iowarp/clio-coder-skills

Use when this workflow is requested: Validated interactive system maps and diagrams as standalone HTML from a typed JSON spec, for one of five diagram types (architecture, workflow, sequence, dataflow, lifecycle). Use when the user asks to visualize architecture, a workflow, a call sequence, a data pipeline, or a state machine, or to map this repository. Not for ad hoc drawings or slide art, and not for Mermaid output; use the artifact tool for plain Markdown. Triggers on "architecture diagram", "system map".

Use when this workflow is requested: Decides the engineering approach for an intent in an interactive session: investigates, proposes two or three genuinely different approaches with trade-offs, recommends, lets the user decide, and writes the decision doc. Not a task-by-task plan; use cut-it. Not a multi-perspective debate; use design-council. Not product intent; use product-intent. Not a typed implementation handoff; use tech-spec. Triggers on "how should we build this", "pick the stack".

Use when this workflow is requested: Searches arXiv, summarizes or compares papers, and builds a compact literature survey as citation-ready, source-linked paper cards. Prefer the Researcher shadow agent for noisy multi-paper retrieval. Triggers on "search arXiv", "summarize an arXiv paper".

Use when this workflow is requested: Structural code search with ast-grep rules: finds code by shape when grep on text is too noisy, and never rewrites it. Not for plain string or filename lookups; use grep or find. Triggers on "structural code search", "ast-grep rule".

Use when this workflow is requested: Turns a finished PRD or architecture doc into a ticket backlog of small stories with verifiable acceptance criteria, confirmed, then created as GitHub issues or in another configured tracker. Not for local sprint slicing into a SPRINT.md; use cut-it. Triggers on "create the stories", "turn this PRD into issues".

Use when this workflow is requested: Proves merged work on the canonical base, inspects and removes associated worktrees through Git, deletes local branches safely, and audits surviving repository refs. Not for creating worktrees; use worktree-create. Not for integrating branches; use worktree-merge. Triggers on "close out this branch", "clean up merged branch".

Use when this workflow is requested: Governs changes to Clio Coder's own source and harness (TUI, skills, agents, tools, prompts, domains): what may change freely, what needs explicit user intent, and how to change it without breaking the architecture. Not for verifying a change against the harness; use clio-coder-test. Triggers on "modify Clio Coder", "change the Clio harness".

Use when this workflow is requested: Verifies a Clio Coder source change against the current contract, smoke, boundary, and application test lanes, including temporary-state and local-provider harnesses. Not for deciding what may change; use clio-coder-dev. Triggers on "test Clio Coder", "verify a Clio source change".

Use when this workflow is requested: Correct-by-construction TypeScript rules (errors as values, parse don't validate, illegal states unrepresentable, deep modules) for writing or refactoring TypeScript when the project has not pinned its own standards. Triggers on "TypeScript coding standards", "errors as values".

Use when this workflow is requested: Writes a durable, redacted, reference-not-copy handoff document when a session winds down or context is about to be compacted or lost, so the next session or agent can continue. Not for orienting at the start of a session; use context-prime. Triggers on "session handoff", "notes for the next session".

Use when this workflow is requested: Orients a fresh session in a repository by loading the last handoff, git state, the project constitution, and active-work signals before acting. Not for writing the handoff; use context-handoff. Triggers on "prime this repository", "catch me up".

Use when this workflow is requested: Handles API keys, tokens, and facility credentials (kerberos tickets, globus and scheduler tokens, ssh agents, netrc) before a tool needs one, after an auth error, when a new secret is supplied, or when one may have leaked. Not for provider target configuration; use clio-coder auth and target settings. Triggers on "API key", "credential missing".

Use when this workflow is requested: Slices an existing plan, PRD, or milestone into an executable sprint of dependency-ordered vertical slices sized for one agent run each, with done-when verification per slice; never fabricates a plan. Not for deciding the approach; use architecture. Triggers on "cut it", "slice this plan".

Use when this workflow is requested: Convenes several expert perspectives that challenge each other on a design decision with real trade-offs before code is written; quick mode runs a single round. Not for a one-question-at-a-time interrogation of a plan; use grill-me. Not for splitting implementation across workers; use dispatch directly. Triggers on "convene a design council", "debate this design".

Use when this workflow is requested: Pre-registers a performance study, numerical comparison, parameter sweep, or benchmark: thresholds, tolerances, environment pins, and verdict conditions locked into the validation contract before any measurement. Not for diagnosing a stalled bug; use scientific-debugging. Triggers on "benchmark these implementations", "pre-register a performance experiment".

Use when this workflow is requested: Turns something noticed mid-session into a tracker issue: captures evidence, dedups against existing issues, composes a labeled issue with acceptance criteria, confirms, and creates it via gh. Not for batch ticket creation from a PRD; use backlog. Not for diagnosing an existing issue; use fix-issue. Triggers on "file a ticket", "open an issue for this".

Use when this workflow is requested: Finds published skills and prepares their Library installation for the operator when the user asks whether a capability exists as a skill. Not for authoring a new skill; use skill-craft. Triggers on "find a skill", "is there a skill for this".

Use when this workflow is requested: Resolves a tracker issue end to end: fetches it, diagnoses only when the issue does not name the code, fixes test-first, and self-reviews against the acceptance criteria, leaving a verified uncommitted change. Not for filing; use file-ticket. Not for committing or PRs; use ship. Triggers on "fix issue 123", "take this ticket".

Use when this workflow is requested: Stress-tests a plan, design, or idea through a phased one-question-at-a-time interview before code is written, ending in a compact decision log. Not for a multi-perspective debate; use design-council. Triggers on "grill me", "interview me about this plan".

Use when this workflow is requested: Launches, drives, or inspects another agent or command in a Herdr pane, tab, or workspace, including a second Clio Coder instance; requires HERDR_ENV=1. Not for background work a plain shell or dispatch already covers. Triggers on "use Herdr", "launch an agent in a Herdr pane".

Use when this workflow is requested: Structure resource interviews into a feasibility map with gaps and alternatives. Triggers on "clio kit materio lab definer".

Use when this workflow is requested: Review supplied materials and provided URLs with citation provenance and explicit gaps. Triggers on "clio kit materio literature reviewer".

Use when this workflow is requested: Synthesize candidate materials-science questions and write researcher-confirmed identity. Triggers on "clio kit materio research explorer".

Use when this workflow is requested: Produce type-specific artifacts for one approved materials-science task and verify the files. Triggers on "clio kit materio task executor".

Use when this workflow is requested: Independently inspect research task outputs against their approved assumptions, artifacts, and evidence. Triggers on "clio kit materio task verifier".

Use when this workflow is requested: Build a resource-aware dependency plan with researcher assumptions and tagged defaults. Triggers on "clio kit materio workflow planner".

Use when this workflow is requested: Turns an idea into a product requirements document through a phase-gated interview, ending in PRD.md plus per-milestone prompt files ready to drive a coding agent. Not for the problem-first product thesis; use product-intent. Triggers on "write a PRD", "spec this product out".

Use when this workflow is requested: Writes a problem-first product document for a greenfield effort: interviews for the problem, evidence, and a falsifiable hypothesis, with zero engineering decisions. Not for engineering decisions; use architecture. Not for turning a locked idea into milestone build prompts; use prd. Triggers on "why are we building this", "write the product thesis".

Use when this workflow is requested: Answers a design question with throwaway code: a clearly marked, runnable, no-persistence prototype whose verdict is kept and whose code is discarded. Not for pre-registered performance experiments; use experiment-protocol. Not for production implementation. Triggers on "throwaway prototype", "mock up this UI".

Use when this workflow is requested: Resolves a merge, rebase, or cherry-pick stopped on conflicts by reconstructing both sides' intent, validating with the project's own checks, and completing the operation. Not for integrating many branches; use worktree-merge. Triggers on "merge conflict", "fix these conflicts".

Use when this workflow is requested: Diagnoses stalled or cross-system failures and wrong, NaN, nondeterministic, or unexpectedly slow scientific results through falsifiable hypotheses across distinct fault classes, with evidence-cited verdicts before any fix. Not for designing benchmarks or pre-registered experiments; use experiment-protocol. Triggers on "wrong scientific results", "nondeterministic HPC code".

Use when this workflow is requested: Modernizes, ports, rewrites, packages, or replaces established scientific software in independently validated stages against an external scientific oracle, settling compatibility and upstream stewardship before calling it complete. Not for an isolated benchmark; use experiment-protocol. Not for diagnosing wrong results; use scientific-debugging. Triggers on "modernize this scientific code", "rewrite this scientific software in Rust".

Use when this workflow is requested: Ships finished work: writes one reviewed atomic commit, keeps maintainer branches local, or pushes a contributor branch to their fork and opens a PR only on explicit intent. Not for producing the change; use fix-issue. Triggers on "ship this", "commit this".

Use when this workflow is requested: Writes, reviews, or prunes a SKILL.md, judging whether its description, body, and length earn their cost. Not for packaging a workflow that just happened; use workflow-distiller. Triggers on "write a SKILL.md", "create a new skill".

Use when this workflow is requested: Builds a feature or fix test-first, red to green at pre-agreed public seams, one vertical slice at a time. Not for designing benchmark criteria; use experiment-protocol. Triggers on "test-driven development", "write the test first".

Use when this workflow is requested: Writes a typed call-stack architecture handoff: code-shaped contracts plus execution flows, implementation-ready for another engineer. User-invoked only. Not for weighing approaches or deciding the design; use architecture first. Triggers on "write a tech spec", "typed call-stack handoff".

Use when this workflow is requested: Packages a workflow that just happened into a reusable SKILL.md: reconstructs it from the session record, checks overlap with installed skills, gates on approval, then writes it following skill-craft. Not for authoring a skill with no prior workflow; use skill-craft. Triggers on "make this workflow a skill", "package what we just did".

Use when this workflow is requested: Stands up one or more git worktrees for parallel work, each on its own branch with gitignored config copied in, dependencies installed, and a verified health check. Not for merging finished worktrees; use worktree-merge. Not for closeout; use branch-closeout. Triggers on "create a git worktree", "set up worktrees for these branches".

Use when this workflow is requested: Integrates finished worktree branches through one throwaway integration branch, testing after each merge and running the full suite before the main line moves, with exact rollback on failure. Not for creating worktrees; use worktree-create. Not for closeout; use branch-closeout. Triggers on "merge my worktrees", "integrate these worktree branches".