RSR standardization: bulk sync 2025-12-10

Automated commit from bulk-commit-push.sh
- Standardized repo structure
- Applied RSR templates
- Synced local changes

🤖 Generated with Claude Code

Author: Jonathan D.A. Jewell

.guix-channel

@@ -0,0 +1,7 @@
+;; echidna - Guix Channel
+;; Add to ~/.config/guix/channels.scm
+
+(channel
+ (version 0)
+ (url "https://github.com/hyperpolymath/echidna")
+ (branch "main"))

.well-known/dc.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<metadata xmlns="http://purl.org/dc/elements/1.1/"
+          xmlns:dcterms="http://purl.org/dc/terms/">
+  <title>echidna</title>
+  <creator>Hyper Polymath</creator>
+  <subject>RSR</subject>
+  <description>RSR-compliant project</description>
+  <publisher>Rhodium Standard</publisher>
+  <date>2025</date>
+  <type>Software</type>
+  <identifier>https://github.com/hyperpolymath/echidna</identifier>
+  <language>en</language>
+  <rights>AGPL-3.0-or-later OR LicenseRef-Palimpsest-0.5</rights>
+  <dcterms:license>https://spdx.org/licenses/AGPL-3.0-or-later.html</dcterms:license>
+  <dcterms:hasVersion>0.1.0</dcterms:hasVersion>
+  <dcterms:isPartOf>RSR Framework</dcterms:isPartOf>
+</metadata>

README.md README.adocREADME.md renamed to README.adoc

@@ -3,9 +3,9 @@ SPDX-License-Identifier: MIT AND Palimpsest-0.6
 SPDX-FileCopyrightText: 2024-2025 ECHIDNA Project Contributors
 -->
 
-# ECHIDNA
+= ECHIDNA
 
-**E**xtensible **C**ognitive **H**ybrid **I**ntelligence for **D**eductive **N**eural **A**ssistance
+*E*xtensible *C*ognitive *H*ybrid *I*ntelligence for *D*eductive *N*eural *A*ssistance
 
 [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSES/MIT.txt)
 [![License: Palimpsest-0.6](https://img.shields.io/badge/License-Palimpsest--0.6-green.svg)](LICENSES/Palimpsest-0.6.txt)
@@ -14,93 +14,93 @@ SPDX-FileCopyrightText: 2024-2025 ECHIDNA Project Contributors
 
 A neurosymbolic theorem proving platform that transforms Quill (Agda-only neural solver) into a universal multi-prover system supporting 12 theorem provers with aspect tagging, OpenCyc integration, and DeepProbLog probabilistic logic.
 
-## Features
+== Features
 
-- **12 Theorem Prover Support**: Universal backend supporting Agda, Coq/Rocq, Lean, Isabelle, Z3, CVC5, Metamath, HOL Light, Mizar, PVS, ACL2, and HOL4
-- **Neurosymbolic AI**: Neural proof synthesis combined with symbolic verification
-- **Aspect Tagging**: Intelligent proof categorization and analysis
-- **OpenCyc Integration**: Common sense reasoning with ontological knowledge
-- **DeepProbLog**: Probabilistic logic programming for uncertain reasoning
-- **4-Language Architecture**: Rust (core), Julia (ML), ReScript (UI), Mercury/Logtalk (logic)
+- *12 Theorem Prover Support*: Universal backend supporting Agda, Coq/Rocq, Lean, Isabelle, Z3, CVC5, Metamath, HOL Light, Mizar, PVS, ACL2, and HOL4
+- *Neurosymbolic AI*: Neural proof synthesis combined with symbolic verification
+- *Aspect Tagging*: Intelligent proof categorization and analysis
+- *OpenCyc Integration*: Common sense reasoning with ontological knowledge
+- *DeepProbLog*: Probabilistic logic programming for uncertain reasoning
+- *4-Language Architecture*: Rust (core), Julia (ML), ReScript (UI), Mercury/Logtalk (logic)
 
-## Quick Start
+== Quick Start
 
-### Prerequisites
+=== Prerequisites
 
-- **Rust** 1.75 or later
-- **Julia** 1.10 or later
-- **Deno** 1.40 or later (for ReScript)
-- **Podman** (NOT Docker)
-- **Just** command runner
+- *Rust* 1.75 or later
+- *Julia* 1.10 or later
+- *Deno* 1.40 or later (for ReScript)
+- *Podman* (NOT Docker)
+- *Just* command runner
 
-### Installation
+=== Installation
 
 ```bash
-# Clone the repository
+= Clone the repository
 git clone https://gitlab.com/non-initiate/rhodinised/quill.git
 cd quill
 
-# Build the project
+= Build the project
 just build
 
-# Run tests
+= Run tests
 just test
 
-# Run ECHIDNA
+= Run ECHIDNA
 just run
 ```
 
-### Using Podman Container
+=== Using Podman Container
 
 ```bash
-# Build container
+= Build container
 podman build -f Containerfile -t echidna:latest .
 
-# Run container
+= Run container
 podman run -it echidna:latest
 ```
 
-## Architecture
+== Architecture
 
-### Prover Tiers
+=== Prover Tiers
 
-**Tier 1** (6 provers - Months 2-4):
+*Tier 1* (6 provers - Months 2-4):
 - Agda - Dependent type theory
 - Coq/Rocq - Interactive theorem prover
 - Lean - Functional programming and proving
 - Isabelle - Higher-order logic
 - Z3 - SMT solver
 - CVC5 - SMT solver
 
-**Tier 2** (3 provers - Months 5-7):
+*Tier 2* (3 provers - Months 5-7):
 - Metamath - Plain text verifier (easiest, start here!)
 - HOL Light - Classical higher-order logic
 - Mizar - Mathematical vernacular
 
-**Tier 3** (2 provers - Months 8-10):
+*Tier 3* (2 provers - Months 8-10):
 - PVS - Specification and verification
 - ACL2 - Applicative Common Lisp
 
-**Tier 4** (1 prover - Months 11-12):
+*Tier 4* (1 prover - Months 11-12):
 - HOL4 - Higher-order logic
 
-### Technology Stack
+=== Technology Stack
 
-- **Rust**: Core logic, FFI, WASM compilation
-- **Julia**: Machine learning components (NO Python allowed!)
-- **ReScript + Deno**: User interface
-- **Mercury/Logtalk**: Optional logic reservoir
+- *Rust*: Core logic, FFI, WASM compilation
+- *Julia*: Machine learning components (NO Python allowed!)
+- *ReScript + Deno*: User interface
+- *Mercury/Logtalk*: Optional logic reservoir
 
-### Key Components
+=== Key Components
 
-- **`echidna_provers.rs`**: Complete Rust trait system (600+ lines)
-- **Aspect Tagging System**: Proof classification and analysis
-- **Neural Solver**: Integration from original Quill project
-- **Universal Prover Abstraction**: Unified interface for all 12 provers
+- *`echidna_provers.rs`*: Complete Rust trait system (600+ lines)
+- *Aspect Tagging System*: Proof classification and analysis
+- *Neural Solver*: Integration from original Quill project
+- *Universal Prover Abstraction*: Unified interface for all 12 provers
 
-## Usage
+== Usage
 
-### Basic Theorem Proving
+=== Basic Theorem Proving
 
 ```rust
 use echidna::prover::{Prover, AgdaProver};
@@ -110,7 +110,7 @@ let result = prover.prove("∀ (n : ℕ) → n + 0 ≡ n")?;
 println!("Proof: {}", result);
 ```
 
-### Using Multiple Provers
+=== Using Multiple Provers
 
 ```rust
 use echidna::prover::{ProverBackend, lean, coq, z3};
@@ -125,69 +125,69 @@ for backend in backends {
 }
 ```
 
-### Neural Proof Synthesis
+=== Neural Proof Synthesis
 
 ```julia
 using ECHIDNA
 
-# Train neural model
+= Train neural model
 model = train_proof_synthesizer(training_data)
 
-# Generate proof candidates
+= Generate proof candidates
 candidates = synthesize_proofs(model, theorem)
 
-# Verify with symbolic prover
+= Verify with symbolic prover
 for candidate in candidates
     if verify_proof(candidate)
         return candidate
     end
 end
 ```
 
-## Development
+== Development
 
-### Building from Source
+=== Building from Source
 
 ```bash
-# Install dependencies
+= Install dependencies
 just deps
 
-# Build all components
+= Build all components
 just build
 
-# Build specific component
+= Build specific component
 just build-rust
 just build-julia
 just build-rescript
 ```
 
-### Running Tests
+=== Running Tests
 
 ```bash
-# Run all tests
+= Run all tests
 just test
 
-# Run specific language tests
+= Run specific language tests
 just test-rust
 just test-julia
 
-# Run integration tests
+= Run integration tests
 just test-integration
 ```
 
-### Quality Checks
+=== Quality Checks
 
 ```bash
-# Run all quality checks
+= Run all quality checks
 just check
 
-# Individual checks
+= Individual checks
 just lint          # REUSE, rustfmt, clippy
 just security      # Trivy, cargo-audit
 just coverage      # Test coverage
 ```
 
-## Documentation
+== Documentation
 
 - [Contributing Guidelines](CONTRIBUTING.md)
 - [Code of Conduct](CODE_OF_CONDUCT.md)
@@ -196,49 +196,49 @@ just coverage      # Test coverage
 - [API Documentation](docs/)
 - [Prover Backend Guides](docs/)
 
-## Roadmap
+== Roadmap
 
-### 12-Month Implementation Plan
+=== 12-Month Implementation Plan
 
-**Months 1-2**: Foundation
+*Months 1-2*: Foundation
 - Deploy RSR/CCCP compliance templates
 - Migrate Python code to Julia
 - Complete Tier 1 infrastructure
 
-**Months 2-4**: Tier 1 Provers
+*Months 2-4*: Tier 1 Provers
 - Coq/Rocq implementation
 - Lean implementation
 - Isabelle implementation
 - Z3 and CVC5 integration
 
-**Months 5-7**: Tier 2 Provers
+*Months 5-7*: Tier 2 Provers
 - Metamath (start here - easiest!)
 - HOL Light
 - Mizar
 
-**Months 8-10**: Tier 3 Provers
+*Months 8-10*: Tier 3 Provers
 - PVS
 - ACL2
 
-**Months 11-12**: Tier 4 and Polish
+*Months 11-12*: Tier 4 and Polish
 - HOL4 implementation
 - Performance optimization
 - Documentation completion
 
-## Contributing
+== Contributing
 
 We welcome contributions! Please see [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.
 
-### Critical Constraints
+=== Critical Constraints
 
-- ❌ **NO PYTHON** - Use Julia for all ML code
-- ✅ **RSR/CCCP Compliance** - Follow Rhodium Standard Repository guidelines
-- ✅ **Justfile PRIMARY** - Use Just, not Make
-- ✅ **GitLab-first** - This is a GitLab project
-- ✅ **Podman not Docker** - Always use Podman
-- ✅ **Dual Licensing** - MIT + Palimpsest v0.6
+- ❌ *NO PYTHON* - Use Julia for all ML code
+- ✅ *RSR/CCCP Compliance* - Follow Rhodium Standard Repository guidelines
+- ✅ *Justfile PRIMARY* - Use Just, not Make
+- ✅ *GitLab-first* - This is a GitLab project
+- ✅ *Podman not Docker* - Always use Podman
+- ✅ *Dual Licensing* - MIT + Palimpsest v0.6
 
-## License
+== License
 
 This project is dual-licensed under:
 
@@ -247,7 +247,7 @@ This project is dual-licensed under:
 
 See [NOTICE](NOTICE) for complete license information.
 
-## Citation
+== Citation
 
 If you use ECHIDNA in your research, please cite:
 
@@ -261,20 +261,20 @@ If you use ECHIDNA in your research, please cite:
 }
 ```
 
-## Acknowledgments
+== Acknowledgments
 
 - Based on the Quill project (Agda neural solver)
 - Built on the shoulders of the theorem proving community
 - See [AUTHORS.md](AUTHORS.md) for contributor list
 
-## Contact
+== Contact
 
-- **GitLab Issues**: https://gitlab.com/non-initiate/rhodinised/quill/-/issues
-- **Merge Requests**: https://gitlab.com/non-initiate/rhodinised/quill/-/merge_requests
-- **Security**: security@echidna-project.org
+- *GitLab Issues*: https://gitlab.com/non-initiate/rhodinised/quill/-/issues
+- *Merge Requests*: https://gitlab.com/non-initiate/rhodinised/quill/-/merge_requests
+- *Security*: security@echidna-project.org
 
 ---
 
-**Version**: 0.1.0
-**Status**: Active Development
-**Last Updated**: 2025-11-22
+*Version*: 0.1.0
+*Status*: Active Development
+*Last Updated*: 2025-11-22