema 13.2)	🤖 + 🧑	3 (REVIEW)	Each reviewer receives the contract BEFORE the paper (Phase 1 metadata-only), commits triggers only for dimensions where its role is eligible, then emits role-scoped Phase 2 scores. `check_phase_conformance.py` enforces the boundary; `editorial_synthesizer_agent` applies per-dimension eligible-seat quantifiers and emits one four-value decision. Templates: `shared/contracts/reviewer/full.json` (panel 5, six dimensions) + `methodology_focus.json` (panel 2).	Synthesizer rejects post-hoc trigger/fatality edits; user sees the pre-commitment and any DA-CRITICAL-vs-Accept escalation
Passport reset boundary (v3.6.3, opt-in)	🤖 (orchestrator)	FULL checkpoints	Opt-in via `ARS_PASSPORT_RESET=1`. Promotes every FULL checkpoint to a context-reset boundary. `systematic-review` mode with the flag ON makes reset mandatory; other modes treat reset as the flag-gated default. New `resume_from_passport=<hash>` mode in `academic-pipeline` lets users resume in a fresh session from the Material Passport ledger alone. Schema 9 `reset_boundary[]` append-only ledger with `kind: boundary` + `kind: resume` entry types; hash via JSON Canonical Form + SHA-256 + canonical placeholder for self-reference safety. Concurrency contract: POSIX `fcntl.flock LOCK_EX` + bounded timeout ≤60s + non-POSIX fail-loudly. Authoritative protocol: `academic-pipeline/references/passport_as_reset_boundary.md`. Validated by `scripts/check_passport_reset_contract.py`.	Flag OFF preserves pre-v3.6.3 continuation behaviour byte-for-byte
Corpus consumer protocol (v3.6.5)	🤖 + Phase 1 agents	1 / 2 (when `literature_corpus[]` present)	Presence-based auto-engage when Material Passport carries non-empty `literature_corpus[]` and parses cleanly. Four Iron Rules (Same criteria / No silent skip / No corpus mutation / Graceful fallback on parse failure). PRE-SCREENED reproducibility block in Search Strategy report (F3 zero-hit + F4a–F4f provenance). Validated by `scripts/check_corpus_consumer_protocol.py` (9 invariants L1-L9 with manifest-driven consumer list).	Parse failure → emit `[CORPUS PARSE FAILURE: <cause>]` and fall back to external-DB-only flow (Iron Rule 4)
Model tiering (v3.16.0, opt-in)	🤖 (dispatch layer)	All stages (agent dispatch)	Never blocks. Opt-in via `ARS_MODEL_TIERING=economy\|quality-boost`. `economy` (frontier-tier session): the 13 execution-type agents dispatch one tier below the session model, floor Opus-class. `quality-boost` (below-frontier session): judgment-type agents at the Stage 2.5/4.5 integrity gates and final-review surfaces step up to the frontier tier; nothing is ever downgraded. Tiers are relative positions, never hard-pinned model ids. Frozen 39-agent classification (26 judgment / 13 execution) in `scripts/model_tiering_manifest.json` + `shared/model_tiering.md`, pinned to each other and to the agent files by `scripts/check_model_tiering.py`.	Unset = byte-equivalent pre-#517 behaviour; unknown value warns once and behaves as unset (fail-open to the safe default)
Stage 5/6 boundary semantics (v3.17.0)	🤖 + 🧑	5 (entry gate), 6 (terminal checkpoint)	Stage 5's "before finalization: always MANDATORY" names exactly one checkpoint — the entry gate between Stage 4.5 PASS and Stage 5 dispatch. Stage 6 gains a defined Stage 5→6 transition, a non-mandatory decline path, a terminal checkpoint after the Process Record is delivered, and canonical terminal-acknowledgement vocabulary (`finish`/`end`/`done`/`confirm`) that sets pipeline global state to `completed`. All five pipeline surfaces (`academic-pipeline/SKILL.md`, `agents/pipeline_orchestrator_agent.md`, `agents/state_tracker_agent.md`, `references/pipeline_state_machine.md`, `references/process_summary_protocol.md`) carry whole-file sha256 content locks in `scripts/check_pipeline_boundary_semantics.py` (66 mutation tests).	Any byte change to a locked surface fails CI until the pinned hash is updated in the same commit
Cross-model handoff envelope (v3.17.0)	🤖 (dispatch layer)	Design freeze (1), Final editorial decision (3), DA critique (3)	Canonical `[CROSS-MODEL-HANDOFF v1]` envelope + normative Python grammar (`scripts/cross_model_handoff.py`) for the #523 owner→dispatcher→owner transport path. Malformed envelope/result → `[CROSS-MODEL-ERROR]` → outcome `unavailable`, never a fabricated judgment; agreement → mechanical fill with no owner re-invocation; divergence → re-invoke the owner with minimum context. `scripts/check_cross_model_handoff_contract.py` pins the contract across all five surfaces.	`ARS_CROSS_MODEL` unset stays byte-equivalent; malformed transport degrades to `unavailable`, never silently treated as a deliverable

7.1 CI workflow enforcement classes (#755)

The files under .github/workflows/ are often described collectively as CI gates, but they enforce at four different strengths (origin: ISO/IEC 42001-spirit gap assessment, finding T-5).

Classes: Blocking — a failure on the guarded event must be fixed (or explicitly bypassed) before proceeding · Advisory — the audited condition warns, never fails · Administrative — produces work items, audits nothing · Post-push detection — triggered by a tag push that has already happened; nothing in GitHub Actions can reject a push after the fact, so a failure is a remediation signal, not prevention (the three tag-only workflows are conventionally called release gates; their stop-power is the maintainer acting on the failure).

One GitHub Actions subtlety the Trigger column accounts for: an unfiltered or paths-only push: trigger ALSO matches tag pushes — GitHub does not evaluate paths filters for tags — so spec-consistency, command-invariants, and freshness-check additionally run on every v* tag push, where their failures are post-push detection exactly like the three tag-only workflows.

Workflow	Trigger	What it checks	Class	Bypass
`spec-consistency.yml`	push (all branches and tags) + PR	the full lint/pytest battery: spec surfaces, contracts, content locks, the pytest manifest	Blocking	none
`pytest.yml`	PR + push to main, both path-filtered (scripts/tests/contracts/config, adapter references, `bibliography_agent`)	adapter + script test suite	Blocking	none
`command-invariants.yml`	push (path-filtered for branch pushes; also every tag push) + PR (all)	SessionStart announce list matches the command inventory; plugin-version ↔ CHANGELOG lockstep; command frontmatter `name` validation	Blocking	none
`repository-hygiene.yml`	PR targeting main + push to main	gitleaks secret scan	Blocking	none
`eval-harness.yml`	PR + push to main, both path-filtered (scoring/generation surfaces + gold sets)	eval gold-set thresholds (aggregate + per-class)	Blocking on `pull_request` events only; report-only on push	`[eval-regression-acknowledged]` in the PR body + ≥1 open tracking-issue URL in this repo
`test-count-monotonic.yml`	PR targeting main	collected test count must not drop	Blocking	`[skip-test-count]` in the PR body (justification requested, not machine-validated)
`pr-closes-issue.yml`	PR targeting main	PR body references an issue via an auto-close keyword	Blocking	`[skip-closes-check]` in the PR body (justification requested, not machine-validated)
`changelog-covers-merges.yml`	PR targeting main; the job runs only when the head branch is `release/**`	every release-worthy merge since the last tag is documented in CHANGELOG	Blocking (ordinary merges rely on the manual CONTRIBUTING fallback)	none
`platform-port-reminder.yml`	PR targeting main	new top-level directory → platform-ports policy reminder	Advisory (one `::warning::`, always exits 0; the merge decision stays with the maintainer)	none
`freshness-check.yml`	weekly schedule + push (two-file path filter for branch pushes; also every tag push) + manual dispatch	PRISMA-trAIce snapshot staleness	Advisory for staleness (warns on stderr, exits 0); malformed protocol metadata is a hard failure	none
`harness-retirement-monthly.yml`	monthly schedule + manual dispatch	opens the monthly prompt-debt audit issue	Administrative	none
`defer-label-gate.yml`	tag push `v*`	open `defer:<tag>` issues must be closed or relabelled	Post-push detection	`[skip-defer-check]` in the tagged commit message
`release-cooldown.yml`	tag push `v*`	paces consecutive release tags	Post-push detection	`[skip-cooldown]` in the commit/tag message
`tag-version-match.yml`	tag push `v*`	re-runs the full version-consistency lint at the tag	Post-push detection	none

Count, honestly stated: 14 workflows — 8 blocking on at least one event class, 2 advisory, 1 administrative, 3 post-push detection.

Inventory sync, the count line, and the bypass tokens are pinned by scripts/check_workflow_classification.py; the class semantics — whether a row honestly describes its workflow's behavior — stay owned by code review, mirroring the degradation-registry posture.

8. ARS Evolution Timeline

timeline
    title ARS evolution timeline
    v3.3 : Semantic Scholar API verification
         : Anti-leakage protocol
         : VLM figure verification
         : Historical score-trajectory concept (retired; current typed carrier deferred)
         : Stage 2 parallelization
    v3.3.1-v3.3.6 : Public contract drift fixes + check_spec_consistency.py
                  : data_access_level + task_type frontmatter
                  : Lint hardening + ground_truth_isolation_pattern
                  : benchmark_report.schema.json + repro_lock on Material Passport
                  : README changelog summaries sync + CI validation
    v3.4.0 : compliance_agent (PRISMA-trAIce + RAISE)
           : Schema 12 compliance_report + compliance_history[]
           : 3-round override ladder + disclosure_addendum
           : freshness check (180-day threshold)
    v3.5.0 : collaboration_depth_agent (advisory observer)
           : shared/collaboration_depth_rubric.md (Wang & Zhang 2026)
           : dialogue_log_ref + collaboration_depth_history[]
           : short-stage guard + ARS_CROSS_MODEL_SAMPLE_INTERVAL
    v3.5.1 : Socratic reading-check probe (opt-in via ARS_SOCRATIC_READING_PROBE)
           : goal-oriented intent only, max-once-per-session
           : decline logged without penalty
    v3.6.2 : Schema 13 Sprint Contract hard gate for reviewers
           : two-phase protocol (paper-blind Phase 1 + paper-visible Phase 2)
           : editorial_synthesizer three-step mechanical protocol + forbidden-ops list
           : full.json (panel 5) + methodology_focus.json (panel 2) templates
    v3.6.3 : Opt-in passport reset boundary (ARS_PASSPORT_RESET=1)
           : resume_from_passport mode + Schema 9 reset_boundary[] ledger
           : JSON Canonical Form + SHA-256 hash with canonical placeholder
           : POSIX fcntl.flock LOCK_EX concurrency contract
    v3.6.4 : Material Passport literature_corpus[] input port (Schema 9 optional)
           : language-neutral adapter contract + 3 reference Python adapters
           : rejection_log.yaml contract (closed enum, always emitted)
           : check_literature_corpus_schema.py + sync_adapter_docs.py CI lints
    v3.6.5 : literature_corpus[] consumer integration in Phase 1
           : bibliography_agent + literature_strategist_agent corpus-first flow
           : 4 Iron Rules + PRE-SCREENED block + F3 zero-hit + F4 provenance
           : check_corpus_consumer_protocol.py (9 invariants, manifest-driven)
    v3.6.7 : Downstream-agent PATTERN PROTECTION (Step 1+2)
           : synthesis_agent A1-A5 + research_architect_agent B1-B5 + report_compiler_agent C1-C3
           : 4 reference glossaries (IRB / psychometric / hedging / word-count)
           : check_v3_6_7_pattern_protection.py (29-test mutation suite)
    v3.6.8 : Generator-Evaluator Contract Gate (v3.6.6 spec ship, naming offset)
           : Schema 13.1 + writer_full / evaluator_full templates
           : two-phase orchestration in academic-paper full mode (Phase 4a/4b + 6a/6b)
           : SC-* mode-gating in check_sprint_contract.py
    v3.7.0 : Claude Code plugin packaging
           : .claude-plugin/{plugin,marketplace}.json + skills/ symlinks
           : 10 slash commands (commands/ars-*.md, model pinned opus/sonnet, no haiku)
           : 3 plugin agents (agents/, byte-identical copies of v3.6.7-hardened
           :   source — mirror-sync lint since #413, model: inherit)
           : SessionStart announce hook (hooks/hooks.json + announce-ars-loaded.sh)
    v3.7.3 : L3 locator infrastructure (claim faithfulness — first half)
           : Three-Layer Citation Emission (synthesis / draft_writer / report_compiler)
           : <!--anchor:kind:value--> on every <!--ref:slug--> (quote / page / section / paragraph / none)
           : contamination_signals advisory (preprint_post_llm_inflection + semantic_scholar_unmatched)
           : check_v3_7_3_three_layer_citation.py + finalizer 5-cell with precedence-zero NO-LOCATOR
    v3.8.0 : L3 claim-faithfulness audit (second half — paired with v3.7.3)
           : claim_ref_alignment_audit_agent (opt-in via ARS_CLAIM_AUDIT=1, default OFF)
           : 5 new passport schemas (claim_audit_result / claim_intent_manifest / claim_drift / uncited_assertion / constraint_violation)
           : 8-row finalizer matrix + 5 new HIGH-WARN classes (formatter REFUSE rules 6-10)
           : Calibration runner (20-tuple gold set, FNR<0.15 + FPR<0.10 acceptance gate)
           : check_claim_audit_consistency.py (38 invariants) + check_v3_8_annotation_literal_sync.py
    v3.8.1 : claim_audit lint hardening (#119 + #120 4×P2 closures)
    v3.8.2 : uncited audit_tool_failure surface (#118)
    v3.9.0 : cross-index triangulation measurement (S2 + OpenAlex + Crossref, 4-tier advisory)
           : openalex_unmatched + crossref_unmatched contamination signals
           : 4-tier advisory (CONTAMINATED-COVERAGE-NOISE / PARTIAL-UNMATCH / TRIANGULATION-UNMATCHED)
    v3.9.1 : client hardening — wrap response-read failures (#129) + manifest_id guard (#130)
    v3.9.2 : Phase scope inflation hot-fix (#133)
           : phase-boundary blocks across 22 single-phase agents
           : intent-clarification gate for ambiguous cross-phase materials
    v3.9.3 : housekeeping — shared client utilities + dedup resolvers (#128)
           : sibling-first dual-path import convention
           : time.monotonic standardization
    v3.9.4 : temporal verification advisory layer (#135)
           : M1 timeline_extraction_agent (Phase 2 sibling)
           : M2 5-pass verifier at Phase 4→5 boundary (P1 arithmetic / P2 anachronism / P3 comparator / P4 causal / P5 deictic)
           : M3 Temporal Integrity Iron Rule in compiler+writer
           : M6 first-party Crossref + pdftotext verification
           : F2 invariant — bibliography_agent.md UNMODIFIED (sha256-guarded)
    v3.9.4.1 : post-ship hotfix (4 codex findings: P1×2 + P2×2)
             : audit() wires citation_provenance through to P2/P4 (spec §3.4 promise)
             : _date_to_interval parses all schema-valid date shapes (YYYY-MM + interval)
             : P4 binds direct-date captures (not only ref markers)
             : citation_provenance.schema.json confidence:high requires presence
    v3.9.4.2 : CI discipline hardening (PR #149 + #153 + #157; codex post-ship 3 of 4 P2)
             : F1 harness-retirement-monthly adds GH_REPO for scheduled runs
             : F2 release-cooldown filters PREV_TAG lookup to v* tags only
             : F3 release-cooldown reads annotated tag subject + accepts hot-fix spelling
             : [skip-cooldown] override now read from both commit message and tag message
             : F4 test-count-monotonic harden reverted (surfaced #154; re-attempt #155)
    v3.10.0 : triangulation terminal policy layer (#127 PR-B, opt-in strict)
            : Kong et al. survey adoptions (commitment ledger #256/#266/#268/#269; domain profiles #259)
            : generalized eval gold set + ranking-lift CI gate (#184)
            : scoped-write guard MVP — PreToolUse fence on 23 single-phase agents (#134)
    v3.11.0 : deterministic citation verification gate (#182)
            : arXiv resolver + four-index contamination matrix k=0..4 (Delta 1)
            : persistent SQLite verification cache + /ars-cache-invalidate (Delta 2)
            : citation_existence terminal policy — default advisory, opt-in strict (Delta 3 / C-V6)
            : unified lookup_verified summary + standalone verification_gate API (Delta 4+5)

9. Skill Modes

Skill	Modes
`deep-research` v2.12.1	full, quick, socratic, review, lit-review, three-way-scan, fact-check, systematic-review (8)
`academic-paper` v3.3.1	full, plan, outline-only, revision, revision-coach, abstract-only, lit-review, format-convert, citation-check, disclosure, rebuttal-audit (11)
`academic-paper-reviewer` v1.11.1	full, re-review, quick, methodology-focus, guided, calibration (6)
`academic-pipeline` v3.21.2	orchestrator (delegates to sub-skill modes) + `resume_from_passport=<hash>` (v3.6.3 — resume a prior pipeline run from a Material Passport reset boundary; no flag required to invoke. The producing session must have set `ARS_PASSPORT_RESET=1` to emit boundary entries.) + `ARS_CLAIM_AUDIT=1` (v3.8 — opt-in Stage 4→5 L3 claim-faithfulness audit gate; default OFF) + v3.9.4 temporal verification advisory layer (M1 timeline_extraction_agent + M2 5-pass verifier at Phase 4→5 + M3 IRON RULE + M6 first-party Crossref/pdftotext)

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ARS Pipeline Architecture (v3.21.2)

How to read

1. Checkpoints (at-a-glance)

2. Pipeline Flow

3. Stage × Dimension Matrix

4. Data Access Level Flow (v3.3.2+)

5. Material Passport `literature_corpus[]` Flow (v3.6.4 input port + v3.6.5 consumers)

6. Skill Dependency Graph

7. Quality Gates

7.1 CI workflow enforcement classes (#755)

8. ARS Evolution Timeline

9. Skill Modes

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ARS Pipeline Architecture (v3.21.2)

How to read

1. Checkpoints (at-a-glance)

2. Pipeline Flow

3. Stage × Dimension Matrix

4. Data Access Level Flow (v3.3.2+)

5. Material Passport literature_corpus[] Flow (v3.6.4 input port + v3.6.5 consumers)

6. Skill Dependency Graph

7. Quality Gates

7.1 CI workflow enforcement classes (#755)

8. ARS Evolution Timeline

9. Skill Modes

5. Material Passport `literature_corpus[]` Flow (v3.6.4 input port + v3.6.5 consumers)