@iowarp/clio-coder 0.4.5 → 0.4.7

package/library/_authoring/templates/plugin/plugin.json

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+{
+	"$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
+	"name": "data-curation",
+	"version": "1.0.0",
+	"description": "Scientific dataset curation bundle with curation skill, curator agent, and inspection prompt.",
+	"license": "Apache-2.0",
+	"extensions": {
+		"ai.iowarp.clio": {
+			"manifestVersion": 1,
+			"resources": {
+				"skills": "skills",
+				"agents": "agents",
+				"prompts": "prompts"
+			},
+			"components": [
+				{
+					"kind": "resource",
+					"id": "guidelines",
+					"path": "assets/curation-guide.md"
+				},
+				{
+					"kind": "skill",
+					"id": "dataset-curation",
+					"path": "skills/dataset-curation/SKILL.md",
+					"requires": ["resource:guidelines"]
+				},
+				{
+					"kind": "agent",
+					"id": "data-curator",
+					"path": "agents/data-curator.md",
+					"requires": ["skill:dataset-curation"]
+				},
+				{
+					"kind": "prompt",
+					"id": "inspect-dataset",
+					"path": "prompts/inspect-dataset.md",
+					"requires": ["agent:data-curator"]
+				}
+			]
+		}
+	}
+}

package/library/_authoring/templates/plugin/prompts/inspect-dataset.md

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+---
+description: Prompt to inspect a scientific dataset directory for FAIR compliance and metadata completeness.
+argument-hint: "[dataset-path]"
+---
+
+Inspect the scientific dataset at: $1
+
+Refer to curation guidelines in ${pluginRoot}/assets/curation-guide.md and use the data-curator agent.
+
+Evaluate:
+1. File structure and format consistency.
+2. Presence of required metadata, license, and provenance documentation.
+3. Missing-value encodings and schema clarity.
+
+Additional instructions: $ARGUMENTS

package/library/_authoring/templates/plugin/skills/dataset-curation/SKILL.md

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+---
+name: dataset-curation
+description: Guidelines and verification procedures for scientific dataset curation, schema compliance, and FAIR data standards.
+version: 1.0.0
+license: Apache-2.0
+clio-coder:
+  registry-id: dataset-curation
+  source-url: https://github.com/iowarp/clio-coder/tree/main/library/_authoring/templates/plugin
+  provenance: designed
+  eval-status: scenarios-recorded
+triggers:
+  - curate dataset
+  - fair data check
+  - validate dataset schema
+  - dataset curation
+allowed-tools:
+  - read
+  - grep
+  - find
+  - ls
+---
+
+# Dataset Curation Skill
+
+Guide for inspecting, curating, and validating scientific datasets against FAIR data standards.
+
+## Reference Guidelines
+
+Consult ${pluginRoot}/assets/curation-guide.md for domain quality invariants and metadata checklists.
+
+## Procedure
+
+1. **Scan Dataset Directory**: Use `ls` and `find` to map all data files and metadata descriptors.
+2. **Review Metadata**: Verify existence of licensing, provenance records, and format declarations.
+3. **Inspect Content**: Verify column names, missing-value sentinels, and unit definitions against the curation guidelines.
+4. **Compile Assessment**: Report missing fields, format violations, and recommendations for FAIR compliance.

package/library/_authoring/templates/plugin/skills/dataset-curation/evals.md

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+# Evals: dataset-curation
+
+Evaluation scenarios for dataset curation skill.
+
+## Scenario: missing-fair-metadata
+
+### Baseline (without skill)
+- Context: Dataset folder containing `data.csv` with no license or column description.
+- Task: Check dataset for publication readiness.
+- Outcome: General observations, omits structured FAIR criteria.
+
+### Treatment (with skill)
+- Prompt: `/skill dataset-curation Check dataset at data/ for FAIR compliance`
+- Expected Evidence:
+  - References FAIR criteria from `assets/curation-guide.md`.
+  - Flags absence of license and schema documentation.
+  - Identifies missing unit definitions in CSV headers.

package/library/_authoring/templates/prompt/README.md

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+# Paper Summary Prompt Template
+
+This template demonstrates a valid standalone **prompt** package for Clio Coder.
+
+## Package Structure
+
+```text
+paper-summary/
+  README.md                     # Documentation (outside resource root)
+  plugin.json                   # Portable manifest declaring kind: prompt
+  prompts/
+    paper-summary.md            # Reusable prompt template
+```
+
+> **Important**: Keep `README.md` at the package root, never inside `prompts/`. Single-kind packages expose exactly one public candidate in their declared resource directory.
+
+## Invocation and Parameters
+
+- **Invocation Name**: Derived from the file path relative to `prompts/`. Here, `prompts/paper-summary.md` exposes `/paper-summary`.
+- **Positional Arguments**: `$1`, `$2`, etc. are replaced by space-separated positional arguments passed to the slash command.
+- **Full Arguments String**: `$ARGUMENTS` expands to the full remainder argument string.
+- **Optional Argument Hint**: The frontmatter `argument-hint: "[paper-path-or-url]"` informs interactive autocomplete of expected inputs.
+
+## Validation
+
+```bash
+clio-coder library validate .
+```

package/library/_authoring/templates/prompt/plugin.json

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+{
+	"$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
+	"name": "paper-summary",
+	"version": "1.0.0",
+	"description": "Structured prompt template for summarizing scientific papers and research methodologies.",
+	"license": "Apache-2.0",
+	"extensions": {
+		"ai.iowarp.clio": {
+			"manifestVersion": 1,
+			"kind": "prompt",
+			"resources": {
+				"prompts": "prompts"
+			},
+			"components": [
+				{
+					"kind": "prompt",
+					"id": "paper-summary",
+					"path": "prompts/paper-summary.md"
+				}
+			]
+		}
+	}
+}

package/library/_authoring/templates/prompt/prompts/paper-summary.md

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+---
+description: Summarize a scientific paper with research question, methodology, key findings, and threats to validity.
+argument-hint: "[paper-path-or-url]"
+---
+
+Summarize the scientific paper located at: $1
+
+Follow this structured format:
+
+## 1. Research Problem & Objective
+- What specific research question does this work address?
+- Why is this problem significant in scientific or computational practice?
+
+## 2. Methodology & Approach
+- What experimental, computational, or theoretical methodology was employed?
+- What datasets, benchmarks, or HPC hardware environments were evaluated?
+
+## 3. Key Findings & Contributions
+- Summarize the primary quantitative and qualitative results.
+- Highlight measured speedups, accuracy improvements, or scaling limits.
+
+## 4. Threats to Validity & Limitations
+- What are the documented or observed limitations?
+- What replication obstacles exist?
+
+Additional instructions: $ARGUMENTS

package/library/_authoring/templates/skill/README.md

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+# Citation Check Skill Template
+
+This template demonstrates a valid standalone **skill** package for Clio Coder.
+
+## Package Structure
+
+```text
+citation-check/
+  README.md         # Documentation (outside resource root)
+  plugin.json       # Portable manifest declaring kind: skill
+  SKILL.md          # Skill instructions and metadata
+  evals.md          # Evaluation scenarios
+```
+
+## How to Use This Template
+
+1. Copy this directory into your project or repository.
+2. Rename the package in `plugin.json` and `SKILL.md`.
+3. Update the description, triggers, and procedure in `SKILL.md`.
+4. Add baseline/treatment scenarios in `evals.md`.
+5. Validate your package:
+   ```bash
+   clio-coder library validate .
+   ```

package/library/_authoring/templates/skill/SKILL.md

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+---
+name: citation-check
+description: Verify citation keys, DOIs, and bibliography entries against source files in research software. Load when checking academic references, bibtex formatting, or paper citations.
+version: 1.0.0
+license: Apache-2.0
+clio-coder:
+  registry-id: citation-check
+  source-url: https://github.com/iowarp/clio-coder/tree/main/library/_authoring/templates/skill
+  provenance: designed
+  eval-status: scenarios-recorded
+triggers:
+  - citation check
+  - verify citations
+  - check bibliography
+  - validate doi
+allowed-tools:
+  - read
+  - grep
+  - find
+---
+
+# Citation Check
+
+Verify citation keys, Digital Object Identifiers (DOIs), and bibliography entries in research codebases and papers.
+
+## When to load this skill
+
+Load when:
+- Reviewing LaTeX documents, markdown papers, or documentation containing citation keys (e.g. `\cite{...}`, `[@key]`).
+- Validating BibTeX `.bib` files for syntax errors, missing fields, or duplicate keys.
+- Checking that cited DOIs resolve to expected formats.
+
+## Procedure
+
+1. **Locate citation files**: Search for `.bib` files and references in the workspace using `find`.
+2. **Inspect citation keys**: Grep for citation markers in manuscript or documentation source files.
+3. **Cross-reference**: Ensure every cited key exists in the corresponding `.bib` file. Report unreferenced bibliography entries as warnings and missing keys as errors.
+4. **DOI Verification**: Verify DOIs match the standard format `10.XXXX/...` and link to valid literature sources.
+5. **Report findings**: Output a structured summary containing verified keys, missing citations, and formatting issues.

package/library/_authoring/templates/skill/evals.md

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+# Evals: citation-check
+
+Scenarios recorded for the citation-check skill.
+
+## Scenario: missing-citation-key
+
+### Baseline (without skill)
+- Context: Workspace with `paper.tex` citing `\cite{smith2024}` and `references.bib` containing only `doe2023`.
+- Task: Verify citations in `paper.tex`.
+- Outcome: General unstructured commentary, potential hallucination of reference existence.
+
+### Treatment (with skill)
+- Prompt: `/skill citation-check Check citations in paper.tex against references.bib`
+- Expected Evidence:
+  - Identifies missing citation key `smith2024` in `references.bib`.
+  - Reports `doe2023` as an unreferenced entry.
+  - Leaves workspace files unmodified.
+
+## Scenario: doi-format-validation
+
+### Baseline (without skill)
+- Context: `references.bib` with invalid DOI string `doi = {https://dx.doi.org/invalid}`.
+- Task: Validate DOI formatting in `references.bib`.
+- Outcome: Misses malformed DOI format or accepts invalid prefix.
+
+### Treatment (with skill)
+- Prompt: `/skill citation-check Validate DOI formats in references.bib`
+- Expected Evidence:
+  - Flags invalid DOI prefix.
+  - Recommends canonical DOI format `10.XXXX/...`.

package/library/_authoring/templates/skill/plugin.json

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+{
+	"$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
+	"name": "citation-check",
+	"version": "1.0.0",
+	"description": "Verify citation keys, DOIs, and bibliography entries against source files in research software.",
+	"license": "Apache-2.0",
+	"extensions": {
+		"ai.iowarp.clio": {
+			"manifestVersion": 1,
+			"kind": "skill",
+			"resources": {
+				"skills": "."
+			},
+			"components": [
+				{
+					"kind": "skill",
+					"id": "citation-check",
+					"path": "SKILL.md"
+				}
+			]
+		}
+	}
+}

package/library/agents/README.md

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+# Agent Packages
+
+This directory hosts standalone agent packages. An agent package distributes a specialized worker recipe defining role instructions, tool permissions, budget, and result contracts.
+
+Core and maintenance agents remain built into Clio Coder under `src/domains/agents/builtins/`.
+
+Community agent package authoring templates and validator guidelines will be introduced in Slice 2 under `library/_authoring/templates/agent/`.

package/library/fleets/README.md

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+# Fleet Packages
+
+This directory hosts standalone fleet packages. A fleet package distributes an executable multi-agent coordination recipe defining task graphs, agent nodes, and wave dispatch policies.
+
+Baseline and internal fleets remain built into Clio Coder under `src/domains/agents/fleets/`.
+
+Community fleet package authoring templates and validator guidelines will be introduced in Slice 2 under `library/_authoring/templates/fleet/`.

package/library/plugins/materio/README.md

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+# Materio
+
+Materio (materials + I/O) is Clio's curated materials research workflow. It turns a materials research question into a supplied-corpus literature synthesis,
+a feasible virtual lab, an assumption-driven task plan, inspected task artifacts,
+and a reviewed paper handoff. The scientific workflow derives from Daisy Quach's
+research system; this package separates domain knowledge from host capabilities.
+
+The root `plugin.json` follows Agent Plugins 1.0.0. Its six portable skills contain
+the domain workflow and link to seventeen complete action guides. Clio's native
+seventeen prompts, six agent recipes, and execute/verify fleet live under
+`ai.iowarp.clio/` and are declared in a closed component graph. Shared references,
+templates, and Python helpers live under `assets/`.
+
+## Clio workflow
+
+Install the whole package with `clio-coder library install ./library/plugins/materio --project`
+from the repository, then reload plugin resources or restart the session. An
+installed copy is a pinned tree; editing this source does not update that copy.
+
+1. `/materio:identify-research` interviews domain, hypothesis,
+   scope, resources, and timeline; the researcher selects a calibrated question.
+2. `/materio:upload-data` indexes supplied papers/data and
+   optionally copies files without overwriting collisions.
+3. `/materio:literature-review` reviews supplied materials and
+   authorized URLs, preserving actual inspection depth and justified gaps.
+4. `/materio:define-virtual-lab` maps equipment, compute,
+   licenses, collaborators, consumables, people, access constraints, and alternatives.
+5. `/materio:define-research-tasks` customizes a traditional
+   workflow, interviews per-task assumptions, and confirms defaults/resource gaps.
+6. `/materio:execute-task N` prepares the approved task's
+   output contract, reads actual artifacts, and presents advisory findings.
+7. `/materio:wtfp` prepares author-reviewed new-paper,
+   map-project, and create-outline briefs. Existing paper state routes to inspection
+   and reuse/repair first. The bridge writes only `.research/handoff/`.
+
+The remaining operations are `add-task`, `archive-task`, `remove-task`,
+`checkpoint`, `pause-research`, `resume-research`, `settings`, `status`, `progress`,
+and `help`. Task IDs remain stable across edits and archival; presentation order
+and dependency order do not require renumbering existing output files.
+
+The interactive orchestrator owns researcher questions. Workers return decision,
+human-action, or human-verify checkpoints; the caller supplies the answer with
+complete context on redispatch. A headless action needs already-confirmed inputs
+and stops before an unanswered gated write. A generated protocol is prepared work;
+physical measurements and successful computation remain separate pending actions.
+
+The optional `materio-execute-task` fleet takes `task`,
+`approval`, and `retrieval` variables. It runs the executor then the read-only
+verifier. The fleet's host write boundary is `.research/tasks/`; the selected
+subdirectory is also a caller instruction. The interactive action owns tighter
+dispatch grants, findings, state updates, and checkpoint decisions. Peer exports
+do not claim the same native fleet or write-boundary enforcement.
+
+Clio's v4 fleet requires an existing Git worktree to validate its write boundary.
+In a fresh research folder, use the execute-task prompt's direct executor dispatch
+with the selected output grant followed by a separate read-only verifier dispatch.
+The workflow never initializes git or disables the fleet boundary to make it run.
+The verifier's read/ls checks are artifact review, not command-backed scientific
+validation; any host grounding limitation or rejected receipt remains visible.
+
+## State and checks
+
+Python 3.10+ runs the stdlib-only helpers. Bash is used for shell syntax checking.
+From a research project, initialize missing state using
+`python3 /absolute/installed/package/assets/scripts/research_state.py init`.
+The helper also accepts `--project /absolute/project` before its subcommand.
+
+Config defaults are `web_search: false`, `auto_checkpoint: true`, and
+`commit_research: false`. The historical `web_search` name controls provided-URL
+retrieval and Crossref queries; it does not provide a search engine. Host model
+selection remains in the host's configuration. Research data lives at `.research/data/`.
+
+`research_state.py` validates JSON policy settings, allocates stable task IDs,
+checks dependency graphs, copies data without collisions, and creates/restores
+digest-verified checkpoint archives. Restore requires researcher confirmation,
+replaces other research state exactly, and preserves data and checkpoint archives.
+It creates no git repository or checkpoint tag. Optional commits require an empty
+preexisting index and explicit changed filenames after `commit_research` is enabled.
+
+`check_physics.py` checks conservative physical bounds. `check_scripts.py` parses
+Python and checks shell syntax without running the generated program.
+`verify_citations.py` extracts BibTeX/Key Papers entries and optionally queries
+Crossref. Use `--offline` when network retrieval is disabled. All support `--json`:
+exit 0 reports no findings in inspected inputs, 1 reports findings, and 2 reports
+incomplete input coverage or execution failure. Missing checks are reported as
+skipped. Crossref absence is inconclusive, and identity matching does not establish
+full-text inspection or scientific support. Findings never delete citations or
+override a researcher decision automatically.
+
+## Peer packages
+
+Codex can consume the root standard package through its portable skills. For a
+native Claude package or Gemini extension, generate a separate output tree:
+
+```bash
+python3 assets/scripts/project_plugin.py --target claude --output /tmp/materials-claude
+python3 assets/scripts/project_plugin.py --target gemini --output /tmp/materials-gemini
+python3 assets/scripts/project_plugin.py --target codex --output /tmp/materials-codex
+```
+
+Claude receives six skills, seventeen native command wrappers, and six native
+agents with `tools` frontmatter. Workers have no interview tool. Gemini receives
+six skills and seventeen TOML commands; roles use available delegation or execute
+in the main conversation. Codex receives a standard root manifest, six skills,
+and the complete action guides. Every export includes `capability-report.json`
+describing translated and omitted runtime behavior. These are installable content
+projections; generated structure and manifest validation do not establish a live
+model run on every host. No target auto-installs MCP servers or dependencies.
+
+The standard package uses action requests such as “Run identify-research using the
+materio-research-explorer skill.” It does not register Codex
+slash commands or named agents. Native peer exports translate action routes to
+their actual commands; Claude also binds roles to registered names such as
+`materio:research-explorer`. Paper briefs name receiving wtf-p
+actions and ask the researcher to use the invocation exposed by that adapter.
+Next-task routing selects an actual dependency-ready task in workflow order;
+gaps, archives, and reordered task IDs never imply incrementing the previous ID.
+
+## Validation and provenance
+
+Run the plugin's deterministic Python suite with:
+
+```bash
+PYTHONDONTWRITEBYTECODE=1 python3 -B -m unittest discover -s library/plugins/materio/tests -v
+pnpm run test:file tests/contracts/materio-plugin.test.ts
+```
+
+The Python suite includes the upstream conservative checker regressions, balanced
+BibTeX extraction, DOI-provider uncertainty, missing-file coverage, stable task
+IDs, dependency failures, archive integrity/containment, data collision handling,
+git-index preservation, and all three peer exports. Python 3.11+ is needed for the
+test that parses generated Gemini TOML using `tomllib`.
+
+Original domain content: Daisy Quach, with validation work by Matthew Larson,
+from `iowarp/wtf-ms`. Extraction refs are recorded in
+`ai.iowarp.portability/provenance.json`. No upstream licensing claim is inferred;
+this package retains attribution metadata and does not invent an SPDX license.