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clarify AE/EP
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‎.github/workflows/ci-hygiene.yml‎

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env:
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PYTHONUNBUFFERED: "1" # WHY: Real-time logging.
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PYTHONIOENCODING: "utf-8" # WHY: Ensure UTF-8 encoding for international characters.
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PYTHON_VERSION: "3.14"
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PYTHON_VERSION: "3.15"
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jobs:
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ci:

‎.markdownlint-cli2.yaml‎

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# ============================================================
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# .markdownlint-cli2.yaml (Markdownlint CLI2 configuration)
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# ============================================================
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# Updated: 2026-05-05
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# Updated: 2026-05-31
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# WHY: Generated and dependency directories are not source content.
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# REQ: Markdown lint should check authored Markdown, not virtual
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# environments, dependency trees, build output, or generated docs.
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- "**/*.md"
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ignores:
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- ".lake/**"
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- "**/.lake/**"
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- ".venv/**"
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- "**/.venv/**"
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- "node_modules/**"

‎.python-version‎

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3.14
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3.15

‎README.md‎

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```shell
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uv self update
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uv python pin 3.14
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uv python pin 3.15
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uvx pre-commit install
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uvx pre-commit run --all-files
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npx markdownlint-cli2 --fix
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```
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Save progress as needed:

‎SE_MANIFEST.toml‎

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# ============================================================
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# .github/SE_MANIFEST.toml
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# SE_MANIFEST.toml (Repository Declaration)
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# ============================================================
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schema = "se-manifest-schema"
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schema_url = "https://github.com/structural-explainability/se-manifest-schema/blob/main/manifest-schema.toml"
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schema_url = "https://raw.githubusercontent.com/structural-explainability/se-manifest-schema/main/manifest-schema.toml"
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# === Identity ===
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# === Framework Context ===
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[meta]
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purpose = "Declares the organization-level GitHub health and governance repository for Structural Explainability."
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framework = "Structural Explainability"
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framework_url = "https://github.com/structural-explainability"
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purpose = "Declares this repository's role in the Structural Explainability ecosystem."
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# === Repository Identity ===
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[repo]
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name = ".github"
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since = "2025"
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summary = "Organization-wide profile for Structural Explainability."
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# === Layer Position ===
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[layer]
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space = "SE"
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space = "structural-explainability"
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role = "administration"
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# === Dependencies ===
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# === Dependency Declarations ===
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[depends]
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required = []
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optional = []
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# === Provided artifacts ===
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# === Provided Artifacts ===
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[provides]
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artifacts = ["README.md", "profile/README.md"]

‎profile/README.md‎

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| [se-theory-neutral-substrate](https://github.com/structural-explainability/se-theory-neutral-substrate) | Neutrality theorem development and defines admissible structure |
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| [se-theory-transformation](https://github.com/structural-explainability/se-theory-transformation) | Defines change pressure and foundational transformation operators, families, composition relations, orthogonality relations, and outcome vocabulary |
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| [se-theory-persistence](https://github.com/structural-explainability/se-theory-persistence) | Defines preservation, breakage, and irrelevance under admissible transformation |
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| [se-theory-identity-regimes](https://github.com/structural-explainability/se-theory-identity-regimes) | Define regime-specific identity behavior, six-regime lower bound, and refinement to nine-regime profiles |
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| [se-theory-identity-regimes](https://github.com/structural-explainability/se-theory-identity-regimes) | Define regime-specific identity behavior, six regime families refined into nine profile kinds |
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| [se-theory-structural-explainability](https://github.com/structural-explainability/se-theory-structural-explainability) | Explains the resulting judgment without collapsing disagreements |
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Note: Each theory repo contains both 1) a TOML encoding and 2) a Lean proof encoding
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This organization is structured around roles:
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| Role | Purpose |
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| ------------------------------------------------------------- | ----------------------------------------------------------------------- |
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| [**Accountable Record Systems**](#accountable-record-systems) | User-facing applications that implement and demonstrate the constraints |
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| [**Specifications**](#early-specifications) | Define what must be true for admissibility |
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| [**Formalizations**](#formalizations) | Demonstrate that specifications are internally consistent |
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| [**Papers**](#papers) | Justify why the constraints are necessary and unavoidable |
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## Early Specifications
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These repositories defined the admissible representational space
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| Role | Purpose |
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| ------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------ |
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| [**Theory Derivation**](#theory-formal-derivation-layer) | Derive and justify the formal contract. |
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| [**Formal Contract and Operational Foundations**](#formal-contract-and-operational-foundations) | Export and enforce the neutral structural constraints used by operational layers. |
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| [**Reference Implementations and Formal Anchors**](#reference-implementations-and-formal-anchors) | Provide optional foundation, interface, and boundary implementations for systems that need shared implementation layers. |
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| [**Specifications**](#normative-and-informative-specifications) | Define structural constraints for admissible representation. |
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| [**Accountable Record Systems**](#accountable-record-systems) | Implement durable record systems that preserve SE structural distinctions. |
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| [**Verification Implementations**](#accountable-record-verification-implementations) | Check record systems, packages, profiles, locks, bundles, and reports against selected contracts. |
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| [**Mapping Examples**](#mapping-examples) | Show bounded conformance examples without extending the neutral core. |
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| [**Source Materials**](#source-materials-govsrc) | Preserve traceable source artifacts for reference by mappings, profiles, and rules. |
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| [**Papers**](#papers) | Explain why the constraints are necessary and unavoidable. |
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## Normative and Informative Specifications
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These repositories define the admissible representational space
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for structurally explainable systems.
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They are normative only in the sense of **defining structural constraints**, not interpretations.
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<details>
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<summary>See more</summary>
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### Structural Explainability (Foundation)
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### Structural Explainability Core Specification
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Defines neutrality and boundary constraints that apply to all downstream systems.
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| Repository | Purpose | Status |
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| --------------------------------------------------------------- | -------------------------------------------------------------- | --------- |
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| [spec-se](https://github.com/structural-explainability/spec-se) | Neutrality and boundary constraints for all downstream systems | Normative |
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### Neutral Substrate (AE / EP)
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### Accountable Entity and Evolution Specifications
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These repositories define the core representational substrate
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for structurally explainable systems.
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These repositories define the accountable-entity and evolution layers
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used by downstream structurally explainable information systems.
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| Repository | Purpose | Status |
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| --------------------------------------------------------------- | ----------------------------------------- | --------- |
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</details>
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## Formalizations
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## Reference Implementations and Formal Anchors
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These repositories **do not define meaning or behavior**.
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They demonstrate that the specifications are internally consistent,
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coherent, and composable under formal reasoning.
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These repositories provide optional reference implementations and formal anchors
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for building information systems on the Structural Explainability theory layer.
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<details>
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<summary>See more</summary>
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### Original / Outdated Foundations
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They are not required by every downstream system.
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Existing information systems may adopt SE by preserving the required structural
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distinctions in their own architectures, schemas, records, and validation processes.
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> ⚠️ The repositories below are archived. Active development has moved to
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> the `se-theory-*` series.
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These repositories exist for systems that need a ready-made foundation,
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a formally anchored implementation vocabulary, or a shared implementation path.
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They instantiate, constrain, or enforce the corresponding specifications without
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replacing the active `se-theory-*` derivation repositories.
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| Repository | Purpose | CI | Description |
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| ------------------------------------------------------------------------------------------------- | ------------------------- | -------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------- |
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| [StructuralExplainability](https://github.com/structural-explainability/StructuralExplainability) | Cross-cutting constraints | ![CI](https://github.com/structural-explainability/StructuralExplainability/actions/workflows/ci-lean.yml/badge.svg?branch=main) | Neutrality and conformance predicates |
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| [NeutralSubstrate](https://github.com/structural-explainability/NeutralSubstrate) | Neutrality theorem | ![CI](https://github.com/structural-explainability/NeutralSubstrate/actions/workflows/ci-lean.yml/badge.svg?branch=main) | Substrates stable under incompatible extensions must be pre-causal and pre-normative |
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| [IdentityRegimes](https://github.com/structural-explainability/IdentityRegimes) | Identity regimes | ![CI](https://github.com/structural-explainability/IdentityRegimes/actions/workflows/ci-lean.yml/badge.svg?branch=main) | Six identity-and-persistence regime (families) are necessary and sufficient for accountability-oriented substrates under neutrality assumptions |
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<details>
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<summary>See more</summary>
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### Neutral Substrate (AE / EP)
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### Optional Foundation Implementations
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These repositories formalize the neutral substrate defined by AE and EP.
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These repositories provide reusable accountable-entity and evolution foundations
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for downstream systems that need them.
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They are reference implementation layers, not universal dependencies.
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| Repository | Purpose | CI | Description |
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| --------------------------------------------------------------------------------------- | --------------------------- | --------------------------------------------------------------------------------------------------------------------------- | ------------------------------------ |
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| [AccountableEntities](https://github.com/structural-explainability/AccountableEntities) | Entity-regime instantiation | ![CI](https://github.com/structural-explainability/AccountableEntities/actions/workflows/ci-lean.yml/badge.svg?branch=main) | Formalization of AE identity regimes |
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| [EvolutionProtocol](https://github.com/structural-explainability/EvolutionProtocol) | Neutral exchange substrate | ![CI](https://github.com/structural-explainability/EvolutionProtocol/actions/workflows/ci-lean.yml/badge.svg?branch=main) | Formalization of EP graph evolution |
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### Interface (CEE)
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### Optional Interface Implementation (CEE)
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This repository formalizes **the structural interface layer**
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over the neutral substrate.
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This repository provides a reusable structural interface for contextual evidence,
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explanation, attestation, and provenance.
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Systems may implement equivalent boundary-respecting structures without depending
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on this repository directly.
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| Repository | Purpose | CI | Description |
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| ------------------------------------------------------- | ------------------- | ----------------------------------------------------------------------------------------------------------- | -------------------------------------------------------- |
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| [CEE](https://github.com/structural-explainability/CEE) | Explanation overlay | ![CI](https://github.com/structural-explainability/CEE/actions/workflows/ci-lean.yml/badge.svg?branch=main) | Structural forms for contextual explanation and evidence |
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### Boundaries (GB / IB)
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### Optional Boundary Implementations (GB / IB)
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These repositories formalize **additional structural boundaries**
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that operate relative to the neutral substrate.
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They keep interpretation from leaking into the neutral substrate.
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These repositories provide reusable governance and interpretation boundary
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implementations.
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They are intended for systems that need explicit boundary machinery rather than
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for systems that already enforce these constraints internally.
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| Repository | Purpose | CI | Description |
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| --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------- |
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| [GovernanceBoundary](https://github.com/structural-explainability/GovernanceBoundary) | Governance boundary | ![CI](https://github.com/structural-explainability/GovernanceBoundary/actions/workflows/ci-lean.yml/badge.svg?branch=main) | Governance |
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| [InterpretationBoundary](https://github.com/structural-explainability/InterpretationBoundary) | Interpretation boundary | ![CI](https://github.com/structural-explainability/InterpretationBoundary/actions/workflows/ci-lean.yml/badge.svg?branch=main) | Conditions under which external frameworks may interpret substrate records |
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### Archived / Superseded Theory Repositories
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> ⚠️ The repositories below are archived. Active development has moved to
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> the `se-theory-*` series.
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| Repository | Purpose | CI | Description |
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| ------------------------------------------------------------------------------------------------- | ------------------------- | -------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------- |
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| [StructuralExplainability](https://github.com/structural-explainability/StructuralExplainability) | Cross-cutting constraints | ![CI](https://github.com/structural-explainability/StructuralExplainability/actions/workflows/ci-lean.yml/badge.svg?branch=main) | Neutrality and conformance predicates |
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| [NeutralSubstrate](https://github.com/structural-explainability/NeutralSubstrate) | Neutrality theorem | ![CI](https://github.com/structural-explainability/NeutralSubstrate/actions/workflows/ci-lean.yml/badge.svg?branch=main) | Substrates stable under incompatible extensions must be pre-causal and pre-normative |
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| [IdentityRegimes](https://github.com/structural-explainability/IdentityRegimes) | Identity regimes | ![CI](https://github.com/structural-explainability/IdentityRegimes/actions/workflows/ci-lean.yml/badge.svg?branch=main) | Six identity-and-persistence regime (families) are necessary and sufficient for accountability-oriented substrates under neutrality assumptions |
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</details>
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## Papers

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