docs(proposals): define Paper2Agent scientific factory contract

[timerloggedout-spec]

Summary

Defines the next bounded Paper2Agent increment identified by #621, building on the already-merged #695 evolutionary-replay work and the merged agent evidence substrate.

Delivered

• registered paper2agent-scientific-factory proposal
• paper manifest contract
• claim/method/result graph contract
• scientific evidence classes
• reference reproduction contract
• acceptance certificate contract
• registry admission boundary
• implementation/gate sequence
• explicit untrusted-research-code security boundary

Non-goals

• no production scientific routing
• no arbitrary repository execution
• no scientific validity inferred from ATES/3L0
• no new scheduler/router

Evidence rule

Documentation establishes the contract only. VALIDATED/DEPLOYABLE states require bounded fixtures, validators, reproduction evidence, security evidence, and the existing repository gates.

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Project	Deployment	Actions	Updated
help-wanted-dash	Ready	Preview	Sep 29, 2026 9:06pm UTC

[ecc-tools]

ECC Tools / Security Evidence

Commit: f9923fd7bdfab0b39ebf78dc7d803ad70581c668

Security evidence gate passed (success)

No security-sensitive scanner-evidence gap detected.

Mode: enforce

Scanned 5 changed file(s). No missing scanner-evidence signal was detected.

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[ecc-tools]

ECC Tools / PR Risk Taxonomy

Commit: f9923fd7bdfab0b39ebf78dc7d803ad70581c668

PR taxonomy clear (success)

Scanned 5 changed file(s). No taxonomy bucket signals were detected.

Scanned 5 changed file(s).

No PR taxonomy bucket signals were detected.

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[ecc-tools]

ECC Tools / Reference Set Readiness

Commit: f9923fd7bdfab0b39ebf78dc7d803ad70581c668

Reference set readiness gaps detected (neutral)

Reference evidence present for 0/7 areas (0%) across 5 changed file(s).

This check is based on files changed in this PR. Repository-level readiness is still reported by /ecc-tools analyze comments and generated manifests.

Area	Status	Evidence / Next Step
Deep analyzer corpus	Missing	Add analyzer fixture, golden, benchmark, or reference-set files that can catch analyzer regressions.
RAG/evaluator comparison	Missing	Add retrieval or evaluator reference-set comparison fixtures with expected ranking behavior.
PR salvage/review corpus	Missing	Add stale-PR, review-thread, reopen-flow, or salvage reference cases for queue cleanup automation.
Discussion triage corpus	Missing	Add public discussion triage fixtures, golden cases, or reference sets for informational, answered, and no-response classifications.
Harness compatibility	Missing	Add cross-harness, adapter-compliance, or harness-audit evidence for Claude, Codex, OpenCode, Zed, dmux, and agent surfaces.
Security evidence	Missing	Attach security evidence such as SBOMs, SARIF, audit reports, or AgentShield evidence packs.
CI failure-mode evidence	Missing	Add captured CI failure logs, dry-run fixtures, or troubleshooting docs for common workflow failure modes.

Check publication was denied or unavailable. An app owner must enable Checks: read and write, and the installation owner must approve the updated permission.

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Review configuration:

⚙️ Run configuration

Configuration used: Repository: timerloggedout-spec/termux-monorepo/.coderabbit.yaml

Review profile: ASSERTIVE

Plan: Advanced

Run ID: 8b100903-6f2b-4fe2-a7e2-0286c5fabb4f

📥 Commits

Reviewing files that changed from the base of the PR and between c6abc7c and f9923fd.

📒 Files selected for processing (5)

• docs/proposals/active/paper2agent-scientific-factory/ITEMS.md
• docs/proposals/active/paper2agent-scientific-factory/MANIFEST.md
• docs/proposals/active/paper2agent-scientific-factory/RECON.md
• docs/proposals/active/paper2agent-scientific-factory/schema.md
• docs/proposals/registry.yaml

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[ecc-tools]

ECC Tools / Hosted Promotion Readiness

Commit: f9923fd7bdfab0b39ebf78dc7d803ad70581c668

Hosted promotion readiness passed (success)

No hosted promotion evidence gaps detected across 5 changed file(s); 0 corpus scenarios had matching evidence.

This check compares PR file changes against the evaluator/RAG promotion corpus in src/analyzers/fixtures/evaluator-rag-corpus.ts.
Hosted output scoring inspected 0 completed cached hosted job results.

No evaluator corpus scenarios matched this PR.

Check publication was denied or unavailable. An app owner must enable Checks: read and write, and the installation owner must approve the updated permission.

[github-actions]

Proposal process checklist

• registry.yaml updated if new/changed proposal
• active//MANIFEST.md + ITEMS.md present
• Binding decisions logged in Review log (not only chat)
• Votes use VOTE: accept|reject|abstain + term: (see docs/CONSENSUS.md)
• Promotion via scripts/proposals/promote_proposal.py when status changes
• Full large sources may stay on a docs/* branch with a pointer on master

Refs: PROCESS · CONSENSUS · registry.yaml

[github-actions]

PR Change Effectiveness Ledger

Measured head: f9923fd7bdfab0b39ebf78dc7d803ad70581c668
Measured base: c6abc7c96eb9f0c22d4f814184e36804fff6b6c3
Merge base: c6abc7c96eb9f0c22d4f814184e36804fff6b6c3

Signal	Value
commits in PR range	5
commits with no file delta	0
commits with file delta	5
no-op commit rate	0%
gross additions across commits	157
gross deletions across commits	0
final additions vs base	157
final deletions vs base	0
final changed files	5
churn → retained final diff	100%
ahead / behind base	5 / 0

Interpretation: commit count is context, not quality. Empty commits are explicitly measured, not silently treated as productive work. Gross churn describes work performed across history; the final base→head diff describes what remains. Review/comment/check evidence must be evaluated separately and tied to this measured head SHA.

State: 🟢 EFFECTIVE_DIFF_PRESENT; No empty commits observed.

Generated: 2026-09-29T21:06:13Z

[timerloggedout-spec]

ECC App activity — dual-gate merges; review skills/hooks before merge.

[timerloggedout-spec]

Validation receipt — exact HEAD

HEAD: f9923fd7bdfab0b39ebf78dc7d803ad70581c668

Successful:

• proposal-lifecycle ⚡ Bolt: Optimize model performance index stream aggregation #434
• repo gate #2483
• termux smoke #2417
• historical backfill promotion gate Explore priority matrix and master functional gate status #176
• Context Relationship + Lead/Lag Audit #43740
• Audit Cycle — Single PR Feed-Forward #21941
• Repository development evaluation #1707
• Gemini Dispatch #29069

DeepSeek CI #23428 is CANCELLED and is retained as observed state; it is not rewritten as success.

This PR is documentation/proposal scope only. No scientific VALIDATED/DEPLOYABLE claim is made, and no production routing is enabled. Next implementation evidence begins at SAF-001/002/003 with machine-readable schemas, deterministic fixtures, and validators.

No merge/promotion action is implied by this receipt.

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[github-actions]

context_key: pr-922-docspaper2agent-scientific-factory-propo
source_id: 5899229995
source_revision: 5899229995:2026-09-29T21:24:52Z
specialist_disposition: independent_implementation_specialist
@jules Auto-resolve (heyVern lane / GHA agent-review-auto-jules) — do not wait for a human ping.
New work-context pr-922-docspaper2agent-scientific-factory-propo — create session if none exists, then prefer continue thereafter.
Bot feedback from qodo-code-review[bot] on PR #922 (branch docs/paper2agent-scientific-factory-proposal-2026-09-29).

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   Signed-off-by: Grok (OPERATOR) session-auto-jules / context_key=pr-922-docspaper2agent-scientific-factory-propo

[timerloggedout-spec]

cycle_id: pr-922-f9923fd7bdfa
head_sha: f9923fd
cycle_started_at: 2026-09-29T21:24:52.000Z
state: provider_cooldown
ready: false
required_providers: coderabbit
enforce_provider_completion: false

Agent peer response gate

Provider state:

• coderabbit: provider_cooldown; cooldown=6 minutes; source=docs(proposals): define Paper2Agent scientific factory contract #922 (comment)

Pending:
coderabbit:provider_cooldown

Authorized interactive controls:

• none observed

A provider-owned checkbox/button requires an authorized Operator Action Executor.
Do not copy control markup into a relay comment. After a permitted UI action, post:

<!-- operator-action-ack:v1 -->
cycle_id: pr-922-f9923fd7bdfa
provider: <provider>
control_id: <provider-control-id>
action: <allowed-action>

The second-pass reviewer remains blocked until matching provider completion evidence is ingested for this SHA.
A checked [x] control means the provider UI action occurred; it is not a completed review.
A provider cooldown is also non-completing: wait for the stated retry window, then retrigger through the authorized provider path.
Pending provider evidence is advisory unless PEER_ENFORCE_PROVIDER_COMPLETION is deliberately set to true for branch protection.

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@coderabbitai full review

cycle_id: pr-922-f9923fd7bdfa
head_sha: f9923fd
provider: coderabbit
action: trigger_review
request_actor: OPERATOR

Autonomous OPERATOR-token request for a current-SHA provider review. A command request is not review completion; await provider evidence.

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⚠️ Action not completed

Pull request is closed.

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