docs(research): formal synthesis paper unifying substrate + e2e framework#52
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…ramework Adds research/formal-synthesis/: a formal, mathematical unification of the cognitive-substrate theory, the end-to-end reliability framework (F1/F2, Δ*, I1-I4, A1-A7, T1-T6), and the forgekit implementation. Central result (Theorem D): reliability = probabilistic instruction layer × deterministic interception layer; neither alone suffices. Three anchor identities proved: impact-oracle blast-radius ≡ change-closure Δ*; assumption gate ≡ amnesia equation; two layers ≡ the Π3-probabilistic/Π2-deterministic design law. Includes: 42-page paper (HTML+PDF), three-way crosswalk (JSON+MD) with the P1/P2/P3 → Π1/Π2/Π3 notation reconciliation, a graded reference set for 15 new sources (9 confirmed / 6 traceable / 0 unverifiable, both future-dated arXiv IDs verified by direct fetch), a merged 47-entry bibliography, and two schematics. The two runnable prototypes are cross-referenced to the existing research/python-prototypes/ trees rather than duplicated.
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| <img src="{{artifact:art_5f049677-4c3c-40f2-8905-dd01c966e9ae}}" alt="The two-layer duality architecture"> |
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When this HTML is opened from the repository, {{artifact:...}} is not a resolvable URL, while the actual PNGs are committed under research/formal-synthesis/figures/. This makes the paper's figures render as broken images despite the README describing the HTML as self-contained; use the committed relative paths or embed the images as data URIs.
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| 1. **The Cognitive Substrate** — five faculties a frozen model structurally lacks | ||
| (memory, learning, imagination, self-correction, impact-awareness) and six | ||
| operating mechanisms M1–M6, with two runnable prototypes. | ||
| 2. **The End-to-End Agent Reliability Framework** (`FRAMEWORK.md`) — failure modes |
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This introduces FRAMEWORK.md as one of the three source bodies for the synthesis, but I checked the repository and there is no FRAMEWORK.md or other non-research/formal-synthesis source for the named End-to-End Agent Reliability Framework. Readers cannot verify the crosswalk/theorem claims from the referenced document, so either add the file or replace this with the actual external/internal link.
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Make the Citations track's 14-verified vs the shipped canonical 15 explicit: the +1 is the founding Agent-as-a-Judge paper (arXiv:2410.10934), added on the track's own recommendation and graded confirmed. Adds count_provenance to the graded reference set (JSON + MD). No other content changes.
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Count reconciliation (14 → 15). The Citations verification track independently verified 14 new sources (8 confirmed / 6 traceable / 0 unverifiable). While disambiguating the 2026 Agent-as-a-Judge survey ( |
…ge changelog latestChanges() matched only the first "## [...]" CHANGELOG section, which after a release is the empty "## [Unreleased]" heading — leaving the status page's "Latest changes" list empty and failing test/pages.test.js:43. Now walks sections in order and uses the first one that actually has bullets. Also bumps ROADMAP's stale "Now" version marker to v0.12.0.
… gitleaks
gitleaks' generic-api-key rule flags the "key" field in
research/formal-synthesis/{graded_reference_set,merged_references}.json —
BibTeX-style citation keys like "wang2023voyager", not secrets. Add a
path-scoped allowlist for these two files.
master auto-bumped past v0.12.0 before this PR's docs-check ran (pull_request CI checks out a merge of this branch into master's current tip). Keep the marker matching master's shipped version.
Resolves the ROADMAP.md "Now" marker conflict in favor of v0.12.1 (master's shipped version after auto-release), consistent with the earlier roadmap fix on this branch.
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Summary
Adds
research/formal-synthesis/— a formal, mathematical unification of threeindependently-developed bodies of work that all describe the same architecture
for making a frozen language model reliable at coding:
FRAMEWORK.md) — F1/F2, Δ*, I1–I4, A1–A7, T1–T6The paper proves these are one object in three vocabularies.
The central result
Instructions raise
p < 1but can never reach 1, so silent misses overntasks go as1 − pⁿ → 1; a deterministic layer multiplies that residual down by(1 − cⱼ)per check but cannot catch the semantic class (undecidable). This is the formal content of never trust a probability engine's output; earn trust with an external check.Three anchor identities (proved, not analogies)
Δ*argmax P(convention∣training)What's in the PR
substrate_synthesis.pdf/.html— the 42-page paper (definitions, Theorem D + proof, the unified A1–A7 TASK loop, invariants I1–I4, theorems T1–T6 with proofs, the 16-row crosswalk, the full 14-mapping Qur'anic epistemology, both prototypes with honest metrics)crosswalk.json/.md— the three-way correspondence, incl. the P1/P2/P3 → Π₁/Π₂/Π₃ notation reconciliation (the paper keeps P1–P3 for model properties, renames the framework primitives Π₁–Π₃)graded_reference_set.json/.md— 15 new sources independently verified: 9 confirmed, 6 traceable, 0 unverifiable. Both future-dated arXiv IDs (2604.26275,2601.05111) were confirmed to resolve to real preprints by direct fetch;2601.05111is disambiguated from the founding Agent-as-a-Judge paper (2410.10934).merged_references.json— full 47-entry bibliography (32 original + 15 new, deduped)figures/— the two-layer duality and the unified TASK loop schematicsThe two runnable prototypes are cross-referenced to the existing
research/python-prototypes/impact_oracle/androuter_gate/trees rather than duplicated.Honesty commitments (carried from the source work)
Review notes
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