Skill Claude CodeCodex
Deterministic benchmark harnesses for public template exemplars. Use when scoring generated project outputs against benchmark manifests, refreshing the default template smoke manifest, checking publication-readiness rubrics, or adding bounded no-network readiness checks for public template outputs.
Skill Claude CodeCodex
Repository-scoped configuration for the template—environment variable templates and default secure/steganography YAML. Use when editing .env patterns, secureconfig defaults, or cross-referencing project manuscript config overrides.
Skill Claude CodeCodex
Skill for the core infrastructure module providing logging, configuration, exception handling, progress tracking, checkpoints, retry logic, pipeline execution, performance monitoring, security, file operations, and multi-project orchestration. Use when setting up logging, loading config, handling errors, running…
Skill Claude CodeCodex
Unified pipeline telemetry — collects per-stage performance metrics (CPU, memory, I/O) and diagnostic events into structured reports (JSON, text).
Skill Claude CodeCodex
Container build and compose assets for the research template. Use when reproducing CI or cloud environments with Docker, following docs/CLOUDDEPLOY.md, or wiring Ollama sidecars via docker-compose.
Skill Claude CodeCodex
Skill for the doctor infrastructure module providing repository-level diagnostics and safe, reversible automated repair. Use when the local checkout is acting up, before opening a bug, when onboarding a fresh clone, or as a periodic health probe. Every mutation is backed up under .doctor/backups/ and journalled in…
Skill Claude CodeCodex
Skill for the documentation infrastructure module providing figure management, image handling, markdown integration, and API glossary generation. Use when managing research figures, inserting images into manuscripts, auto-numbering figures, or generating API documentation.
Skill Claude CodeCodex
Skill for the fonds module — discovery, validation, scope, and private-sidecar symlink sync for the top-level fonds/ directory (archival collection units such as bibliographies, contact registries, and dataset catalogs). Use when discovering fonds (discoverfonds), resolving a fond path (resolvefondroot), validating…
Skill Claude CodeCodex
Skill for the LLM infrastructure module providing local Large Language Model integration via Ollama. Covers client initialization, prompt templates, output validation, manuscript review generation, conversation context, and CLI usage. Use when querying LLMs, generating manuscript reviews, validating LLM outputs, or…
Skill Claude CodeCodex
Methods orchestration contract builder for template projects. Use when mapping pipeline stages, manuscript methods, artifact manifests, evidence registries, figures, claim ledgers, experiment plans, and validation commands into one reproducible methods plan.
Skill Claude CodeCodex
Python CLI and menu orchestration for pipeline runs — project slug validation, interactive picker, PipelineRunner wrapping PipelineExecutor, per-stage logs, secure pipeline wrapper. Use when extending run.sh behavior, fixing menu/CLI routing, or testing discovery helpers.
Skill Claude CodeCodex
Skill for the project management infrastructure module providing multi-project discovery, structure validation, and metadata extraction. Use when discovering active projects, validating project directory structure, or extracting project configuration metadata.
Skill Claude CodeCodex
Improves codebase quality via the desloppify CLI — install, exclude noise, scan, and drive the next/resolve execution loop to raise strict score. Use when the user invokes /desloppify, asks for tech-debt cleanup, desloppify, strict score, or codebase health scanning.
Skill Claude CodeCodex
Keep Codex, Claude Code, and Hermes workflows aligned through portable skills, explicit runtime adapters, and shared MCP contracts.
Skill Claude CodeCodex
Reduce an ambiguous technical problem to verified facts, constraints, and explicit decisions before proposing a solution.
Skill Claude CodeCodex
Use Model Context Protocol tools safely through schema inspection, least-privilege selection, explicit approvals, bounded execution, and result verification.
Skill Claude CodeCodex
Adversarially test a design, implementation, agent workflow, or tool surface for realistic failure and abuse paths within authorized scope.
Skill Claude CodeCodex
Analyze a change as part of a wider system by mapping boundaries, dependencies, feedback loops, delays, incentives, and leverage points.
Skill Claude CodeCodex
Use when the user needs to run GitNexus CLI commands like analyze/index a repo, check status, clean the index, generate a wiki, or list indexed repos. Examples: "Index this repo", "Reanalyze the codebase", "Generate a wiki".
Skill Claude CodeCodex
Use when the user is debugging a bug, tracing an error, or asking why something fails. Examples: "Why is X failing?", "Where does this error come from?", "Trace this bug".
Skill Claude CodeCodex
Use when the user asks how code works, wants to understand architecture, trace execution flows, or explore unfamiliar parts of the codebase. Examples: "How does X work?", "What calls this function?", "Show me the auth flow".
Skill Claude CodeCodex
Use when the user asks about GitNexus itself — available tools, how to query the knowledge graph, MCP resources, graph schema, or workflow reference. Examples: "What GitNexus tools are available?", "How do I use GitNexus?".
Skill Claude CodeCodex
Use when the user wants to know what will break if they change something, or needs safety analysis before editing code. Examples: "Is it safe to change X?", "What depends on this?", "What will break?".
Skill Claude CodeCodex
Use when the user wants to rename, extract, split, move, or restructure code safely. Examples: "Rename this function", "Extract this into a module", "Refactor this class", "Move this to a separate file".