CRQ-46: crq document index

[jmikedupont2]

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CRQ-46-crq-document-index.md

Change Request: crq document index

CRQ Document Index: A Guide to the Lattice Idea Framework's Conceptual Development

This document serves as an index and guide to the various Conceptual Research Questions (CRQ) documents that detail the development, implications, and applications of the Lattice Idea Framework. Each CRQ document explores a specific facet of the framework, contributing to its comprehensive understanding.

Index of CRQ Documents

• Zos Sequence Self-Application: Iterative Attribute Expansion

  • Description: Explores the meta-application of the zos sequence to itself, demonstrating how it iteratively expands the descriptive attributes of models by adding new predicates, aspects, or morphisms.

• Lattice Code Generation and Mapping: Addressing and Organizing Knowledge

  • Description: Details how the parameters of the lattice code generator define the address of generated objects within the lattice, and the process of generating a directory hierarchy that reflects the lattice, followed by mapping existing code into this structure by similarity.

• LLM Communication Protocol: Audited, Controlled, Curried, and Continuable

  • Description: Outlines the conceptual design for a robust communication protocol for LLMs, emphasizing auditing, control, currying for contextual pre-filling, and continuation for stateful interaction.

• Rust Code Generation for Lattice Structures: Programmatic Construction of the Framework

  • Description: Describes the process of programmatically generating Rust code for the Lattice Idea Framework's core structures using syn and quote, and the creation of a callable code generation module.

• Conceptual Rust Implementation: The Lattice of Types

  • Description: Details the conceptual Rust implementation of the Lattice Idea Framework's core data structures using enums, structs, traits, and generics, representing the multi-layered lattice.

• K-Value Type Semantics: Expanding Predicate Granularity in the Lattice

  • Description: Defines the semantic interpretation of different k-value types (2, 3, 5, 7, ..., 19) within the lattice, mapping them to boolean predicates, relational statements, contextualized statements, and higher-order models.

• Meta-Lattice Application: N-grams on K=19 Tuples for a Level 2 Lattice

  • Description: Proposes applying n-gram analysis to the values of k=19 tuples, creating a "Level 2 Lattice" and demonstrating the recursive and fractal nature of the framework.

• Concrete Lattice Analysis Example: Identifying Repeating Patterns in N-grams

  • Description: Outlines a specific analytical workflow for finding repeating elements and patterns within selected top N n-grams across specific layers, demonstrating practical application.

• Audited and Controlled LLM Interaction: Ensuring Trust and Transparency in Knowledge Extraction

  • Description: Focuses on the critical aspects of auditing and control within the LLM communication protocol, emphasizing how the lattice provides the framework for traceability, control, and reliability.

• Open-Source Language and Compiler Classification: The 1k Repo Grounding

  • Description: Proposes classifying open-source programming languages and compilers within the framework, emphasizing "vibes" and "memes," and the crucial assertion that understanding one repository requires grounding from approximately 1,000 others.

This index will be updated as new CRQ documents are developed, providing a comprehensive overview of the Lattice Idea Framework's evolving conceptual landscape.

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PR Type

Enhancement, Documentation

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Description

• Major Lattice Framework Implementation: Complete implementation of the Lattice Idea Framework with core type system, code generation utilities, and multiple applications demonstrating lattice-based classification and analysis
• Comprehensive Tool Suite: Added multiple specialized tools including submodule collector, project file lattice builder, git project reader, and report analyzer with extensive functionality
• Code Generation System: Implemented procedural macro utilities for generating Rust lattice structures, including value types, lattice layers, and instance management
• Repository Analysis Tools: Created sophisticated repository search simulator, meta-lattice model, and grand unified search system for large-scale codebase analysis
• Documentation and Standardization: Added extensive CRQ documentation covering lattice applications, testing frameworks, and development methodologies
• Development Infrastructure: Enhanced Nix flake with new packages and development tools, added comprehensive test suites and benchmarking infrastructure
• GitHub Integration Scripts: Created workflow automation scripts for CRQ processing, GitHub CLI wrappers, and repository management
• Generated Code Structures: Produced complete lattice type definitions and placeholder implementations for multi-layered framework demonstration

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Diagram Walkthrough

flowchart LR
  A["Core Lattice Types"] --> B["Code Generation"]
  B --> C["Generated Structures"]
  A --> D["Classification Apps"]
  D --> E["Repository Analysis"]
  E --> F["Search & Mapping"]
  G["Development Tools"] --> H["Submodule Collector"]
  G --> I["Project File Builder"]
  J["Documentation"] --> K["CRQ Standards"]
  J --> L["Testing Framework"]
  M["Infrastructure"] --> N["Nix Configuration"]
  M --> O["GitHub Scripts"]

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File Walkthrough

	Relevant files
Configuration changes	2 files flake.nix Enhanced Nix flake with submodule-collector package and development tools flake.nix • Removed empty line at the beginning of the file • Added new submodule-collector package derivation with Rust build configuration • Added multiple development tools including jq, valgrind, Emacs packages, and formatting tools +34/-1    shell.nix Added valgrind to development shell dependencies                  shell.nix • Added pkgs.valgrind to the buildInputs list for development shell +1/-1
Enhancement	54 files lib.rs Lattice code generation library with procedural macro utilities lattice_code_generator/src/lib.rs • New library providing code generation utilities for the Lattice Idea Framework • Implements functions to generate Rust enums, structs, and traits using syn and quote • Includes comprehensive test suite for generated code validation +296/-0  main.rs Git submodule collector tool with recursive scanning capabilities submodule-collector/src/main.rs • New command-line tool for scanning Git repositories and submodules recursively • Collects detailed repository information including remote URLs, paths, and branches • Outputs comprehensive JSON reports with error handling for failed repositories +279/-0  main.rs Project file lattice builder with predicate-based classification project_file_lattice_builder/src/main.rs • New application that constructs a conceptual lattice of project files • Implements file classification using word predicates and lattice hierarchy • Includes comprehensive test suite for predicate extraction and classification +202/-0  lattice_mapper_app.rs Lattice mapper application for code similarity classification src/lattice_mapper_app.rs • New application demonstrating code mapping into pre-generated lattice structures • Implements similarity-based classification using predicate matching • Bridges lattice structure generation with repository search functionality +209/-0  lattice_types.rs Core lattice type definitions with multi-layered framework src/lattice_types.rs • Defines conceptual lattice type system using Rust enums, structs, and traits • Implements multi-layered lattice with different value types and n-gram instances • Includes demonstration of lattice construction with boolean and three-value types +196/-0  repo_search_simulator.rs Repository search simulator with predicate-based similarity matching src/repo_search_simulator.rs • Simulates repository search functionality using predicate-based classification • Implements search-by-example across mock repositories with similarity scoring • Demonstrates lattice framework application to large codebase analysis +202/-0  meta_lattice_model.rs Self-referential meta-lattice model for framework introspection src/meta_lattice_model.rs • Meta-model implementation that analyzes the lattice framework itself • Demonstrates self-referential capacity with conceptual similarity finding • Embodies the framework's ability to model its own structure +153/-0  analyze_strings.rs String analysis module with n-gram processing and ontology mapping report-analyzer-rs/src/analyze_strings.rs • String analysis module with token collection and frequency counting • Implements n-gram generation and analysis with emoji ontology application • Provides suggested rule generation based on token patterns +171/-0  lattice_classifier_app.rs Lattice classifier application for predicate-based text analysis src/lattice_classifier_app.rs • Classification application using generated lattice structures • Implements predicate-based text classification with word predicates • Demonstrates search-by-example functionality within lattice framework +188/-0  lib.rs Git project reader library with comprehensive repository information extraction git_project_reader/src/lib.rs • Library for reading Git project information including tracked files and status • Implements comprehensive test suite with temporary repository creation • Provides structured data collection from Git repositories +174/-0  grand_unified_search.rs Grand unified search system concept with self-analysis capabilities src/grand_unified_search.rs • Conceptual outline for grand unified search system across repositories • Demonstrates self-parsing, similarity search, and LLM interaction concepts • Provides framework for large-scale code analysis and knowledge extraction +148/-0  lattice_model.rs Core lattice model with value types and predicate classification src/lattice_model.rs • Core lattice model definitions with value types and layer structures • Implements traits for value counting and lattice layer management • Provides predicate classifier for text analysis within lattice framework +136/-0  word_predicate_analyzer.rs Word predicate analyzer with n-gram generation and lattice integration src/word_predicate_analyzer.rs • Word predicate analysis using lattice type definitions • Implements text tokenization and n-gram generation for predicate analysis • Demonstrates integration with lattice structure for text processing +95/-0    main.rs Lattice structure generator with hierarchical directory creation lattice_structure_generator/src/main.rs • Generates structured lattice hierarchy with parameterized layer creation • Creates directory structure representing lattice organization • Demonstrates conceptual mapping of existing code into lattice bins +82/-0    lib.rs ZOS lattice builder integration with project file classification src/lib.rs • Added build_zos_lattice function for project file classification • Integrates lattice model with file processing and predicate extraction • Provides structured approach to organizing project files in lattice layers +78/-0    main.rs Lattice generator application for code structure creation lattice_generator_app/src/main.rs • Application for generating lattice code structures to files • Uses lattice code generator library to create complete type definitions • Outputs generated code to organized directory structure +56/-0    main.rs Initial report analyzer main implementation with CLI interface report-analyzer-rs/src/main.rs • Added new main.rs file for report analyzer with command-line argument parsing using clap • Implemented basic report loading and analysis functionality with JSON deserialization • Added calls to analyze_strings module for string analysis and emoji application • Included commented-out calls to various analysis functions for future implementation +50/-0    program_self_description.rs Self-describing program implementation for lattice framework demonstration src/program_self_description.rs • Created a conceptual Rust program demonstrating self-description capabilities • Implemented functions to describe the program itself and search for similar programs • Added meta-assertion functionality reflecting the theoretical framework's postulates • Demonstrates the "word as predicate" model and program similarity concepts +37/-0    lcp.rs Longest common prefix analysis implementation for repository data report-analyzer-rs/src/lcp.rs • Implemented longest common prefix (LCP) analysis functionality • Added find_longest_common_prefix function for string comparison • Created perform_lcp_analysis to analyze repository paths and URLs • Included print function for displaying LCP analysis results +51/-0    my_profiling_bench.rs Performance benchmarking infrastructure with iai-callgrind integration benches/my_profiling_bench.rs • Added performance benchmarking setup using iai_callgrind library • Created benchmark functions for add function and git config parsing • Implemented dummy function for demonstration of profiling capabilities • Set up benchmark group configuration for performance testing +36/-0    types.rs Core type definitions for report analyzer with CLI support report-analyzer-rs/src/types.rs • Defined core data structures for report analysis including SubmoduleInfo, RepoInfo, FailedRepoInfo • Added Report struct with repositories and failed repositories tracking • Implemented command-line arguments structure with clap Parser derive • Created Ontology type for emoji mapping functionality +47/-0    analyze_names.rs Repository name analysis with frequency counting implementation report-analyzer-rs/src/analyze_names.rs • Implemented repository name analysis functionality using regex patterns • Added extraction of repository names from GitHub URLs • Created frequency counting for repository and submodule names • Included processing of nested repository structures +30/-0    value_type.rs Generated ValueType enum implementation for lattice framework generated_lattice_code/value_type.rs • Generated Rust code for ValueType enum with prime value variants • Implemented count method for retrieving value type counts • Added zos_sequence function returning vector of value types • Created comprehensive enum covering bit, three-value, five-value, and prime value types +1/-0      value_type.rs Duplicate ValueType enum in alternative structure directory generated_lattice_structure/value_type.rs • Duplicate of generated lattice code for value type enum • Contains identical implementation of ValueType enum and methods • Represents alternative output location for generated code +1/-0      analyze_orgs.rs Organization analysis with frequency counting from GitHub URLs report-analyzer-rs/src/analyze_orgs.rs • Implemented organization analysis functionality using regex for GitHub URLs • Added extraction of organization names from repository URLs • Created frequency counting for organizations across repositories • Included processing of failed repositories for comprehensive analysis +26/-0    lattice_struct.rs Generated Lattice struct with dynamic layer management system generated_lattice_code/lattice_struct.rs • Generated main Lattice struct with dynamic layer management • Implemented LatticeLayerTrait for polymorphic layer handling • Added methods for creating, adding layers, and describing lattice structure • Created trait object system for handling different layer types +1/-0      lattice_struct.rs Duplicate Lattice struct in alternative structure directory generated_lattice_structure/lattice_struct.rs • Duplicate of generated lattice struct implementation • Contains identical Lattice struct and trait definitions • Represents alternative output location for generated code +1/-0      instance_struct.rs Generated Instance struct for n-gram representation in lattice generated_lattice_code/instance_struct.rs • Generated Instance struct for representing n-grams and code snippets • Implemented generic structure with ID, n-gram size, and units vector • Added constructor and description methods for instance management • Created validation for n-gram size consistency +1/-0      instance_struct.rs Duplicate Instance struct in alternative structure directory generated_lattice_structure/instance_struct.rs • Duplicate of generated instance struct implementation • Contains identical Instance struct with generic type support • Represents alternative output location for generated code +1/-0      lattice_layer_struct.rs Generated LatticeLayer struct for value type organization generated_lattice_code/lattice_layer_struct.rs • Generated LatticeLayer struct for organizing instances by value type • Implemented layer management with value type validation • Added methods for creating layers, adding instances, and description • Created type-safe layer organization system +1/-0      lattice_layer_struct.rs Duplicate LatticeLayer struct in alternative structure directory generated_lattice_structure/lattice_layer_struct.rs • Duplicate of generated lattice layer struct implementation • Contains identical LatticeLayer struct and methods • Represents alternative output location for generated code +1/-0      duplicates.rs Duplicate repository URL analysis and reporting implementation report-analyzer-rs/src/duplicates.rs • Implemented duplicate URL analysis functionality for repositories • Added functions to identify and report duplicate repository URLs • Created mapping of URLs to multiple paths for duplicate detection • Included comprehensive reporting of duplicate findings +25/-0    input.rs Input handling implementation for CLI arguments and data loading report-analyzer-rs/src/input.rs • Implemented input handling functions for command-line arguments and data loading • Added parse_args function using clap for argument parsing • Created load_data function for JSON report and ontology loading • Included error handling for file reading and JSON deserialization +22/-0    apply_emojis.rs Emoji ontology application system for text enhancement      report-analyzer-rs/src/apply_emojis.rs • Implemented emoji ontology application functionality • Added text replacement system using ontology mappings • Created sorted key processing for longest-match replacement • Included optional ontology handling for emoji enhancement +18/-0    names_analysis.rs Names analysis display with emoji ontology integration      report-analyzer-rs/src/names_analysis.rs • Implemented names analysis printing functionality with emoji support • Added sorting and display of most frequent repository/submodule names • Created top-10 display with emoji ontology integration • Included handling for empty name collections +14/-0    org_analysis.rs Organization analysis display with emoji ontology support report-analyzer-rs/src/org_analysis.rs • Implemented organization analysis printing functionality • Added sorting and display of most frequent organizations • Created top-10 display with emoji ontology support • Included handling for empty organization collections +13/-0    main.rs Git repository testing application with git2 integration  git_test_repo/src/main.rs • Created simple Git repository testing application using git2 crate • Implemented repository opening and validation functionality • Added current directory detection and repository path display • Created basic Git repository interaction example +10/-0    instance_1.rs Placeholder instance implementation for k=2 layer                generated_lattice_structure/layer_k_2/instance_1.rs • Added placeholder code for instance 1 in k=2 layer • Created template for 2-value type instance implementation • Included comments describing intended structure and purpose +3/-0      instance_0.rs Placeholder instance implementation for k=3 layer (instance 0) generated_lattice_structure/layer_k_3/instance_0.rs • Added placeholder code for instance 0 in k=3 layer • Created template for 3-value type instance implementation • Included comments describing intended structure and purpose +3/-0      instance_1.rs Placeholder instance implementation for k=3 layer (instance 1) generated_lattice_structure/layer_k_3/instance_1.rs • Added placeholder code for instance 1 in k=3 layer • Created template for 3-value type instance implementation • Included comments describing intended structure and purpose +3/-0      has_value_count_impls.rs Generated HasValueCount trait implementation for bool type generated_lattice_code/has_value_count_impls.rs • Generated implementation of HasValueCount trait for bool type • Added value count method returning 2 for boolean type • Created foundation for trait implementation system +1/-0      has_value_count_impls.rs Duplicate HasValueCount implementation in alternative structure directory generated_lattice_structure/has_value_count_impls.rs • Duplicate of generated HasValueCount implementation • Contains identical trait implementation for bool type • Represents alternative output location for generated code +1/-0      has_value_count_trait.rs Generated HasValueCount trait definition for value counting generated_lattice_code/has_value_count_trait.rs • Generated HasValueCount trait definition • Added trait method for returning value count as u8 • Created foundation for generic value counting system +1/-0      has_value_count_trait.rs Duplicate HasValueCount trait in alternative structure directory generated_lattice_structure/has_value_count_trait.rs • Duplicate of generated HasValueCount trait definition • Contains identical trait definition and method signature • Represents alternative output location for generated code +1/-0      standardize_and_move_crqs.sh CRQ document standardization and organization script          tools/gh_scripts/standardize_and_move_crqs.sh • Created comprehensive bash script for CRQ document standardization • Implemented dry-run mode and robust CRQ number calculation • Added filename and header standardization with validation • Included automatic renaming and moving of CRQ files to standardized directory +149/-0  create_crq_workflow.sh CRQ workflow automation script with GitHub integration      tools/gh_scripts/create_crq_workflow.sh • Created workflow script for CRQ processing and GitHub integration • Implemented branch creation, task.md generation, and PR creation • Added CRQ content extraction and GitHub CLI integration • Created automated workflow for CRQ document processing +79/-0    boot.sh Boot orchestration script with session recording and crash recovery boot.sh • Created orchestration script for tmux session recording with asciinema • Implemented crash recovery checks with git status and diff logging • Added log processor integration and comprehensive logging system • Created session management and recovery workflow +38/-0    gh_extract_actors.sh GitHub actor extraction script for repository analysis      tools/gh_scripts/gh_extract_actors.sh • Created script to extract unique actors from GitHub issues and comments • Implemented JSON parsing with jq for actor identification • Added GitHub CLI integration for issue and comment data retrieval • Created comprehensive actor analysis from repository activity +41/-0    gh_workflows_view.sh GitHub workflow run viewing script wrapper                              tools/gh_scripts/gh_workflows_view.sh • Created simple wrapper script for viewing GitHub Actions workflow runs • Added parameter validation and usage instructions • Implemented direct pass-through to gh run view command +7/-0      gh_workflows_rerun.sh GitHub workflow re-run script wrapper                                        tools/gh_scripts/gh_workflows_rerun.sh • Created wrapper script for re-running GitHub Actions workflows • Added parameter validation and usage instructions • Implemented direct pass-through to gh run rerun command +7/-0      gh_issues_view.sh GitHub issue viewing script wrapper                                            tools/gh_scripts/gh_issues_view.sh • Created wrapper script for viewing GitHub issue details • Added parameter validation and usage instructions • Implemented direct pass-through to gh issue view command +7/-0      gh_prs_view.sh GitHub pull request viewing script wrapper                              tools/gh_scripts/gh_prs_view.sh • Created wrapper script for viewing GitHub pull request details • Added parameter validation and usage instructions • Implemented direct pass-through to gh pr view command +7/-0      gh_prs_checkout.sh GitHub pull request checkout script wrapper                            tools/gh_scripts/gh_prs_checkout.sh • Created wrapper script for checking out GitHub pull requests locally • Added parameter validation and usage instructions • Implemented direct pass-through to gh pr checkout command +7/-0      gh_prs_create.sh GitHub pull request creation script wrapper                            tools/gh_scripts/gh_prs_create.sh • Created simple wrapper script for creating GitHub pull requests • Implemented direct pass-through to gh pr create command • Added parameter forwarding for flexible PR creation +3/-0
Tests	3 files git-config-parser.rs Enhanced git-config-parser with comprehensive test coverage src/bin/git-config-parser.rs • Added comprehensive test suite for Git configuration parsing functions • Tests cover empty configs, comments, multiple sections, and submodule parsing • Removed unused import and improved code quality +131/-1  main_execution_test.rs Integration test for project file lattice builder binary  project_file_lattice_builder/tests/main_execution_test.rs • Added integration test for project file lattice builder binary execution • Implemented test to verify binary exists and runs successfully • Added stdout content validation for expected output messages • Created comprehensive test for main execution workflow +23/-0    main_execution_test.rs Integration test for submodule collector binary with help validation submodule-collector/tests/main_execution_test.rs • Added integration test for submodule collector binary execution • Implemented test using --help flag to verify basic functionality • Added validation for expected help message content in stdout • Created test to ensure binary exists and executes properly +24/-0
Miscellaneous	1 files instance_0.rs Generated lattice structure placeholder for layer k=2 instance generated_lattice_structure/layer_k_2/instance_0.rs • Generated placeholder file for lattice layer k=2 instance 0 • Represents conceptual implementation for 2-value type lattice structure +3/-0
Documentation	5 files submodule_report.json Complete submodule dependency mapping and inventory report submodule_report.json • Added comprehensive JSON report containing 2021 lines documenting all Git submodules and repositories • Includes repository URLs, local paths, and nested submodule structures • Maps extensive vendor dependencies across multiple projects including lattice-introspector, minizinc-introspector, and git-submodule-tools-rs +2021/-0 CRQ-48-lattice-and-quine-relay.md Lattice framework application to multi-language quine relay docs/crq_standardized/CRQ-48-lattice-and-quine-relay.md • Introduces concept of applying Lattice Idea Framework to 128-language quine relay • Proposes language-specific predicate extraction and generate-and-test methodology • Describes mapping quine relay transformations as lattice morphisms • Outlines implications for universal code understanding and cross-language generation +38/-0    structured_testing_framework.md Structured testing framework for lattice-based knowledge extraction docs/structured_testing_framework.md • Defines systematic testing framework based on Lattice Idea principles • Outlines lattice-guided test case generation and predicate-driven assertions • Describes layered evaluation methodology from simple to complex predicates • Includes test construction examples for different lattice layers and value types +38/-0    CRQ-003-deep-dive-and-reflection-on-nix-development-environment-graph.md Nix development environment dependency graph analysis framework docs/crq_standardized/CRQ-003-deep-dive-and-reflection-on-nix-development-environment-graph.md • Documents analysis methodology for Nix development environment dependency graph • Outlines systematic examination of nodes, edges, and transitive dependencies • Describes reflection process for understanding build complexity and optimization opportunities • Includes partial progress notes on devshell_graph.dot file analysis +58/-0    CRQ-51-meta-lattice-application.md Meta-lattice recursive application for Level 2 pattern analysis docs/crq_standardized/CRQ-51-meta-lattice-application.md • Proposes recursive application of lattice framework to create Level 2 Lattice • Describes n-gram analysis on k=19 tuple components for higher-order pattern discovery • Explains fractal nature of knowledge representation and meta-classification capabilities • Outlines implications for enhanced abstraction and grounding of complex models +32/-0
Additional files	101 files .git_commit_message.txt +0/-3      Cargo.toml +10/-1    README.md +102/-0  SOP_Nix_Graph_Reflection.md +88/-0    abstract_mathematical_idea.tex +76/-0    concept_word_as_predicate.md +20/-0    creative_expressions.md +106/-0  CRQ-004-rust-documentation-rustdoc-updates-for-binaries.md +35/-0    CRQ-005-readme-md-updates.md +34/-0    CRQ-006-formal-qa-procedures-and-standard-operating-procedures-sops-development.md +37/-0    CRQ-007-comprehensive-project-testing.md +37/-0    CRQ-008-the-crq-of-crqs.md +36/-0    CRQ-009-git-project-reader-library-and-integration.md +37/-0    CRQ-010-sop-documentation-and-cargo-lock-update.md +38/-0    CRQ-011-github-cli-sops-and-wrapper-scripts.md +46/-0    CRQ-012-integrate-git-submodule-tools-into-lattice-system.md +32/-0    CRQ-013-integrate-gitoxide-into-lattice-system.md +32/-0    CRQ-014-integrate-magoo-into-lattice-system.md +32/-0    CRQ-015-integrate-naersk-into-lattice-system.md +32/-0    CRQ-016-integrate-submod-into-lattice-system.md +32/-0    CRQ-017-submodule-lattice-integration-crqs-and-task-files.md +36/-0    CRQ-018-the-branch-as-a-holistic-development-unit.md +39/-0    CRQ-019-one-to-one-mapping-of-crq-to-branch-and-pull-request.md +38/-0    CRQ-020-braindump-update-and-crq-status-reflection.md +34/-0    CRQ-024-new-sops-for-crq-driven-development.md +35/-0    CRQ-025-rust-code-generation-for-lattice-structures-programmatic-construction-of-the-framework.md +36/-0    CRQ-026-zos-sequence-self-application-iterative-attribute-expansion.md +31/-0    CRQ-027-Open_Source_Language_and_Compiler_Classification_The_1k_Repo_Grounding.md +40/-0    CRQ-28-audited-llm-interaction.md +38/-0    CRQ-29-conceptual-rust-lattice-types.md +56/-0    CRQ-30-concrete-lattice-analysis-example.md +54/-0    CRQ-31-crq-001-review-git-log-patch.md +7/-0      CRQ-32-crq-002-automate-sops-to-rust.md +3/-0      CRQ-33-crq-002-submodule-report-function-development.md +44/-0    CRQ-34-crq-003-context-introspector.md +3/-0      CRQ-35-crq-004-formalize-interaction-procedure.md +3/-0      CRQ-36-crq-005-strategic-alignment.md +3/-0      CRQ-37-crq-006-process-unification-kether-review.md +3/-0      CRQ-38-crq-007-gitmodules-recon.md +3/-0      CRQ-39-crq-008-category-theory-hott-submodules.md +3/-0      CRQ-40-crq-009-grand-unified-framework.md +3/-0      CRQ-41-crq-009-grand-unified-framework-zoomed-in.md +3/-0      CRQ-42-crq-009-grand-unified-framework-zoomed-out.md +3/-0      CRQ-43-crq-010-dynamic-information-flow.md +3/-0      CRQ-44-crq-011-bott-periodicity.md +3/-0      CRQ-45-crq-012-naersk-integration.md +3/-0      CRQ-46-crq-document-index.md +40/-0    CRQ-47-k-value-type-semantics.md +41/-0    CRQ-49-lattice-code-generation-and-mapping.md +45/-0    CRQ-50-llm-communication-protocol.md +40/-0    CRQ-52-orchestration-layer-architecture.md +50/-0    CRQ-53-recursive-decomposition.md +40/-0    grand_unified_search_architecture.md +43/-0    Meme_CRQ_Commit_Message.md +11/-0    gta.md +7/-0      gta1.md +3/-0      oss_language_classification.md +35/-0    resonance_analysis.md +29/-0    scalable_analysis_of_large_repositories.md +40/-0    SOP_AI_Agent_Management_via_PRs.md +57/-0    SOP_Bootstrap_CRQ_Hypothesis_Implementation.md +45/-0    SOP_Branch_Driven_Development_Philosophy.md +59/-0    SOP_CRQ_as_Commit_Message.md +28/-0    SOP_Coding_Standards.md +28/-0    SOP_GH_CLI_Check_Issues.md +93/-0    SOP_GH_CLI_Check_PRs.md +101/-0  SOP_GH_CLI_Check_Workflows.md +84/-0    SOP_Integrated_Binary_Workflow.md +60/-0    SOP_Refactoring_with_CRQ_Branches.md +49/-0    SOP_Using_Git_Config_Parser.md +62/-0    SOP_Using_Project_File_Lattice_Builder.md +49/-0    SOP_Using_Submodule_Collector.md +52/-0    sops-debugging-submodule-counting.md +68/-0    sops-github-issue-workflow.md +44/-0    sops-herding-ai-flock.md +59/-0    sops-whistle-while-you-work.md +71/-0    task_git-submodule-tools_lattice_integration.md +21/-0    task_gitoxide_lattice_integration.md +23/-0    task_magoo_lattice_integration.md +15/-0    task_naersk_lattice_integration.md +22/-0    task_submod_lattice_integration.md +15/-0    emacs.sh +1/-0      Cargo.toml +15/-0    Cargo.toml +7/-0      gitoxide +1/-1      section_combinatorial_analysis.tex +2/-0      section_conclusion.tex +6/-0      section_functions_and_enumeration.tex +4/-0      section_instances_and_algebraic_composition.tex +17/-0    section_introduction.tex +2/-0      section_multi_layered_model.tex +11/-0    section_n_grams_and_core_topologies.tex +14/-0    section_primorial_base_sequence.tex +4/-0      section_proposed_application.tex +11/-0    Cargo.toml +9/-0      Cargo.toml +9/-0      Cargo.toml +9/-0      memes.md +3/-0      ontology.json +63/-0    Cargo.toml +7/-0      Additional files not shown

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⚡ Recommended focus areas for review Compile Error In the generated LatticeLayer code, the field is declared as Vec but add_instance pushes an Instance, which will not compile. The instances field should be Vec<Instance> and related methods should iterate over Instance. #[derive(Debug, Clone)] pub struct LatticeLayer<T: HasValueCount + std::fmt::Debug> { pub value_type: ValueType, pub instances: Vec<T>, } impl<T: HasValueCount + std::fmt::Debug> LatticeLayer<T> { pub fn new(value_type: ValueType) -> Self { Self { value_type, instances: Vec::new() } } pub fn add_instance(&mut self, instance: Instance<T>) { assert_eq!(instance.units[0].value_count(), self.value_type.count(), "Instance unit value count must match layer's value type"); self.instances.push(instance); } pub fn describe(&self) { Compile Error The entire file content is wrapped in triple quotes and includes invalid string/formatting, making it non-Rust syntax. This will fail to compile and should be rewritten as valid Rust (remove the leading/trailing triple quotes and fix the embedded string formatting). """//! This program conceptually outlines a "Grand Unified Search" system in Rust. //! It aims to demonstrate how a program could parse its own code, search for similar //! programs within a vast repository (like 10k submodules), and interact with LLMs //! for knowledge extraction, all within the framework of our defined lattice. // NOTE: This is a conceptual outline. Actual implementation of semantic code parsing, // LLM communication with currying/continuation, and deep submodule tool integration // would require significant external libraries, complex logic, and a robust // communication infrastructure, which are beyond the scope of this single file. use std::fs; use std::path::{Path, PathBuf}; // --- Conceptual Lattice Components --- // These structs represent the theoretical elements of our lattice, // which would be used to "address" and classify code patterns and knowledge. #[derive(Debug, PartialEq, Eq, Hash, Clone)] struct Predicate { name: String, // In Model 1, this is a bit (0 or 1) indicating presence/absence. // In higher layers, it could represent more complex values. value: u8, } #[derive(Debug, Clone)] struct CodeLatticeAddress { // Example: A unique identifier for a code pattern or knowledge unit. // This would be derived from the lattice's structure (layer, n-gram, etc.). address_components: Vec<String>, } // --- Core Functionality Placeholders --- /// Conceptually parses Rust code using `syn` to extract structural predicates. /// In a real implementation, this would involve detailed AST traversal. fn conceptual_syn_parse_and_extract_predicates(code: &str) -> Vec<Predicate> { println!(" [Conceptual Parsing] Analyzing code to extract predicates..."); // Placeholder for actual `syn` parsing logic. // For demonstration, we'll just look for some keywords. let mut predicates = Vec::new(); if code.contains("fn main") { predicates.push(Predicate { name: "has_main_function".to_string(), value: 1 }); } if code.contains("struct") { predicates.push(Predicate { name: "defines_struct".to_string(), value: 1 }); } if code.contains("impl") { predicates.push(Predicate { name: "has_impl_block".to_string(), value: 1 }); } if code.contains("use std::") { predicates.push(Predicate { name: "uses_std_lib".to_string(), value: 1 }); } println!(" Extracted {} conceptual predicates.", predicates.len()); predicates } /// Conceptually queries an LLM for help or knowledge extraction. /// In a real implementation, this would involve secure API calls, /// prompt engineering, and response parsing. fn conceptual_llm_query(query_text: &str, context_lattice_address: &CodeLatticeAddress) -> String { println!(" [Conceptual LLM Query] Asking LLM for help..."); println!(" Query: "{}"", query_text); println!(" Context Lattice Address: {:?}", context_lattice_address); // Placeholder for LLM interaction. "LLM_RESPONSE: Based on your query and the lattice context, here's some conceptual knowledge." .to_string() } /// Conceptually interacts with the submodule tool to list/access repositories. /// In a real implementation, this would involve executing shell commands /// or using a Rust crate that wraps git submodule functionality. fn conceptual_submodule_tool_list_repos() -> Vec<PathBuf> { println!(" [Conceptual Submodule Tool] Listing repositories..."); // Placeholder for actual submodule tool interaction. // For demonstration, return a few dummy paths. vec![ PathBuf::from("/data/data/com.termux.nix/files/home/pick-up-nix/source/github/meta-introspector/submodules/git_test_repo/src/main.rs"), PathBuf::from("/data/data/com.termux.nix/files/home/pick-up-nix/source/github/meta-introspector/submodules/report-analyzer-rs/src/main.rs"), PathBuf::from("/data/data/com.termux.nix/files/home/pick-up-nix/source/github/meta-introspector/submodules/src/program_self_description.rs"), PathBuf::from("/data/data/com.termux.nix/files/home/pick-up-nix/source/github/meta-introspector/submodules/src/meta_lattice_model.rs"), ] } /// The core search logic: reads its own code, extracts predicates, /// and then searches other programs for similarity based on these predicates. fn grand_unified_search() -> Result<(), Box<dyn std::error::Error>> { println!("--- Grand Unified Search Initiated ---"); // Step 1: Self-parsing and predicate extraction println!(" [Step 1] Self-analysis: Parsing this program's own code."); let self_code_path = PathBuf::from(file!()); // Path to this source file let self_code = fs::read_to_string(&self_code_path)?; let self_predicates = conceptual_syn_parse_and_extract_predicates(&self_code); let self_lattice_address = CodeLatticeAddress { address_components: vec!["self_model".to_string(), "layer1".to_string()], }; println!(" This program's conceptual predicates: {:?}", self_predicates); // Step 2: Search other programs in submodules println!(" [Step 2] Searching for similar programs in submodules."); let all_rust_files = conceptual_submodule_tool_list_repos(); // Get all Rust files (conceptual) for file_path in all_rust_files { if file_path == self_code_path { continue; // Skip self } println!(" Analyzing: {:?}", file_path); let other_code = fs::read_to_string(&file_path)?; let other_predicates = conceptual_syn_parse_and_extract_predicates(&other_code); // Conceptual similarity check based on shared predicates let mut shared_count = 0; for self_p in &self_predicates { if other_predicates.contains(self_p) { shared_count += 1; } } if shared_count > 0 { println!(" -> Found {} shared predicates with {:?}. Considered similar.", shared_count, file_path); // Step 3: Conceptual LLM interaction for deeper insight let llm_response = conceptual_llm_query( &format!("Explain the core function of {:?} based on these predicates: {:?}", file_path, other_predicates), &self_lattice_address, ); println!(" LLM Insight: {}", llm_response); } else { println!(" -> No shared conceptual predicates with {:?}. Not considered similar.", file_path); } } println!(" --- Grand Unified Search Concluded ---"); Ok(()) } fn main() -> Result<(), Box<dyn std::error::Error>> { grand_unified_search() } "" Possible Issue In generate_and_analyze_ngrams, comparing **n_gram to a String and pushing **count uses incorrect dereferencing. Use n_gram.as_str() != compressed_n_gram and *count (or clone/format appropriately). The current double deref will not compile. // Collect suggestions if **n_gram != compressed_n_gram { // Fixed type mismatch suggested_rules.push((n_gram.to_string(), **count)); } // For the next iteration, we want the compressed version of the n-gram // if it was actually compressed, otherwise the original n-gram. // We also need to ensure we're not adding duplicates or single emojis that are already compressed. next_iteration_tokens.push(compressed_n_gram.replace(" ", ""));

[qodo-merge-pro]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
Possible issue	Fix invalid enum and methods The enum implementation is syntactically invalid and the count method never returns a value. Also, constructors for payload variants are called without arguments. Implement proper match arms with return values and supply payloads in zos_sequence. generated_lattice_code/value_type.rs [1] -# [derive (Debug , PartialEq , Eq , Clone , Copy)] pub enum ValueType { Bit , ThreeValue , FiveValue , PrimeValue7 (u8) , PrimeValue11 (u8) , PrimeValue13 (u8) , PrimeValue17 (u8) , PrimeValue19 (u8) , } impl ValueType { pub fn count (& self) -> u8 { match self { ValueType :: Bit , ValueType :: ThreeValue , ValueType :: FiveValue , ValueType :: PrimeValue7 (p) , ValueType :: PrimeValue11 (p) , ValueType :: PrimeValue13 (p) , ValueType :: PrimeValue17 (p) , ValueType :: PrimeValue19 (p) , } } pub fn zos_sequence () -> Vec < ValueType > { vec ! [ValueType :: Bit , ValueType :: ThreeValue , ValueType :: FiveValue , ValueType :: PrimeValue7 , ValueType :: PrimeValue11 , ValueType :: PrimeValue13 , ValueType :: PrimeValue17 , ValueType :: PrimeValue19 ,] } } +#[derive(Debug, PartialEq, Eq, Clone, Copy)] +pub enum ValueType { + Bit, + ThreeValue, + FiveValue, + PrimeValue7(u8), + PrimeValue11(u8), + PrimeValue13(u8), + PrimeValue17(u8), + PrimeValue19(u8), +} +impl ValueType { + pub fn count(&self) -> u8 { + match self { + ValueType::Bit => 2, + ValueType::ThreeValue => 3, + ValueType::FiveValue => 5, + ValueType::PrimeValue7(_) => 7, + ValueType::PrimeValue11(_) => 11, + ValueType::PrimeValue13(_) => 13, + ValueType::PrimeValue17(_) => 17, + ValueType::PrimeValue19(_) => 19, + } + } + + pub fn zos_sequence() -> Vec<ValueType> { + vec![ + ValueType::Bit, + ValueType::ThreeValue, + ValueType::FiveValue, + ValueType::PrimeValue7(7), + ValueType::PrimeValue11(11), + ValueType::PrimeValue13(13), + ValueType::PrimeValue17(17), + ValueType::PrimeValue19(19), + ] + } +} + [To ensure code accuracy, apply this suggestion manually] Suggestion importance[1-10]: 10 __ Why: The suggestion correctly identifies that the generated code is syntactically invalid and will not compile, fixing multiple critical errors in the count and zos_sequence methods.	High
	Fix layer storage and validation instances stores T but you push Instance, causing a type mismatch. Also, calling value_count() on a unit requires indexing and will panic if empty. Store Vec<Instance> and compare T::value_count() to the layer value count. generated_lattice_code/lattice_layer_struct.rs [1] -# [derive (Debug , Clone)] pub struct LatticeLayer < T : HasValueCount + std :: fmt :: Debug > { pub value_type : ValueType , pub instances : Vec < T > , } impl < T : HasValueCount + std :: fmt :: Debug > LatticeLayer < T > { pub fn new (value_type : ValueType) -> Self { Self { value_type , instances : Vec :: new () } } pub fn add_instance (& mut self , instance : Instance < T >) { assert_eq ! (instance . units [0] . value_count () , self . value_type . count () , "Instance unit value count must match layer's value type") ; self . instances . push (instance) ; } pub fn describe (& self) { println ! ("\n--- Lattice Layer: {:?} (k={}) ---" , self . value_type , self . value_type . count ()) ; for instance in & self . instances { instance . describe () ; } } } +#[derive(Debug, Clone)] +pub struct LatticeLayer<T: HasValueCount + std::fmt::Debug> { + pub value_type: ValueType, + pub instances: Vec<Instance<T>>, +} +impl<T: HasValueCount + std::fmt::Debug> LatticeLayer<T> { + pub fn new(value_type: ValueType) -> Self { + Self { value_type, instances: Vec::new() } + } + + pub fn add_instance(&mut self, instance: Instance<T>) { + assert_eq!( + T::value_count(), + self.value_type.count(), + "Instance unit value count must match layer's value type" + ); + self.instances.push(instance); + } + + pub fn describe(&self) { + println!("\n--- Lattice Layer: {:?} (k={}) ---", self.value_type, self.value_type.count()); + for instance in &self.instances { + instance.describe(); + } + } +} + [To ensure code accuracy, apply this suggestion manually] Suggestion importance[1-10]: 10 __ Why: The suggestion correctly identifies a critical type mismatch where an Instance<T> is pushed into a Vec<T>, which would cause a compilation failure, and provides a correct fix.	High
	Fix missing Result return type The main function returns Ok(()) but is not declared to return a Result type. This will cause a compilation error since Ok(()) can only be returned from functions with a Result return type. src/lattice_mapper_app.rs [136-209] -fn main() { +fn main() -> Result<(), Box<dyn std::error::Error>> { println!("\n--- Lattice Mapper Application ---"); ... Ok(()) } [To ensure code accuracy, apply this suggestion manually] Suggestion importance[1-10]: 9 __ Why: The suggestion correctly identifies a compilation error where the main function returns Ok(()) without being declared to return a Result type.	High
	Remove invalid triple quote syntax The file starts with triple quotes which is invalid Rust syntax. Rust uses //! for module-level documentation comments, not triple quotes. This will prevent the file from compiling. src/grand_unified_search.rs [1-148] -"""//! This program conceptually outlines a "Grand Unified Search" system in Rust. +//! This program conceptually outlines a "Grand Unified Search" system in Rust. //! It aims to demonstrate how a program could parse its own code, search for similar //! programs within a vast repository (like 10k submodules), and interact with LLMs //! for knowledge extraction, all within the framework of our defined lattice. ... -"" [To ensure code accuracy, apply this suggestion manually] Suggestion importance[1-10]: 9 __ Why: The suggestion correctly points out that the entire file is wrapped in triple quotes, which is invalid Rust syntax and will cause a compilation error.	High
	Fix header number extraction The first grep doesn’t use PCRE, so \K is treated literally and the match always fails. Use a single PCRE-enabled grep to extract the number, ensuring headers are detected correctly and numbering isn’t corrupted. tools/gh_scripts/standardize_and_move_crqs.sh [43] -CRQ_NUMBER_FROM_HEADER=$(grep -m 1 "^# CRQ-\K[0-9]+" "$CRQ_FILE_PATH" | grep -oP 'CRQ-\K[0-9]+') +CRQ_NUMBER_FROM_HEADER=$(grep -oP -m1 '^# CRQ-\K[0-9]+' "$CRQ_FILE_PATH") [To ensure code accuracy, apply this suggestion manually] Suggestion importance[1-10]: 8 __ Why: The suggestion correctly identifies that the grep command uses a PCRE-specific feature \K without enabling PCRE, which would cause it to fail, and provides a correct and more efficient fix.	Medium
High-level	Fix layer/unit type mismatch The build_zos_lattice function in src/lib.rs incorrectly attempts to add bool-based instances to layers defined as ThreeValue, which will cause a runtime panic due to an assertion in LatticeLayer::add_instance. The fix is to ensure the ValueType of the layer matches the type of the instances being added. Examples: src/lib.rs [27-29] src/lattice_model.rs [79-80] Solution Walkthrough: Before: // In src/lib.rs pub fn build_zos_lattice(...) -> Lattice { // ... // Layer is created for 3-value types, but its generic type is `bool` (2-value) let mut crq_documentation_layer = LatticeLayer::<bool>::new(ValueType::ThreeValue); // ... for (file_path_str, file_extension, conceptual_content) in files { // ... // An instance with `bool` units is created let instance = Instance::new(..., predicates.into_iter().map(|wp| wp.0).collect()); // This call will panic at runtime crq_documentation_layer.add_instance(instance); } // ... } // In src/lattice_model.rs impl<T: HasValueCount> LatticeLayer<T> { pub fn add_instance(&mut self, instance: Instance<T>) { // This assertion fails: T::value_count() (2 for bool) != self.value_type.count() (3 for ThreeValue) assert_eq!(T::value_count(), self.value_type.count(), ...); self.instances.push(instance); } } After: // In src/lib.rs pub fn build_zos_lattice(...) -> Lattice { // ... // Option 1: Align layer type with instance type. let mut crq_documentation_layer = LatticeLayer::<bool>::new(ValueType::Bit); // ... for (file_path_str, file_extension, conceptual_content) in files { // ... let instance = Instance::new(..., predicates.into_iter().map(|wp| wp.0).collect()); // This call will now succeed. crq_documentation_layer.add_instance(instance); } // ... } // In src/lattice_model.rs // (No changes needed here, the assertion correctly caught the bug) impl<T: HasValueCount> LatticeLayer<T> { pub fn add_instance(&mut self, instance: Instance<T>) { assert_eq!(T::value_count(), self.value_type.count(), ...); self.instances.push(instance); } } Suggestion importance[1-10]: 9 __ Why: This suggestion correctly identifies a critical runtime panic in the build_zos_lattice function, where a LatticeLayer initialized for ThreeValue types is incorrectly populated with bool instances, causing an assertion failure.	High
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[jmikedupont2]

please review this ticket, look at the crq and help us plan next steps

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