Error

status=failed

Result

Handle

task_f09a2b5dd6f2480987550cc9f20340a2

Pending

false

Result

Created At

2026-10-27T07:49:43.679318+00:00

Error

null

Input Requests

null

Last Updated At

2026-10-27T07:49:44.489049+00:00

Meta

Io.Modelcontextprotocol/Serverinfo

Name

CLIO shell

Version

4.1.0

Poll Interval Ms

5000

Result

Content

• {"command":"cd /home/user/clio-agent && ls plugins/ && find plugins -maxdepth 5 \( -iname 'SKILL.md' -o -name 'plugin.json' \) | sort","cwd":"/home/user/clio-agent/.cloud-run/f18/ws-f18","exit_code":2,"timed_out":false,"timeout_s":0.0,"stdout":"","stdout_truncated":false,"stderr":"ls: cannot access 'plugins/': No such file or directory\n","stderr_truncated":false}

Iserror

false

Resulttype

complete

Structuredcontent

Command

cd /home/user/clio-agent && ls plugins/ && find plugins -maxdepth 5 \( -iname 'SKILL.md' -o -name 'plugin.json' \) | sort

Cwd

/home/user/clio-agent/.cloud-run/f18/ws-f18

Exit Code

2

Stderr

ls: cannot access 'plugins/': No such file or directory

Stderr Truncated

false

Stdout

Stdout Truncated

false

Timed Out

false

Timeout S

0.0

Result Type

complete

Status

completed

Status Message

null

Task Id

gaRLCA7FO9MrR8kMwY4V1audL2IEfpbnKP36DiXD_tw

Ttl Ms

900000

Status

failed

Handle

task_e6d7a5e4fa854972a88c5323775a02ca

Pending

false

Result

Created At

2026-10-27T07:49:48.338879+00:00

Error

null

Input Requests

null

Last Updated At

2026-10-27T07:49:51.120314+00:00

Meta

Io.Modelcontextprotocol/Serverinfo

Name

CLIO shell

Version

4.1.0

Poll Interval Ms

5000

Result

Content

• {"command":"cd /home/user/clio-agent && find . -type d -name 'plugins' -not -path '/node_modules/' 2>/dev/null | head -20; echo ---; find . \( -name 'plugin.json' -o -iname 'SKILL.md' \) -not -path '/node_modules/' 2>/dev/null | head -100","cwd":"/home/user/clio-agent/.cloud-run/f18/ws-f18","exit_code":0,"timed_out":false,"timeout_s":0.0,"stdout":"./src/clio_agent/plugins\n./.cloud-run/f18/ws-f18/plugins\n./.cloud-run/f17/ws-f17/clio_agent/plugins\n./scripts/live_verification/agents/task-testing/plugins\n./scripts/live_verification/agents/v2ex-avenues/plugins\n./scripts/live_verification/agents/task-subagent-testing/plugins\n./scripts/live_verification/agents/v2-stress/plugins\n./scripts/live_verification/agents/web-testing/plugins\n./scripts/live_verification/agents/v2ex-testing/plugins\n./tests/fixtures/plugin_marketplace/plugins\n./.venv/lib/python3.14/site-packages/mypy/plugins\n./external/gact-tui/tui/internal/plugins\n./external/clio-agent-marketplace/testing/plugins\n./external/clio-agent-marketplace/plugins\n---\n./src/clio_agent/plugins/builtin/orchestration/skills/author-a-flow/SKILL.md\n./src/clio_agent/plugins/builtin/orchestration/plugin.json\n./src/clio_agent/plugins/builtin/fleet/skills/update-models/SKILL.md\n./src/clio_agent/plugins/builtin/fleet/plugin.json\n./src/clio_agent/plugins/builtin/core/skills/planning/SKILL.md\n./src/clio_agent/plugins/builtin/core/plugin.json\n./src/clio_agent/plugins/builtin/memory/plugin.json\n./.cloud-run/f18/ws-f18/plugins/wordle-demo/plugin.json\n./.cloud-run/f18/ws-f18/plugins/ssh/plugin.json\n./.cloud-run/f18/ws-f18/plugins/latex/skills/author-latex-pdf/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/latex/plugin.json\n./.cloud-run/f18/ws-f18/plugins/materials/skills/material-properties/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/materials/skills/nickel-superalloys/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/materials/skills/heat-treatment/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/materials/skills/microstructure/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/materials/skills/metallic-materials/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/materials/skills/materials-science/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/materials/plugin.json\n./.cloud-run/f18/ws-f18/plugins/mechanical-testing/skills/mechanical-testing/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/mechanical-testing/skills/experimental-data-acquisition/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/mechanical-testing/skills/tensile-testing/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/mechanical-testing/skills/load-frame-capability/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/mechanical-testing/plugin.json\n./.cloud-run/f18/ws-f18/plugins/adios/skills/adios2/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/adios/plugin.json\n./.cloud-run/f18/ws-f18/plugins/slurm/skills/hpc-batch-jobs/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/slurm/plugin.json\n./.cloud-run/f18/ws-f18/plugins/clio-search/plugin.json\n./.cloud-run/f18/ws-f18/plugins/science-log/skills/run-a-study/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/science-log/plugin.json\n./.cloud-run/f18/ws-f18/plugins/visuals/skills/geometry-to-glb/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/visuals/skills/review-visual-presentation/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/visuals/skills/create-dashboard/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/visuals/skills/present-interactive-analysis/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/visuals/skills/create-diagram/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/visuals/plugin.json\n./.cloud-run/f18/ws-f18/plugins/phenotyping/skills/treatment-response/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/phenotyping/skills/phenotyping-onboarding-checks/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/phenotyping/skills/phenotyping-report/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/phenotyping/skills/size-and-growth-traits/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/phenotyping/skills/physiology-signals/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/phenotyping/plugin.json\n./.cloud-run/f18/ws-f18/plugins/deep-research/plugin.json\n./.cloud-run/f18/ws-f18/plugins/earthscope/skills/acquire-earthscope-gnss/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/earthscope/plugin.json\n./.cloud-run/f18/ws-f18/plugins/clio-data/skills/convert-scientific-data/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/clio-data/skills/assess-data-quality/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/clio-data/plugin.json\n./.cloud-run/f18/ws-f18/plugins/web/plugin.json\n./.cloud-run/f18/ws-f18/plugins/geodesy/skills/resolve-region/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/geodesy/skills/gnss-time-series/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/geodesy/skills/count-stations-in-region/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/geodesy/skills/station-catalogs/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/geodesy/skills/compare-station-coverage/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/geodesy/plugin.json\n./.cloud-run/f18/ws-f18/plugins/workspace/plugin.json\n./.cloud-run/f18/ws-f18/plugins/data-onboarding/skills/onboard-dataset/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/data-onboarding/skills/evidence-and-claims/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/data-onboarding/skills/audit-dataset/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/data-onboarding/plugin.json\n./.cloud-run/f18/ws-f18/plugins/shell/plugin.json\n./.cloud-run/f18/ws-f18/plugins/fatigue/skills/crack-initiation/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/fatigue/skills/fatemi-socie/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/fatigue/skills/defect-driven-fatigue/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/fatigue/skills/multiaxial-fatigue/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/fatigue/skills/fatigue-life-prediction/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/fatigue/skills/fatigue-mechanics/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/fatigue/skills/high-cycle-fatigue/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/fatigue/skills/fracture-mechanics/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/fatigue/plugin.json\n./.cloud-run/f18/ws-f18/plugins/geo/plugin.json\n./.cloud-run/f18/ws-f18/plugins/factorio/skills/maintain-scientific-dossier/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/factorio/skills/evidence-fanout/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/factorio/skills/frame-research-problem/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/factorio/skills/audit-scientific-package/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/factorio/skills/coordinate-scientific-work/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/factorio/plugin.json\n./.cloud-run/f18/ws-f18/plugins/manufacturing-processes/skills/am-process-parameters/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/manufacturing-processes/skills/additive-manufacturing/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/manufacturing-processes/skills/manufacturability/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/manufacturing-processes/skills/post-processing/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/manufacturing-processes/skills/build-orientation/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/manufacturing-processes/plugin.json\n./.cloud-run/f18/ws-f18/plugins/opendocument/skills/edit-opendocument/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/opendocument/plugin.json\n./.cloud-run/f18/ws-f18/plugins/morphorm/skills/morphorm/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/morphorm/plugin.json\n./.cloud-run/f18/ws-f18/plugins/parquet/skills/parquet/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/parquet/plugin.json\n./.cloud-run/f18/ws-f18/plugins/docx/skills/work-with-word/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/docx/skills/edit-ooxml-word/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/docx/plugin.json\n./.cloud-run/f18/ws-f18/plugins/abaqus/skills/visualize-topology-optimization/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/abaqus/skills/abaqus/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/abaqus/skills/tosca/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/abaqus/skills/abaqus-visualization/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/abaqus/plugin.json\n./.cloud-run/f18/ws-f18/plugins/scientific-method/skills/data-visualization/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/scientific-method/skills/scientific-data-analysis/SKILL.md\n./.cloud-run/f18/ws-f18/plugins/scientific-method/skills/scientific-writing/SKILL.md\n","stdout_truncated":false,"stderr":"","stderr_truncated":false}

Iserror

false

Resulttype

complete

Structuredcontent

Command

cd /home/user/clio-agent && find . -type d -name 'plugins' -not -path '*/node_modules/*' 2>/dev/null | head -20; echo ---; find . \( -name 'plugin.json' -o -iname 'SKILL.md' \) -not -path '*/node_modules/*' 2>/dev/null | head -100

Cwd

/home/user/clio-agent/.cloud-run/f18/ws-f18

Exit Code

0

Stderr

Stderr Truncated

false

Stdout

./src/clio_agent/plugins
./.cloud-run/f18/ws-f18/plugins
./.cloud-run/f17/ws-f17/clio_agent/plugins
./scripts/live_verification/agents/task-testing/plugins
./scripts/live_verification/agents/v2ex-avenues/plugins
./scripts/live_verification/agents/task-subagent-testing/plugins
./scripts/live_verification/agents/v2-stress/plugins
./scripts/live_verification/agents/web-testing/plugins
./scripts/live_verification/agents/v2ex-testing/plugins
./tests/fixtures/plugin_marketplace/plugins
./.venv/lib/python3.14/site-packages/mypy/plugins
./external/gact-tui/tui/internal/plugins
./external/clio-agent-marketplace/testing/plugins
./external/clio-agent-marketplace/plugins
---
./src/clio_agent/plugins/builtin/orchestration/skills/author-a-flow/SKILL.md
./src/clio_agent/plugins/builtin/orchestration/plugin.json
./src/clio_agent/plugins/builtin/fleet/skills/update-models/SKILL.md
./src/clio_agent/plugins/builtin/fleet/plugin.json
./src/clio_agent/plugins/builtin/core/skills/planning/SKILL.md
./src/clio_agent/plugins/builtin/core/plugin.json
./src/clio_agent/plugins/builtin/memory/plugin.json
./.cloud-run/f18/ws-f18/plugins/wordle-demo/plugin.json
./.cloud-run/f18/ws-f18/plugins/ssh/plugin.json
./.cloud-run/f18/ws-f18/plugins/latex/skills/author-latex-pdf/SKILL.md
./.cloud-run/f18/ws-f18/plugins/latex/plugin.json
./.cloud-run/f18/ws-f18/plugins/materials/skills/material-properties/SKILL.md
./.cloud-run/f18/ws-f18/plugins/materials/skills/nickel-superalloys/SKILL.md
./.cloud-run/f18/ws-f18/plugins/materials/skills/heat-treatment/SKILL.md
./.cloud-run/f18/ws-f18/plugins/materials/skills/microstructure/SKILL.md
./.cloud-run/f18/ws-f18/plugins/materials/skills/metallic-materials/SKILL.md
./.cloud-run/f18/ws-f18/plugins/materials/skills/materials-science/SKILL.md
./.cloud-run/f18/ws-f18/plugins/materials/plugin.json
./.cloud-run/f18/ws-f18/plugins/mechanical-testing/skills/mechanical-testing/SKILL.md
./.cloud-run/f18/ws-f18/plugins/mechanical-testing/skills/experimental-data-acquisition/SKILL.md
./.cloud-run/f18/ws-f18/plugins/mechanical-testing/skills/tensile-testing/SKILL.md
./.cloud-run/f18/ws-f18/plugins/mechanical-testing/skills/load-frame-capability/SKILL.md
./.cloud-run/f18/ws-f18/plugins/mechanical-testing/plugin.json
./.cloud-run/f18/ws-f18/plugins/adios/skills/adios2/SKILL.md
./.cloud-run/f18/ws-f18/plugins/adios/plugin.json
./.cloud-run/f18/ws-f18/plugins/slurm/skills/hpc-batch-jobs/SKILL.md
./.cloud-run/f18/ws-f18/plugins/slurm/plugin.json
./.cloud-run/f18/ws-f18/plugins/clio-search/plugin.json
./.cloud-run/f18/ws-f18/plugins/science-log/skills/run-a-study/SKILL.md
./.cloud-run/f18/ws-f18/plugins/science-log/plugin.json
./.cloud-run/f18/ws-f18/plugins/visuals/skills/geometry-to-glb/SKILL.md
./.cloud-run/f18/ws-f18/plugins/visuals/skills/review-visual-presentation/SKILL.md
./.cloud-run/f18/ws-f18/plugins/visuals/skills/create-dashboard/SKILL.md
./.cloud-run/f18/ws-f18/plugins/visuals/skills/present-interactive-analysis/SKILL.md
./.cloud-run/f18/ws-f18/plugins/visuals/skills/create-diagram/SKILL.md
./.cloud-run/f18/ws-f18/plugins/visuals/plugin.json
./.cloud-run/f18/ws-f18/plugins/phenotyping/skills/treatment-response/SKILL.md
./.cloud-run/f18/ws-f18/plugins/phenotyping/skills/phenotyping-onboarding-checks/SKILL.md
./.cloud-run/f18/ws-f18/plugins/phenotyping/skills/phenotyping-report/SKILL.md
./.cloud-run/f18/ws-f18/plugins/phenotyping/skills/size-and-growth-traits/SKILL.md
./.cloud-run/f18/ws-f18/plugins/phenotyping/skills/physiology-signals/SKILL.md
./.cloud-run/f18/ws-f18/plugins/phenotyping/plugin.json
./.cloud-run/f18/ws-f18/plugins/deep-research/plugin.json
./.cloud-run/f18/ws-f18/plugins/earthscope/skills/acquire-earthscope-gnss/SKILL.md
./.cloud-run/f18/ws-f18/plugins/earthscope/plugin.json
./.cloud-run/f18/ws-f18/plugins/clio-data/skills/convert-scientific-data/SKILL.md
./.cloud-run/f18/ws-f18/plugins/clio-data/skills/assess-data-quality/SKILL.md
./.cloud-run/f18/ws-f18/plugins/clio-data/plugin.json
./.cloud-run/f18/ws-f18/plugins/web/plugin.json
./.cloud-run/f18/ws-f18/plugins/geodesy/skills/resolve-region/SKILL.md
./.cloud-run/f18/ws-f18/plugins/geodesy/skills/gnss-time-series/SKILL.md
./.cloud-run/f18/ws-f18/plugins/geodesy/skills/count-stations-in-region/SKILL.md
./.cloud-run/f18/ws-f18/plugins/geodesy/skills/station-catalogs/SKILL.md
./.cloud-run/f18/ws-f18/plugins/geodesy/skills/compare-station-coverage/SKILL.md
./.cloud-run/f18/ws-f18/plugins/geodesy/plugin.json
./.cloud-run/f18/ws-f18/plugins/workspace/plugin.json
./.cloud-run/f18/ws-f18/plugins/data-onboarding/skills/onboard-dataset/SKILL.md
./.cloud-run/f18/ws-f18/plugins/data-onboarding/skills/evidence-and-claims/SKILL.md
./.cloud-run/f18/ws-f18/plugins/data-onboarding/skills/audit-dataset/SKILL.md
./.cloud-run/f18/ws-f18/plugins/data-onboarding/plugin.json
./.cloud-run/f18/ws-f18/plugins/shell/plugin.json
./.cloud-run/f18/ws-f18/plugins/fatigue/skills/crack-initiation/SKILL.md
./.cloud-run/f18/ws-f18/plugins/fatigue/skills/fatemi-socie/SKILL.md
./.cloud-run/f18/ws-f18/plugins/fatigue/skills/defect-driven-fatigue/SKILL.md
./.cloud-run/f18/ws-f18/plugins/fatigue/skills/multiaxial-fatigue/SKILL.md
./.cloud-run/f18/ws-f18/plugins/fatigue/skills/fatigue-life-prediction/SKILL.md
./.cloud-run/f18/ws-f18/plugins/fatigue/skills/fatigue-mechanics/SKILL.md
./.cloud-run/f18/ws-f18/plugins/fatigue/skills/high-cycle-fatigue/SKILL.md
./.cloud-run/f18/ws-f18/plugins/fatigue/skills/fracture-mechanics/SKILL.md
./.cloud-run/f18/ws-f18/plugins/fatigue/plugin.json
./.cloud-run/f18/ws-f18/plugins/geo/plugin.json
./.cloud-run/f18/ws-f18/plugins/factorio/skills/maintain-scientific-dossier/SKILL.md
./.cloud-run/f18/ws-f18/plugins/factorio/skills/evidence-fanout/SKILL.md
./.cloud-run/f18/ws-f18/plugins/factorio/skills/frame-research-problem/SKILL.md
./.cloud-run/f18/ws-f18/plugins/factorio/skills/audit-scientific-package/SKILL.md
./.cloud-run/f18/ws-f18/plugins/factorio/skills/coordinate-scientific-work/SKILL.md
./.cloud-run/f18/ws-f18/plugins/factorio/plugin.json
./.cloud-run/f18/ws-f18/plugins/manufacturing-processes/skills/am-process-parameters/SKILL.md
./.cloud-run/f18/ws-f18/plugins/manufacturing-processes/skills/additive-manufacturing/SKILL.md
./.cloud-run/f18/ws-f18/plugins/manufacturing-processes/skills/manufacturability/SKILL.md
./.cloud-run/f18/ws-f18/plugins/manufacturing-processes/skills/post-processing/SKILL.md
./.cloud-run/f18/ws-f18/plugins/manufacturing-processes/skills/build-orientation/SKILL.md
./.cloud-run/f18/ws-f18/plugins/manufacturing-processes/plugin.json
./.cloud-run/f18/ws-f18/plugins/opendocument/skills/edit-opendocument/SKILL.md
./.cloud-run/f18/ws-f18/plugins/opendocument/plugin.json
./.cloud-run/f18/ws-f18/plugins/morphorm/skills/morphorm/SKILL.md
./.cloud-run/f18/ws-f18/plugins/morphorm/plugin.json
./.cloud-run/f18/ws-f18/plugins/parquet/skills/parquet/SKILL.md
./.cloud-run/f18/ws-f18/plugins/parquet/plugin.json
./.cloud-run/f18/ws-f18/plugins/docx/skills/work-with-word/SKILL.md
./.cloud-run/f18/ws-f18/plugins/docx/skills/edit-ooxml-word/SKILL.md
./.cloud-run/f18/ws-f18/plugins/docx/plugin.json
./.cloud-run/f18/ws-f18/plugins/abaqus/skills/visualize-topology-optimization/SKILL.md
./.cloud-run/f18/ws-f18/plugins/abaqus/skills/abaqus/SKILL.md
./.cloud-run/f18/ws-f18/plugins/abaqus/skills/tosca/SKILL.md
./.cloud-run/f18/ws-f18/plugins/abaqus/skills/abaqus-visualization/SKILL.md
./.cloud-run/f18/ws-f18/plugins/abaqus/plugin.json
./.cloud-run/f18/ws-f18/plugins/scientific-method/skills/data-visualization/SKILL.md
./.cloud-run/f18/ws-f18/plugins/scientific-method/skills/scientific-data-analysis/SKILL.md
./.cloud-run/f18/ws-f18/plugins/scientific-method/skills/scientific-writing/SKILL.md

Stdout Truncated

false

Timed Out

false

Timeout S

0.0

Result Type

complete

Status

completed

Status Message

null

Task Id

V7gF2CteQsCowp2pWi-phSkLbQjLR80Rj7plPr8W_sc

Ttl Ms

900000

Status

completed

Handle

task_afb74d3610f84632a298572f2a245134

Pending

false

Result

Created At

2026-10-27T07:50:01.579087+00:00

Error

null

Input Requests

null

Last Updated At

2026-10-27T07:50:03.417535+00:00

Meta

Io.Modelcontextprotocol/Serverinfo

Name

CLIO shell

Version

4.1.0

Poll Interval Ms

5000

Result

Content

• {"command":"cd /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins && for f in */plugin.json; do echo "##### $f"; head -c 1500 $f; echo; done","cwd":"/home/user/clio-agent/.cloud-run/f18/ws-f18","exit_code":0,"timed_out":false,"timeout_s":0.0,"stdout":"##### abaqus/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "abaqus",\n "version": "0.6.0",\n "description": "The Abaqus program: scripting, running and auditing Abaqus/Standard and Explicit packages, Tosca optimization runs, 3D views and report figures of meshes and results, the abaqus-topology views, and the abaqus_engineer subagent.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "abaqus",\n "tosca",\n "fea",\n "simulation"\n ],\n "extensions": {\n "ai.iowarp.clio": {\n "requires": [\n "shell"\n ]\n }\n }\n}\n\n##### adios/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "adios",\n "version": "1.0.0",\n "description": "Inspect ADIOS2 BP4 and BP5 output through clio-kit's adios MCP server (list, variables, steps, attributes, one variable at one step), with the adios2 skill: directory layout, steps and variables, shape/start/count, global and local arrays, blocks, attributes, the Python FileReader and Stream APIs, bpls, engines and operators.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "adios2",\n "bp5",\n "scientific-data"\n ]\n}\n\n##### appl-core/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "appl-core",\n "version": "0.3.0",\n "description": "OPAL's APPL-CORE source plugin: the mission of the appl-core agent and the APPL-CORE export contract (export_version 6, other versions refused) for plant-phenotyping data from ORNL's phenotyping facility, read from each export's own files. General onboarding and phenotyping methods come from the data-onboarding and phenotyping plugins.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "phenotyping",\n "plants",\n "appl-core",\n "opal",\n "ornl"\n ],\n "extensions": {\n "ai.iowarp.clio": {\n "requires": [\n "data-onboarding",\n "phenotyping",\n "parquet"\n ]\n }\n }\n}\n\n##### characterization/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "characterization",\n "version": "0.6.0",\n "description": "Materials characterization method: X-ray CT and porosity, surface roughness and optical profilometry, fractography, and cross-technique defect synthesis, with the characterization_expert subagent.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "characterization",\n "xct",\n "microscopy"\n ]\n}\n\n##### clio-data/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "clio-data",\n "version": "1.0.0",\n "description": "The clio-data agent's plugin: its mission, assess-data-quality (what a variable states, checks, comparisons, visual checks) and convert-scientific-data (the HDF5/ADIOS2 to Parquet dtype map, skip-or-ask rules, and a bundled converter that reads back and verifies rows, nulls, NaNs, dtypes and per-column checksums).",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "hdf5",\n "adios2",\n "parquet",\n "conversion",\n "data-quality"\n ],\n "extensions": {\n "ai.iowarp.clio": {\n "requires": [\n "data-onboarding",\n "hdf5",\n "adios",\n "parquet"\n ]\n }\n }\n}\n\n##### clio-search/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "clio-search",\n "version": "0.2.0",\n "description": "Search and read the connected CLIO service's conversations, message passages and workspace files, with real navigable source links.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "search",\n "conversations",\n "workspace"\n ]\n}\n\n##### connected-data/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "connected-data",\n "version": "1.0.1",\n "description": "Connect research data sources and work with the National Data Platform and knowledge stores.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "data",\n "ndp",\n "knowledge"\n ]\n}\n\n##### data-onboarding/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "data-onboarding",\n "version": "1.0.0",\n "description": "General habits for unfamiliar datasets: read the self-description, inventory and audit tables with bundled scripts (sentinels, empty and near-duplicate columns, flags against data, join keys, declared against actual counts), keep an experiment card in the workspace, audit in a child agent, and state evidence plainly.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "datasets",\n "onboarding",\n "data-quality",\n "provenance"\n ]\n}\n\n##### deep-research/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "deep-research",\n "version": "0.3.0",\n "description": "Deep web research as a flow: a planner chooses research directions, repeatable web researcher subagents investigate them in parallel, an independent web-enabled critic returns a typed audit (verified claims with fetched source and quote, rejected claims, gaps), gaps are researched within bounded rounds, and a Markdown report is written only from verified claims.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "research",\n "web",\n "citations",\n "report",\n "flow"\n ],\n "extensions": {\n "ai.iowarp.clio": {\n "requires": [\n "delegation"\n ]\n }\n }\n}\n\n##### delegation/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "delegation",\n "version": "1.1.0",\n "description": "Delegate work: to a copy of the delegating agent, to the generic read-only explore, planner and review roles, to one of the agent's defined subagents, or to any installed agent.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "delegation",\n "subagents",\n "tasks"\n ]\n}\n\n##### document-production/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "document-production",\n "version": "0.2.0",\n "description": "Document production practice: edit the canonical source, preserve Office and OpenDocument packages, validate the native format, review the rendered result, and apply anchored artifact review comments.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "documents",\n "office",\n "opendocument",\n "latex",\n "review"\n ],\n "extensions": {\n "ai.iowarp.clio": {\n "requires": [\n "documents",\n "document-runtime"\n ]\n }\n }\n}\n\n##### document-runtime/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "document-runtime",\n "version": "1.0.0",\n "description": "CLIO's managed document toolchain: converters, fonts and bounded document inspection.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "documents",\n "runtime"\n ],\n "extensions": {\n "ai.iowarp.clio": {\n "requires": [\n "shell"\n ]\n }\n }\n}\n\n##### documents/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n","stdout_truncated":true,"stdout_spill":{"status":"spilled","reason":"shell_output_spilled","path":"/root/.local/state/clio-agent/workspaces/4839f65ddaa6bee8f9e9e2fe/tool-output/sess_b095500427c6/sh_20261027T075001_c863acfd.stdout.txt","relative_path":"/root/.local/state/clio-agent/workspaces/4839f65ddaa6bee8f9e9e2fe/tool-output/sess_b095500427c6/sh_20261027T075001_c863acfd.stdout.txt","total_bytes":27454,"total_lines":1028,"head_lines":264,"tail":"{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "visuals",\n "version": "1.2.0",\n "description": "Interactive analysis, dashboards, diagrams, 3D geometry for the mesh viewport (geometry-to-glb) and rendered visual review in CLIO's side panel.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "a2ui",\n "visuals",\n "dashboards",\n "diagrams",\n "3d"\n ]\n}\n\n##### weather/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "weather",\n "version": "1.0.0",\n "description": "Weather forecasts for a place.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "weather"\n ]\n}\n\n##### web/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "web",\n "version": "1.0.0",\n "description": "Fetch web pages and search the web through clio-kit's web MCP server.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "web",\n "search",\n "fetch"\n ]\n}\n\n##### wordle-demo/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "wordle-demo",\n "version": "0.1.0",\n "description": "A Wordle bench for studies of solving strategy: a generated, versioned list of pronounceable five-letter pseudo-words, games whose answers are drawn from a secret seed the agent never sees, strict per-guess feedback, and a live board wall.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "wordle",\n "game",\n "study",\n "demo"\n ]\n}\n\n##### workspace/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "workspace",\n "version": "1.1.0",\n "description": "Read, search and edit files in the session workspace, and view images.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "files",\n "workspace"\n ]\n}\n\n##### xlsx/plugin.json\n{\n "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",\n "name": "xlsx",\n "version": "1.0.0",\n "description": "Create, edit and analyze spreadsheets and CSV/TSV tables.",\n "author": {\n "name": "IoWarp Team"\n },\n "license": "BSD-3-Clause",\n "keywords": [\n "excel",\n "xlsx",\n "spreadsheets",\n "documents"\n ],\n "extensions": {\n "ai.iowarp.clio": {\n "requires": [\n "document-runtime"\n ]\n }\n }\n}\n\n","tail_lines":109},"stderr":"","stderr_truncated":false}

Iserror

false

Resulttype

complete

Structuredcontent

Command

cd /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins && for f in */plugin.json; do echo "##### $f"; head -c 1500 $f; echo; done

Cwd

/home/user/clio-agent/.cloud-run/f18/ws-f18

Exit Code

0

Stderr

Stderr Truncated

false

Stdout

##### abaqus/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "abaqus",
  "version": "0.6.0",
  "description": "The Abaqus program: scripting, running and auditing Abaqus/Standard and Explicit packages, Tosca optimization runs, 3D views and report figures of meshes and results, the abaqus-topology views, and the abaqus_engineer subagent.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "abaqus",
    "tosca",
    "fea",
    "simulation"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "shell"
      ]
    }
  }
}

##### adios/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "adios",
  "version": "1.0.0",
  "description": "Inspect ADIOS2 BP4 and BP5 output through clio-kit's adios MCP server (list, variables, steps, attributes, one variable at one step), with the adios2 skill: directory layout, steps and variables, shape/start/count, global and local arrays, blocks, attributes, the Python FileReader and Stream APIs, bpls, engines and operators.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "adios2",
    "bp5",
    "scientific-data"
  ]
}

##### appl-core/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "appl-core",
  "version": "0.3.0",
  "description": "OPAL's APPL-CORE source plugin: the mission of the appl-core agent and the APPL-CORE export contract (export_version 6, other versions refused) for plant-phenotyping data from ORNL's phenotyping facility, read from each export's own files. General onboarding and phenotyping methods come from the data-onboarding and phenotyping plugins.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "phenotyping",
    "plants",
    "appl-core",
    "opal",
    "ornl"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "data-onboarding",
        "phenotyping",
        "parquet"
      ]
    }
  }
}

##### characterization/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "characterization",
  "version": "0.6.0",
  "description": "Materials characterization method: X-ray CT and porosity, surface roughness and optical profilometry, fractography, and cross-technique defect synthesis, with the characterization_expert subagent.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "characterization",
    "xct",
    "microscopy"
  ]
}

##### clio-data/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "clio-data",
  "version": "1.0.0",
  "description": "The clio-data agent's plugin: its mission, assess-data-quality (what a variable states, checks, comparisons, visual checks) and convert-scientific-data (the HDF5/ADIOS2 to Parquet dtype map, skip-or-ask rules, and a bundled converter that reads back and verifies rows, nulls, NaNs, dtypes and per-column checksums).",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "hdf5",
    "adios2",
    "parquet",
    "conversion",
    "data-quality"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "data-onboarding",
        "hdf5",
        "adios",
        "parquet"
      ]
    }
  }
}

##### clio-search/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "clio-search",
  "version": "0.2.0",
  "description": "Search and read the connected CLIO service's conversations, message passages and workspace files, with real navigable source links.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "search",
    "conversations",
    "workspace"
  ]
}

##### connected-data/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "connected-data",
  "version": "1.0.1",
  "description": "Connect research data sources and work with the National Data Platform and knowledge stores.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "data",
    "ndp",
    "knowledge"
  ]
}

##### data-onboarding/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "data-onboarding",
  "version": "1.0.0",
  "description": "General habits for unfamiliar datasets: read the self-description, inventory and audit tables with bundled scripts (sentinels, empty and near-duplicate columns, flags against data, join keys, declared against actual counts), keep an experiment card in the workspace, audit in a child agent, and state evidence plainly.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "datasets",
    "onboarding",
    "data-quality",
    "provenance"
  ]
}

##### deep-research/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "deep-research",
  "version": "0.3.0",
  "description": "Deep web research as a flow: a planner chooses research directions, repeatable web researcher subagents investigate them in parallel, an independent web-enabled critic returns a typed audit (verified claims with fetched source and quote, rejected claims, gaps), gaps are researched within bounded rounds, and a Markdown report is written only from verified claims.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "research",
    "web",
    "citations",
    "report",
    "flow"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "delegation"
      ]
    }
  }
}

##### delegation/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "delegation",
  "version": "1.1.0",
  "description": "Delegate work: to a copy of the delegating agent, to the generic read-only explore, planner and review roles, to one of the agent's defined subagents, or to any installed agent.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "delegation",
    "subagents",
    "tasks"
  ]
}

##### document-production/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "document-production",
  "version": "0.2.0",
  "description": "Document production practice: edit the canonical source, preserve Office and OpenDocument packages, validate the native format, review the rendered result, and apply anchored artifact review comments.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "documents",
    "office",
    "opendocument",
    "latex",
    "review"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "documents",
        "document-runtime"
      ]
    }
  }
}

##### document-runtime/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "document-runtime",
  "version": "1.0.0",
  "description": "CLIO's managed document toolchain: converters, fonts and bounded document inspection.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "documents",
    "runtime"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "shell"
      ]
    }
  }
}

##### documents/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",

Stdout Spill

Complete saved output · 27,454 bytes

##### abaqus/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "abaqus",
  "version": "0.6.0",
  "description": "The Abaqus program: scripting, running and auditing Abaqus/Standard and Explicit packages, Tosca optimization runs, 3D views and report figures of meshes and results, the abaqus-topology views, and the abaqus_engineer subagent.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "abaqus",
    "tosca",
    "fea",
    "simulation"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "shell"
      ]
    }
  }
}

##### adios/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "adios",
  "version": "1.0.0",
  "description": "Inspect ADIOS2 BP4 and BP5 output through clio-kit's adios MCP server (list, variables, steps, attributes, one variable at one step), with the adios2 skill: directory layout, steps and variables, shape/start/count, global and local arrays, blocks, attributes, the Python FileReader and Stream APIs, bpls, engines and operators.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "adios2",
    "bp5",
    "scientific-data"
  ]
}

##### appl-core/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "appl-core",
  "version": "0.3.0",
  "description": "OPAL's APPL-CORE source plugin: the mission of the appl-core agent and the APPL-CORE export contract (export_version 6, other versions refused) for plant-phenotyping data from ORNL's phenotyping facility, read from each export's own files. General onboarding and phenotyping methods come from the data-onboarding and phenotyping plugins.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "phenotyping",
    "plants",
    "appl-core",
    "opal",
    "ornl"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "data-onboarding",
        "phenotyping",
        "parquet"
      ]
    }
  }
}

##### characterization/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "characterization",
  "version": "0.6.0",
  "description": "Materials characterization method: X-ray CT and porosity, surface roughness and optical profilometry, fractography, and cross-technique defect synthesis, with the characterization_expert subagent.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "characterization",
    "xct",
    "microscopy"
  ]
}

##### clio-data/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "clio-data",
  "version": "1.0.0",
  "description": "The clio-data agent's plugin: its mission, assess-data-quality (what a variable states, checks, comparisons, visual checks) and convert-scientific-data (the HDF5/ADIOS2 to Parquet dtype map, skip-or-ask rules, and a bundled converter that reads back and verifies rows, nulls, NaNs, dtypes and per-column checksums).",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "hdf5",
    "adios2",
    "parquet",
    "conversion",
    "data-quality"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "data-onboarding",
        "hdf5",
        "adios",
        "parquet"
      ]
    }
  }
}

##### clio-search/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "clio-search",
  "version": "0.2.0",
  "description": "Search and read the connected CLIO service's conversations, message passages and workspace files, with real navigable source links.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "search",
    "conversations",
    "workspace"
  ]
}

##### connected-data/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "connected-data",
  "version": "1.0.1",
  "description": "Connect research data sources and work with the National Data Platform and knowledge stores.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "data",
    "ndp",
    "knowledge"
  ]
}

##### data-onboarding/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "data-onboarding",
  "version": "1.0.0",
  "description": "General habits for unfamiliar datasets: read the self-description, inventory and audit tables with bundled scripts (sentinels, empty and near-duplicate columns, flags against data, join keys, declared against actual counts), keep an experiment card in the workspace, audit in a child agent, and state evidence plainly.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "datasets",
    "onboarding",
    "data-quality",
    "provenance"
  ]
}

##### deep-research/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "deep-research",
  "version": "0.3.0",
  "description": "Deep web research as a flow: a planner chooses research directions, repeatable web researcher subagents investigate them in parallel, an independent web-enabled critic returns a typed audit (verified claims with fetched source and quote, rejected claims, gaps), gaps are researched within bounded rounds, and a Markdown report is written only from verified claims.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "research",
    "web",
    "citations",
    "report",
    "flow"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "delegation"
      ]
    }
  }
}

##### delegation/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "delegation",
  "version": "1.1.0",
  "description": "Delegate work: to a copy of the delegating agent, to the generic read-only explore, planner and review roles, to one of the agent's defined subagents, or to any installed agent.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "delegation",
    "subagents",
    "tasks"
  ]
}

##### document-production/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "document-production",
  "version": "0.2.0",
  "description": "Document production practice: edit the canonical source, preserve Office and OpenDocument packages, validate the native format, review the rendered result, and apply anchored artifact review comments.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "documents",
    "office",
    "opendocument",
    "latex",
    "review"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "documents",
        "document-runtime"
      ]
    }
  }
}

##### document-runtime/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "document-runtime",
  "version": "1.0.0",
  "description": "CLIO's managed document toolchain: converters, fonts and bounded document inspection.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "documents",
    "runtime"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "shell"
      ]
    }
  }
}

##### documents/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "documents",
  "version": "1.0.0",
  "description": "Every document format CLIO works with: PDF, Word, spreadsheets, presentations, LaTeX and OpenDocument.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "documents",
    "pack"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "kind": "pack",
      "members": [
        "pdf",
        "docx",
        "xlsx",
        "pptx",
        "latex",
        "opendocument"
      ]
    }
  }
}

##### docx/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "docx",
  "version": "1.0.0",
  "description": "Create, edit and review Word documents.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "word",
    "docx",
    "documents"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "document-runtime"
      ]
    }
  }
}

##### earthscope/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "earthscope",
  "version": "0.5.0",
  "description": "The earthscope agent's L2 source plugin: its mission, acquisition of EarthScope GNSS station catalogs and position time series from the National Data Platform (discovered, never assumed), the earthscope-stations A2UI catalog for picking stations on a map, and the typed workflow_state for acquisition. GNSS methods come from the geodesy plugin.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "earthscope",
    "gnss",
    "ndp",
    "stations"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "ndp",
        "geo",
        "geodesy"
      ],
      "workflow_state": {
        "sections": {
          "geospatial": {
            "status_ranks": {
              "resolved": 4,
              "ambiguous": 2,
              "blocked": 1
            }
          },
          "catalog": {
            "status_ranks": {
              "metadata_found": 4,
              "candidates_found": 4,
              "no_candidates": 3,
              "blocked": 1
            }
          },
          "acquisition": {
            "status_ranks": {
              "staged": 5,
              "metadata_only": 4,
              "blocked": 2,
              "missing": 1
            },
            "readiness": {
              "field": "analysis_ready",
              "ready_status": "staged",
              "r
##### factorio/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "factorio",
  "version": "0.7.0",
  "description": "Factorio's identity and research process: its mission, specialist roster and working practice; the coordination, framing, study-log, audit and evidence fan-out skills; and its research-process subagents (methodologist, virtual lab, evidence researcher with its leaf and critic lanes, simulation methodologist, independent reviewer).",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "factorio",
    "research",
    "manufacturing"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "delegation",
        "science-log"
      ]
    }
  }
}

##### fatigue/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "fatigue",
  "version": "0.6.0",
  "description": "Fatigue and failure method: regime and mechanism, high-cycle and multiaxial fatigue, critical-plane (Fatemi-Socie) and defect-driven life prediction, fracture mechanics and crack initiation, with the fatigue_failure_expert subagent.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "fatigue",
    "fracture",
    "failure-analysis"
  ]
}

##### fea-methods/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "fea-methods",
  "version": "0.6.0",
  "description": "Finite-element and topology-optimization method, independent of any program: formulating a study, meshing and convergence, boundary conditions, structural response, reading stress and strain, and stating and interpreting an optimization problem.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "fea",
    "finite-element",
    "topology-optimization",
    "simulation"
  ]
}

##### geo/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "geo",
  "version": "1.0.0",
  "description": "Geocode places, filter points by radius and query geospatial features through clio-kit's geo MCP server.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "geo",
    "geospatial"
  ]
}

##### geodesy/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "geodesy",
  "version": "1.0.0",
  "description": "GNSS geodesy methods for any network: position time series (frames, trajectory models with rate, offsets and seasonal terms, noise and rate uncertainty) with a bundled fit, station catalogs read without guessing columns, region resolution, and station-coverage comparison over any discovered catalog.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "geodesy",
    "gnss",
    "time-series",
    "stations"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "geo"
      ]
    }
  }
}

##### hdf5/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "hdf5",
  "version": "1.2.0",
  "description": "Open and inspect HDF5 files through clio-kit's hdf5 MCP server, with the HDF5 team's `hdf5` skill: how to use the tools with bounded reads, and reference guides on layout, chunking, filters, cloud and parallel access, drivers and clio-core ingest.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "hdf5",
    "scientific-data"
  ]
}

##### hidden-law-bench/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "hidden-law-bench",
  "version": "0.1.0",
  "description": "A simulated bench apparatus whose governing law is drawn from a secret seed: controllable inputs with stated ranges, noisy readings of the time for ten cycles, every reading's history by branch, and a live readings view.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "bench",
    "apparatus",
    "study",
    "demo"
  ]
}

##### latex/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "latex",
  "version": "1.0.0",
  "description": "Author LaTeX documents and build them to PDF.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "latex",
    "pdf",
    "documents"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "document-runtime"
      ]
    }
  }
}

##### manufacturing-processes/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "manufacturing-processes",
  "version": "0.6.0",
  "description": "How a design becomes a part: process families (additive and conventional), additive process parameters and their defects, build orientation, manufacturability checks, post-processing and surface finishing, and the manufacturing_expert subagent.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "manufacturing",
    "additive-manufacturing",
    "process"
  ]
}

##### manufacturing/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "manufacturing",
  "version": "0.6.0",
  "description": "Manufacturing and materials science method, independent of any simulation program: materials, manufacturing processes, characterization, mechanical testing, fatigue and failure, and finite-element and topology-optimization method. Programs such as Abaqus or Morphorm are separate plugins an agent selects alongside it.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "manufacturing",
    "materials",
    "pack"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "kind": "pack",
      "members": [
        "materials",
        "manufacturing-processes",
        "characterization",
        "mechanical-testing",
        "fatigue",
        "fea-methods"
      ]
    }
  }
}

##### materials/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "materials",
  "version": "0.6.0",
  "description": "Materials science method for metallic parts: processing-structure-property reasoning, metallic material classes, nickel superalloys as a family, microstructure description and measurement, heat treatment and material property claims, and the materials_scientist subagent.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "materials",
    "metallurgy",
    "microstructure"
  ]
}

##### mechanical-testing/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "mechanical-testing",
  "version": "0.6.0",
  "description": "Mechanical testing method: test and fatigue-campaign design against named standards, tensile testing, load frame and instrumentation capability, and data acquisition, with the mechanical_testing_expert subagent.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "testing",
    "tensile",
    "fatigue"
  ]
}

##### morphorm/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "morphorm",
  "version": "0.6.0",
  "description": "The Morphorm topology-optimization program: Cubit mesh, input deck, XMLGenerator, batch run and restarts, with bundled checks of the Exodus mesh, the generated XML settings and the optimizer diagnostics.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "morphorm",
    "topology-optimization",
    "simulation"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "shell"
      ]
    }
  }
}

##### ndp/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "ndp",
  "version": "1.0.0",
  "description": "Search National Data Platform datasets and stage their resources through clio-kit's ndp MCP server.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "ndp",
    "datasets"
  ]
}

##### opendocument/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "opendocument",
  "version": "1.0.0",
  "description": "Create and edit OpenDocument text, spreadsheets and presentations.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "opendocument",
    "odt",
    "ods",
    "odp",
    "documents"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "document-runtime"
      ]
    }
  }
}

##### pandas/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "pandas",
  "version": "1.0.0",
  "description": "Load, profile, filter and summarize tabular data through clio-kit's pandas MCP server.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "pandas",
    "tables",
    "csv"
  ]
}

##### parquet/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "parquet",
  "version": "1.1.0",
  "description": "Parquet through clio-kit's parquet MCP server (single-file summaries, slices, previews and aggregates) and the parquet skill: footer, row groups and statistics, physical and logical types, hive partitioning, bounded scans with pyarrow or DuckDB, and write options.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "parquet",
    "tables"
  ]
}

##### pdf/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "pdf",
  "version": "1.0.0",
  "description": "Read, review and produce PDF documents.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "pdf",
    "documents"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "document-runtime"
      ]
    }
  }
}

##### phenotyping/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "phenotyping",
  "version": "1.0.0",
  "description": "Plant-phenotyping methods for any source: design and identity checks with MIAPPE-style example schemas and a validator, size and growth traits, treatment and genotype response, fluorescence and spectral signals, and phenotyping reports.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "phenotyping",
    "plants",
    "miappe"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "data-onboarding"
      ]
    }
  }
}

##### plot/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "plot",
  "version": "1.0.0",
  "description": "Render static plots (line, scatter, histogram, heatmap, time series) through clio-kit's plot MCP server.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "plot",
    "figures"
  ]
}

##### pptx/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "pptx",
  "version": "1.0.0",
  "description": "Create, edit and review PowerPoint presentations.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "powerpoint",
    "pptx",
    "presentations",
    "documents"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "document-runtime"
      ]
    }
  }
}

##### science-log/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "science-log",
  "version": "1.0.1",
  "description": "A study's questions, hypotheses, experiments, observations, evidence, reframes and conclusions as typed, linked log entries, with sources read from the recorded calls, measurements as data, and the run-a-study method.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "science",
    "study",
    "hypotheses",
    "provenance"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "delegation",
        "orchestration"
      ]
    }
  }
}

##### scientific-method/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "scientific-method",
  "version": "0.7.0",
  "description": "General scientific practice for every science agent: method choice and study design, literature search and review, research gaps, citations, data analysis, statistics, uncertainty, figures, scientific writing, and non-interactive task runs.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "research",
    "methodology",
    "literature",
    "statistics"
  ]
}

##### shell/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "shell",
  "version": "1.0.0",
  "description": "A shell in the session workspace, with CLIO's managed execution runtime.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "shell",
    "execution"
  ]
}

##### slurm/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "slurm",
  "version": "0.6.0",
  "description": "Slurm batch jobs: submit, record job ids, wait in bounded low-output steps with a bundled helper, and read a failed job's output before resubmitting.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "slurm",
    "hpc",
    "batch"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "shell"
      ]
    }
  }
}

##### spotter/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "spotter",
  "version": "0.5.0",
  "description": "SPOTTER's forensic watcher: provider-aware execution and artifact lineage across Flowcept, CMF and CLIO's native journal, captured-attention inspection, and skills for investigating and alerting on unexplained deviations in a watched CLIO session.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "provenance",
    "forensics",
    "lineage",
    "attention"
  ]
}

##### ssh/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "ssh",
  "version": "1.0.0",
  "description": "Run commands on a configured remote host over SSH.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "ssh",
    "hpc",
    "remote"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "shell"
      ]
    }
  }
}

##### visuals/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "visuals",
  "version": "1.2.0",
  "description": "Interactive analysis, dashboards, diagrams, 3D geometry for the mesh viewport (geometry-to-glb) and rendered visual review in CLIO's side panel.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "a2ui",
    "visuals",
    "dashboards",
    "diagrams",
    "3d"
  ]
}

##### weather/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "weather",
  "version": "1.0.0",
  "description": "Weather forecasts for a place.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "weather"
  ]
}

##### web/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "web",
  "version": "1.0.0",
  "description": "Fetch web pages and search the web through clio-kit's web MCP server.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "web",
    "search",
    "fetch"
  ]
}

##### wordle-demo/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "wordle-demo",
  "version": "0.1.0",
  "description": "A Wordle bench for studies of solving strategy: a generated, versioned list of pronounceable five-letter pseudo-words, games whose answers are drawn from a secret seed the agent never sees, strict per-guess feedback, and a live board wall.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "wordle",
    "game",
    "study",
    "demo"
  ]
}

##### workspace/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "workspace",
  "version": "1.1.0",
  "description": "Read, search and edit files in the session workspace, and view images.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "files",
    "workspace"
  ]
}

##### xlsx/plugin.json
{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "xlsx",
  "version": "1.0.0",
  "description": "Create, edit and analyze spreadsheets and CSV/TSV tables.",
  "author": {
    "name": "IoWarp Team"
  },
  "license": "BSD-3-Clause",
  "keywords": [
    "excel",
    "xlsx",
    "spreadsheets",
    "documents"
  ],
  "extensions": {
    "ai.iowarp.clio": {
      "requires": [
        "document-runtime"
      ]
    }
  }
}

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false

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Task Id

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Ttl Ms

900000

Status

completed

Handle

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Pending

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Result

Created At

2026-10-27T07:50:01.401923+00:00

Error

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Last Updated At

2026-10-27T07:50:03.781699+00:00

Meta

Io.Modelcontextprotocol/Serverinfo

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CLIO shell

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4.1.0

Poll Interval Ms

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Result

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Cwd

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Exit Code

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Stderr

Stderr Truncated

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Stdout

=== abaqus: 19 files, skills: 4
=== adios: 6 files, skills: 1
=== appl-core: 15 files, skills: 1
=== characterization: 10 files, skills: 5
=== clio-data: 9 files, skills: 2
=== clio-search: 7 files, skills: 0
=== connected-data: 14 files, skills: 2
=== data-onboarding: 16 files, skills: 3
=== deep-research: 17 files, skills: 0
=== delegation: 8 files, skills: 0
=== document-production: 8 files, skills: 1
=== document-runtime: 9 files, skills: 2
=== documents: 1 files, skills: 0
=== docx: 9 files, skills: 2
=== earthscope: 12 files, skills: 1
=== factorio: 34 files, skills: 5
=== fatigue: 13 files, skills: 8
=== fea-methods: 9 files, skills: 6
=== geo: 2 files, skills: 0
=== geodesy: 12 files, skills: 5
=== hdf5: 26 files, skills: 1
=== hidden-law-bench: 12 files, skills: 0
=== latex: 4 files, skills: 1
=== manufacturing-processes: 10 files, skills: 5
=== manufacturing: 1 files, skills: 0
=== materials: 11 files, skills: 6
=== mechanical-testing: 9 files, skills: 4
=== morphorm: 9 files, skills: 1
=== ndp: 2 files, skills: 0
=== opendocument: 3 files, skills: 1
=== pandas: 2 files, skills: 0
=== parquet: 6 files, skills: 1
=== pdf: 7 files, skills: 2
=== phenotyping: 16 files, skills: 5
=== plot: 2 files, skills: 0
=== pptx: 9 files, skills: 2
=== science-log: 4 files, skills: 1
=== scientific-method: 14 files, skills: 11
=== shell: 5 files, skills: 0
=== slurm: 7 files, skills: 1
=== spotter: 32 files, skills: 3
=== ssh: 2 files, skills: 0
=== visuals: 19 files, skills: 5
=== weather: 2 files, skills: 0
=== web: 2 files, skills: 0
=== wordle-demo: 13 files, skills: 0
=== workspace: 4 files, skills: 0
=== xlsx: 4 files, skills: 2

./abaqus/.lint-l3
./abaqus/ai.iowarp.clio/a2ui/abaqus-topology/catalog.clio.json
./abaqus/ai.iowarp.clio/a2ui/abaqus-topology/catalog.json
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./abaqus/ai.iowarp.clio/subagents/abaqus_engineer.py
./abaqus/lint-denylist.txt
./abaqus/skills/abaqus-visualization/scripts/fea_glb.py
./abaqus/skills/abaqus-visualization/scripts/odb_to_glb.py
./abaqus/skills/abaqus-visualization/scripts/render_view.py
./abaqus/tests/test_abaqus_topology_catalog.py
./abaqus/tests/test_fea_glb.py
./adios/.lint-l3
./adios/lint-denylist.txt
./adios/mcp.json
./adios/tests/test_adios_plugin.py
./appl-core/.lint-l3
./appl-core/ai.iowarp.clio/prompt/mission.md
./appl-core/ai.iowarp.clio/prompt/outputs.md
./appl-core/ai.iowarp.clio/prompt/views.md
./appl-core/evals/README.md
./appl-core/evals/behavioral-cases.json
./appl-core/evals/scripts/evaluate_appl_core.py
./appl-core/evals/scripts/make_variants.py
./appl-core/lint-denylist.txt
./appl-core/tests/appl_core_fixtures.py
./appl-core/tests/conftest.py
./appl-core/tests/test_appl_evals.py
./appl-core/tests/test_appl_levels.py
./characterization/.lint-l3
./characterization/ai.iowarp.clio/prompt/subagents/characterization_expert.md
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./characterization/lint-denylist.txt
./clio-data/.lint-l3
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./clio-data/lint-denylist.txt
./clio-data/skills/convert-scientific-data/scripts/convert_to_parquet.py
./clio-data/tests/test_clio_data_plugin.py
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./clio-search/.lint-l3
./clio-search/ai.iowarp.clio/prompt/mission.md
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./connected-data/skills/work-with-ndp/references/catalog-authoring.md
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./connected-data/skills/work-with-ndp/scripts/inspect_capture.py
./connected-data/skills/work-with-ndp/scripts/prepare_dataset.py
./connected-data/tests/test_ndp_skill_helpers.py
./data-onboarding/.lint-l3
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./data-onboarding/skills/onboard-dataset/scripts/_tables.py
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./data-onboarding/skills/onboard-dataset/scripts/card.py
./data-onboarding/skills/onboard-dataset/scripts/flag_check.py
./data-onboarding/skills/onboard-dataset/scripts/inventory.py
./data-onboarding/skills/onboard-dataset/scripts/join_keys.py
./data-onboarding/tests/conftest.py
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./deep-research/.lint-l3
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./document-production/.lint-l3

Stdout Spill

Complete saved output · 9,098 bytes

=== abaqus: 19 files, skills: 4
=== adios: 6 files, skills: 1
=== appl-core: 15 files, skills: 1
=== characterization: 10 files, skills: 5
=== clio-data: 9 files, skills: 2
=== clio-search: 7 files, skills: 0
=== connected-data: 14 files, skills: 2
=== data-onboarding: 16 files, skills: 3
=== deep-research: 17 files, skills: 0
=== delegation: 8 files, skills: 0
=== document-production: 8 files, skills: 1
=== document-runtime: 9 files, skills: 2
=== documents: 1 files, skills: 0
=== docx: 9 files, skills: 2
=== earthscope: 12 files, skills: 1
=== factorio: 34 files, skills: 5
=== fatigue: 13 files, skills: 8
=== fea-methods: 9 files, skills: 6
=== geo: 2 files, skills: 0
=== geodesy: 12 files, skills: 5
=== hdf5: 26 files, skills: 1
=== hidden-law-bench: 12 files, skills: 0
=== latex: 4 files, skills: 1
=== manufacturing-processes: 10 files, skills: 5
=== manufacturing: 1 files, skills: 0
=== materials: 11 files, skills: 6
=== mechanical-testing: 9 files, skills: 4
=== morphorm: 9 files, skills: 1
=== ndp: 2 files, skills: 0
=== opendocument: 3 files, skills: 1
=== pandas: 2 files, skills: 0
=== parquet: 6 files, skills: 1
=== pdf: 7 files, skills: 2
=== phenotyping: 16 files, skills: 5
=== plot: 2 files, skills: 0
=== pptx: 9 files, skills: 2
=== science-log: 4 files, skills: 1
=== scientific-method: 14 files, skills: 11
=== shell: 5 files, skills: 0
=== slurm: 7 files, skills: 1
=== spotter: 32 files, skills: 3
=== ssh: 2 files, skills: 0
=== visuals: 19 files, skills: 5
=== weather: 2 files, skills: 0
=== web: 2 files, skills: 0
=== wordle-demo: 13 files, skills: 0
=== workspace: 4 files, skills: 0
=== xlsx: 4 files, skills: 2

./abaqus/.lint-l3
./abaqus/ai.iowarp.clio/a2ui/abaqus-topology/catalog.clio.json
./abaqus/ai.iowarp.clio/a2ui/abaqus-topology/catalog.json
./abaqus/ai.iowarp.clio/a2ui/abaqus-topology/instructions.md
./abaqus/ai.iowarp.clio/prompt/capabilities.md
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./abaqus/ai.iowarp.clio/subagents/abaqus_engineer.py
./abaqus/lint-denylist.txt
./abaqus/skills/abaqus-visualization/scripts/fea_glb.py
./abaqus/skills/abaqus-visualization/scripts/odb_to_glb.py
./abaqus/skills/abaqus-visualization/scripts/render_view.py
./abaqus/tests/test_abaqus_topology_catalog.py
./abaqus/tests/test_fea_glb.py
./adios/.lint-l3
./adios/lint-denylist.txt
./adios/mcp.json
./adios/tests/test_adios_plugin.py
./appl-core/.lint-l3
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./appl-core/ai.iowarp.clio/prompt/outputs.md
./appl-core/ai.iowarp.clio/prompt/views.md
./appl-core/evals/README.md
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./appl-core/tests/test_appl_evals.py
./appl-core/tests/test_appl_levels.py
./characterization/.lint-l3
./characterization/ai.iowarp.clio/prompt/subagents/characterization_expert.md
./characterization/ai.iowarp.clio/subagents/characterization_expert.py
./characterization/lint-denylist.txt
./clio-data/.lint-l3
./clio-data/ai.iowarp.clio/prompt/mission.md
./clio-data/lint-denylist.txt
./clio-data/skills/convert-scientific-data/scripts/convert_to_parquet.py
./clio-data/tests/test_clio_data_plugin.py
./clio-data/tests/test_convert_to_parquet.py
./clio-search/.lint-l3
./clio-search/ai.iowarp.clio/prompt/mission.md
./clio-search/ai.iowarp.clio/prompt/reporting.md
./clio-search/ai.iowarp.clio/prompt/search.md
./clio-search/ai.iowarp.clio/tools/builtin.py
./clio-search/lint-denylist.txt
./connected-data/ai.iowarp.clio/tools/builtin.py
./connected-data/skills/work-with-ndp/examples/hosted-resources.json
./connected-data/skills/work-with-ndp/examples/replay-segment.sse
./connected-data/skills/work-with-ndp/references/catalog-authoring.md
./connected-data/skills/work-with-ndp/references/discovery-and-analysis.md
./connected-data/skills/work-with-ndp/references/scientific-stream-analysis.md
./connected-data/skills/work-with-ndp/references/services-and-streams.md
./connected-data/skills/work-with-ndp/references/worked-examples.md
./connected-data/skills/work-with-ndp/scripts/inspect_capture.py
./connected-data/skills/work-with-ndp/scripts/prepare_dataset.py
./connected-data/tests/test_ndp_skill_helpers.py
./data-onboarding/.lint-l3
./data-onboarding/lint-denylist.txt
./data-onboarding/skills/onboard-dataset/scripts/_tables.py
./data-onboarding/skills/onboard-dataset/scripts/audit_columns.py
./data-onboarding/skills/onboard-dataset/scripts/card.py
./data-onboarding/skills/onboard-dataset/scripts/flag_check.py
./data-onboarding/skills/onboard-dataset/scripts/inventory.py
./data-onboarding/skills/onboard-dataset/scripts/join_keys.py
./data-onboarding/tests/conftest.py
./data-onboarding/tests/onboarding_fixtures.py
./data-onboarding/tests/test_onboarding_levels.py
./data-onboarding/tests/test_onboarding_scripts.py
./deep-research/.lint-l3
./deep-research/ai.iowarp.clio/audit.py
./deep-research/ai.iowarp.clio/evidence.py
./deep-research/ai.iowarp.clio/flows/deep_research.py
./deep-research/ai.iowarp.clio/prompt/mission.md
./deep-research/ai.iowarp.clio/prompt/options.md
./deep-research/ai.iowarp.clio/prompt/report.md
./deep-research/ai.iowarp.clio/prompt/subagents/critic.md
./deep-research/ai.iowarp.clio/prompt/subagents/researcher.md
./deep-research/ai.iowarp.clio/report.py
./deep-research/ai.iowarp.clio/subagents/critic.py
./deep-research/ai.iowarp.clio/subagents/researcher.py
./deep-research/lint-denylist.txt
./deep-research/tests/test_audit_continuity.py
./deep-research/tests/test_deep_research_flow.py
./deep-research/tests/test_report_actions.py
./delegation/ai.iowarp.clio/prompt/child.md
./delegation/ai.iowarp.clio/prompt/parent.md
./delegation/ai.iowarp.clio/prompt/subagents/explore.md
./delegation/ai.iowarp.clio/prompt/subagents/planner.md
./delegation/ai.iowarp.clio/prompt/subagents/review.md
./delegation/ai.iowarp.clio/subagents/roles.py
./delegation/ai.iowarp.clio/tools/builtin.py
./document-production/.lint-l3
./document-production/ai.iowarp.clio/prompt/mission.md
./document-production/ai.iowarp.clio/prompt/native-formats.md
./document-production/ai.iowarp.clio/prompt/shell-conversions.md
./document-production/lint-denylist.txt
./document-production/skills/review-document-artifact/references/anchor-semantics.md
./document-runtime/ai.iowarp.clio/prompt/runtime.md
./document-runtime/ai.iowarp.clio/tools/builtin.py
./document-runtime/skills/edit-markdown-html/references/document-quality.md
./document-runtime/skills/inspect-office-package/references/part-ownership.md
./document-runtime/skills/inspect-office-package/scripts/package_guard.py
./document-runtime/tests/test_package_guard.py
./docx/skills/edit-ooxml-word/references/word-ooxml.md
./docx/skills/work-with-word/examples/README.md
./docx/skills/work-with-word/examples/create-reference-report.mjs
./docx/skills/work-with-word/references/docx-js.md
./docx/skills/work-with-word/references/python-docx-editing.md
./docx/skills/work-with-word/references/report-design.md
./earthscope/.lint-l3
./earthscope/README.md
./earthscope/ai.iowarp.clio/a2ui/earthscope-stations/catalog.clio.json
./earthscope/ai.iowarp.clio/a2ui/earthscope-stations/catalog.json
./earthscope/ai.iowarp.clio/a2ui/earthscope-stations/instructions.md
./earthscope/ai.iowarp.clio/prompt/mission.md
./earthscope/ai.iowarp.clio/prompt/views.md
./earthscope/lint-denylist.txt
./earthscope/tests/test_a2ui_catalog.py
./earthscope/tests/test_earthscope_plugin.py
./factorio/.lint-l3
./factorio/README.md
./factorio/ai.iowarp.clio/prompt/mission.md
./factorio/ai.iowarp.clio/prompt/practice.md
./factorio/ai.iowarp.clio/prompt/specialists.md
./factorio/ai.iowarp.clio/prompt/subagents/evidence_critic.md
./factorio/ai.iowarp.clio/prompt/subagents/evidence_leaf.md
./factorio/ai.iowarp.clio/prompt/subagents/evidence_researcher.md
./factorio/ai.iowarp.clio/prompt/subagents/independent_reviewer.md
./factorio/ai.iowarp.clio/prompt/subagents/research_methodologist.md
./factorio/ai.iowarp.clio/prompt/subagents/simulation_methodologist.md
./factorio/ai.iowarp.clio/prompt/subagents/virtual_lab.md
./factorio/ai.iowarp.clio/subagents/evidence_critic.py
./factorio/ai.iowarp.clio/subagents/evidence_leaf.py
./factorio/ai.iowarp.clio/subagents/evidence_researcher.py
./factorio/ai.iowarp.clio/subagents/independent_reviewer.py
./factorio/ai.iowarp.clio/subagents/research_methodologist.py
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./factorio/evals/README.md
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./factorio/evals/scripts/evaluate_factorio.py
./factorio/lint-denylist.txt
./factorio/skills/coordinate-scientific-work/references/decision-criteria.md
./factorio/skills/evidence-fanout/references/fanout-lifecycle.md
./factorio/skills/evidence-fanout/references/source-integrity.md
./factorio/tests/fixtures/behavioral-results.json
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Outcomes

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  Handle

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  Kind

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  Task Id

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• Accepted

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  Assignment

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  Handle

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  Kind

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  Task Id

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• Accepted

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  Assignment

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  Handle

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  Kind

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  Task Id

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• Accepted

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  Assignment

  Review the skills of these plugins under /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/: connected-data, earthscope, geodesy, spotter, slurm, science-log. For each plugin read plugin.json (including extensions.ai.iowarp.clio.requires), every skills/*/SKILL.md (and the references/ files they cite), and list the files the plugin ships. Report, PLUGIN BY PLUGIN and skill by skill, with file path and quoted/line-referenced evidence: (1) unclear instructions; (2) contradictions with another skill (same plugin or any other plugin under plugins/); (3) references to tools, scripts, files, MCP servers, subagents or other skills that the plugin does not ship and that are not provided by a plugin in its requires (verify each on the filesystem). Do not modify anything. Only report issues you verified; say 'none found' for clean plugins.

  Handle

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  Provider Id

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  Task Id

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• Accepted

  true

  Assignment

  Review the skills of these plugins under /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/: document-production, document-runtime, docx, pdf, pptx, xlsx, latex, opendocument, visuals. For each plugin read plugin.json (including extensions.ai.iowarp.clio.requires), every skills/*/SKILL.md, and list the files the plugin ships. Report, PLUGIN BY PLUGIN and skill by skill, with file path and quoted/line-referenced evidence: (1) unclear instructions; (2) contradictions with another skill (same plugin or any other plugin under plugins/ — pay attention to overlap between docx/work-with-word and edit-ooxml-word, xlsx, pptx, pdf, latex, opendocument, document-production); (3) references to tools, scripts, files, MCP servers or other skills that the plugin does not ship and that are not provided by a plugin in its requires (verify each on the filesystem). Do not modify anything. Only report issues you verified; say 'none found' for clean plugins.

  Handle

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  Kind

  Subagent

  Model

  Asked

  Effort

  Ran

  Model Id

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  Provider Id

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  Reasons

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  Session Id

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  Task Id

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• Accepted

  true

  Assignment

  Review the skills of these plugins under /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/: factorio, scientific-method, morphorm. For each plugin read plugin.json (including extensions.ai.iowarp.clio.requires), every skills/*/SKILL.md (and the references/ files they cite), and list the files the plugin ships (subagents, prompts, evals). Report, PLUGIN BY PLUGIN and skill by skill, with file path and quoted/line-referenced evidence: (1) unclear instructions; (2) contradictions with another skill (same plugin or any other plugin under plugins/); (3) references to tools, scripts, files, subagents, MCP servers or other skills that the plugin does not ship and that are not provided by a plugin in its requires (verify each on the filesystem). Do not modify anything. Only report issues you verified; say 'none found' for clean plugins.

  Handle

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  Kind

  Subagent

  Model

  Asked

  Effort

  Ran

  Model Id

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  Provider Id

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  Reasons

  Source

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  Session Id

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  Task Id

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Spawned

• Accepted

  true

  Assignment

  Review the skills of these plugins under /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/: abaqus, fea-methods, mechanical-testing, characterization. For each plugin read plugin.json (including extensions.ai.iowarp.clio.requires), every skills/*/SKILL.md, and list the files the plugin ships (scripts, references, ai.iowarp.clio/tools, mcp.json, prompt files, subagents). Report, PLUGIN BY PLUGIN and skill by skill, with file path and quoted/line-referenced evidence: (1) unclear instructions (ambiguous, missing steps, undefined terms); (2) contradictions with another skill (same plugin or any other plugin under plugins/); (3) references to tools, scripts, files, subagents, other skills or MCP servers that the plugin does not ship and that are not provided by a plugin listed in its requires (verify each by checking the filesystem, do not assume). Do not modify anything. Only report issues you verified; say 'none found' for clean plugins.

  Handle

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  Kind

  Subagent

  Model

  Asked

  Effort

  Ran

  Model Id

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  Provider Id

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  Reasons

  Source

  inherited

  Session Id

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  Task Id

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• Accepted

  true

  Assignment

  Review the skills of these plugins under /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/: fatigue, materials, manufacturing-processes. For each plugin read plugin.json (including extensions.ai.iowarp.clio.requires), every skills/*/SKILL.md, and list the files the plugin ships. Report, PLUGIN BY PLUGIN and skill by skill, with file path and quoted/line-referenced evidence: (1) unclear instructions; (2) contradictions with another skill (same plugin or any other plugin under plugins/, e.g. conflicting numeric values, conventions, or procedures); (3) references to tools, scripts, files, subagents, other skills or MCP servers that the plugin does not ship and that are not provided by a plugin listed in its requires (verify each on the filesystem). Do not modify anything. Only report issues you verified; say 'none found' for clean plugins.

  Handle

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  Kind

  Subagent

  Model

  Asked

  Effort

  Ran

  Model Id

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  Provider Id

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  Reasons

  Source

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  Session Id

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  Task Id

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• Accepted

  true

  Assignment

  Review the skills of these plugins under /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/: data-onboarding, clio-data, adios, hdf5, parquet, appl-core, phenotyping. For each plugin read plugin.json (including extensions.ai.iowarp.clio.requires), every skills/*/SKILL.md, and list the files the plugin ships (scripts, mcp.json, prompts, evals). Report, PLUGIN BY PLUGIN and skill by skill, with file path and quoted/line-referenced evidence: (1) unclear instructions; (2) contradictions with another skill (same plugin or any other plugin under plugins/); (3) references to tools, scripts, files, MCP servers or other skills that the plugin does not ship and that are not provided by a plugin listed in its requires (verify each on the filesystem; note e.g. skills that rely on plugins missing from requires). Do not modify anything. Only report issues you verified; say 'none found' for clean plugins.

  Handle

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  Kind

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  Model

  Asked

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  Provider Id

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  Reasons

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  Task Id

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• Accepted

  true

  Assignment

  Review the skills of these plugins under /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/: connected-data, earthscope, geodesy, spotter, slurm, science-log. For each plugin read plugin.json (including extensions.ai.iowarp.clio.requires), every skills/*/SKILL.md (and the references/ files they cite), and list the files the plugin ships. Report, PLUGIN BY PLUGIN and skill by skill, with file path and quoted/line-referenced evidence: (1) unclear instructions; (2) contradictions with another skill (same plugin or any other plugin under plugins/); (3) references to tools, scripts, files, MCP servers, subagents or other skills that the plugin does not ship and that are not provided by a plugin in its requires (verify each on the filesystem). Do not modify anything. Only report issues you verified; say 'none found' for clean plugins.

  Handle

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  Kind

  Subagent

  Model

  Asked

  Effort

  Ran

  Model Id

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  Provider Id

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  Reasons

  Source

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  Session Id

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  Task Id

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• Accepted

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  Assignment

  Review the skills of these plugins under /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/: document-production, document-runtime, docx, pdf, pptx, xlsx, latex, opendocument, visuals. For each plugin read plugin.json (including extensions.ai.iowarp.clio.requires), every skills/*/SKILL.md, and list the files the plugin ships. Report, PLUGIN BY PLUGIN and skill by skill, with file path and quoted/line-referenced evidence: (1) unclear instructions; (2) contradictions with another skill (same plugin or any other plugin under plugins/ — pay attention to overlap between docx/work-with-word and edit-ooxml-word, xlsx, pptx, pdf, latex, opendocument, document-production); (3) references to tools, scripts, files, MCP servers or other skills that the plugin does not ship and that are not provided by a plugin in its requires (verify each on the filesystem). Do not modify anything. Only report issues you verified; say 'none found' for clean plugins.

  Handle

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  Kind

  Subagent

  Model

  Asked

  Effort

  Ran

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  Provider Id

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  Reasons

  Source

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  Session Id

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  Task Id

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• Accepted

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  Assignment

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  Handle

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  Kind

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  Asked

  Effort

  Ran

  Model Id

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  Provider Id

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  Reasons

  Source

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  {"answer": "# Review of abaqus, fea-methods, mechanical-testing and characterization\n\nI found no missing files. The recurring problem is cross-plugin skill references that are not covered by requires. I also found undefined terms and one contradiction on units.\n\nBase path: /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/. Every file named below was read directly.\n\n## What each plugin ships\n\n| Plugin | requires (plugin.json) | Shipped files |\n|---|---|---|\n| abaqus | [\"shell\"] | 4 skills (abaqus, abaqus-visualization, tosca, visualize-topology-optimization); skills/abaqus-visualization/scripts/{fea_glb,odb_to_glb,render_view}.py; ai.iowarp.clio/a2ui/abaqus-topology/{catalog.clio.json,catalog.json,instructions.md}; ai.iowarp.clio/prompt/{capabilities.md,views.md,subagents/abaqus_engineer.md}; ai.iowarp.clio/subagents/abaqus_engineer.py; tests/{test_abaqus_topology_catalog.py,test_fea_glb.py}; .lint-l3; lint-denylist.txt |\n| fea-methods | none (no extensions block) | 6 skills (finite-element-analysis, structural-analysis, boundary-conditions, meshing, stress-strain-analysis, topology-optimization); no ai.iowarp.clio directory |\n| mechanical-testing | none | 4 skills; ai.iowarp.clio/prompt/subagents/mechanical_testing_expert.md; ai.iowarp.clio/subagents/mechanical_testing_expert.py |\n| characterization | none | 5 skills; ai.iowarp.clio/prompt/subagents/characterization_expert.md; ai.iowarp.clio/subagents/characterization_expert.py |\n\n- Not shipped by any of the four: none has mcp.json, ai.iowarp.clio/tools, or scripts outside abaqus-visualization.\n- Skill folders: the other skill folders hold only SKILL.md. The name-search scans visited exactly 6, 4 and 5 files for fea-methods, mechanical-testing and characterization. I did not list those folders one by one.\n- Pack membership: manufacturing/plugin.json lists characterization, mechanical-testing and fea-methods as pack members, but not abaqus.\n\n## abaqus\n\n### Dangling references (verified)\nAll of these skills exist elsewhere under plugins/, but abaqus requires only shell.\n- fea-methods skills. skills/abaqus/SKILL.md says "The method behind each modelling choice is in finite-element-analysis, meshing, boundary-conditions and stress-strain-analysis". skills/tosca/SKILL.md and prompt/subagents/abaqus_engineer.md reference topology-optimization. All live in fea-methods/skills/.\n- hpc-batch-jobs. It is referenced in skills/abaqus/SKILL.md §3 ("load hpc-batch-jobs") and in abaqus_engineer.md. It lives in slurm/skills/hpc-batch-jobs/.\n- Subagent coverage. abaqus_engineer.py declares plugins=[\"workspace\",\"shell\",\"fea-methods\",\"manufacturing-processes\",\"slurm\"], so the subagent path is covered. A direct skill load without the subagent is not.\n- Catalog skill names. a2ui-catalog-abaqus-topology is named in views.md and in visualize-topology-optimization/SKILL.md. A repo-wide text search for that string found no match, but the search hit its time limit. The catalog directory does exist at ai.iowarp.clio/a2ui/abaqus-topology/. I could not confirm the skill id, nor the "clio-workspace catalog" cited by abaqus-visualization.\n- uv. The viz skill depends on uv run, but uv is not a declared requirement. I did not check whether it is present.\n\n### Contradiction (verified)\n- Units. abaqus/SKILL.md §1 says "Abaqus has none of its own: every input must use one consistent set, stated in the package". abaqus-visualization/SKILL.md hard-codes "S_MISES in MPa, U_MAG in mm". A model in SI-m/Pa would be mislabelled. The viz skill should take units from the package.\n\n### Unclear instructions (verified from text)\n- No status for a failed run. abaqus §4 defines GENERATED_NOT_EXECUTED, SOLVER_EXECUTED ("the run finished and its status and message files were read") and VALIDATED. §3 admits a job can write an ODB and still fail to converge. A non-converged or failed run has no label.\n- Older Abaqus releases. abaqus-visualization says odb_to_glb.py needs "Abaqus 2024 or newer, Python 3". abaqus §1 covers Python 2 releases. Nothing says what to do for pre-2024.\n- tosca: "Convert the manual to text once and search it". It does not say where the manual is or what tool converts it.\n- "approved formulation" and "accepted decision". abaqus §2 and §4, tosca Return, and abaqus_engineer.md all lean on these. No skill says where the formulation or decision record lives. topology-optimization §1 has the same gap ("decision with its owner").\n- Flags the viz skill does not document.\n - visualize-topology-optimization §2 and §3 use odb_to_glb.py --iso ISO_VALUE and render_view.py --frame --threshold DENSITY:ISO:1.\n - abaqus-visualization documents neither.\n - I did not open the scripts, so I cannot say whether the flags exist.\n- Script paths. visualize-topology-optimization §2 calls odb_to_glb.py with no path, "next to the ODBs", but fea_glb.py via SKILL_ROOT. The first form needs the reader to infer the copy step from the other skill.\n- Placeholders. LAST_CYCLE.odb, SAVE.inp/<last>/…_optimized.odb and ISO_SMOOTHING.stl are not defined as inputs.\n\n### Verified clean\n- Events abaqus.topology.reviewed (catalog.clio.json line 37) and abaqus.topology.figure-requested (line 60) exist.\n- Surfaces topology-compare and topology-history appear in instructions.md.\n- clio.mesh-viewport.v1 is the catalog kernel (catalog.clio.json line 9). ParameterSlider aliases clio.slider.v1 (instructions.md line 5).\n- The three scripts named in abaqus-visualization exist.\n- abaqus_engineer.py points at prompt/subagents/abaqus_engineer.md, which exists.\n\n## fea-methods\n\n### Dangling references\n- topology-optimization/SKILL.md §4 references manufacturability. It exists in manufacturing-processes/skills/, but fea-methods has no requires.\n- Its "a Tosca or a Morphorm skill" resolves to abaqus/skills/tosca and morphorm/skills/morphorm. These are program plugins, so the reference is acceptable.\n\n### Unclear instructions\n- structural-analysis refers to "finite-element-analysis's nonlinear treatment (large deflection, contact, plasticity, buckling…)". finite-element-analysis/SKILL.md has no nonlinear-treatment section, only a list of idealizations. The reference does not lead anywhere.\n- meshing: "refine until the reported quantity changes by less than a stated tolerance". It gives no default or guidance for the tolerance, so a choice is left unspecified.\n- finite-element-analysis mentions "dynamic/fatigue-cycle treatment" with no pointer to the fatigue plugin.\n\n### Contradictions\nNone found. The GENERATED_NOT_EXECUTED wording matches abaqus and topology-optimization. The stress-at-density-penalized-model caveat in topology-optimization §4 matches tosca and visualize-topology-optimization.\n\n## mechanical-testing\n\n### Dangling references\n- mechanical-testing/SKILL.md ("Fit them with a method that handles censoring (statistics)") and mechanical_testing_expert.md reference statistics. It exists at scientific-method/skills/statistics, but the plugin has no requires.\n- mechanical_testing_expert.py declares plugins=[\"workspace\",\"shell\",\"manufacturing\",\"scientific-method\"], so the subagent path is covered. A direct skill load is not.\n- The sibling skills tensile-testing, load-frame-capability and experimental-data-acquisition exist.\n\n### Unclear instructions\n- experimental-data-acquisition: "a stated multiple of the highest frequency of interest". The skill gives no number or default.\n- mechanical-testing: "Report them, or a specimen effect will be mistaken for a material effect". It does not say in what form, or against which standard's fields.\n\n### Contradictions\nNone found.\n\n## characterization\n\n### Dangling references\nAll of these exist elsewhere, but the plugin has no requires.\n\n| Reference | Location of target | Cited in |\n|---|---|---|\n| microstructure | materials/skills/microstructure | defect-characterization, xct, characterization_expert.md |\n| additive-manufacturing | manufacturing-processes/skills/ | defect-characterization |\n| am-process-parameters | manufacturing-processes/skills/ | defect-characterization, xct |\n| post-processing | manufacturing-processes/skills/ | surface-roughness |\n| build-orientation | manufacturing-processes/skills/ | surface-roughness |\n| defect-driven-fatigue | fatigue/skills/ | defect-characterization, xct |\n\n- Subagent coverage. The subagent declares plugins=[\"workspace\",\"shell\",\"manufacturing\",\"scientific-method\"]. The manufacturing pack's members are materials, manufacturing-processes, characterization, mechanical-testing, fatigue and fea-methods, so the subagent path is covered.\n- Description gap. The plugin description (plugin.json) never mentions microstructure, yet characterization_expert.md routes phase and grain questions to it. It is not shipped here.\n- The same-plugin references (xct, fractography, optical-profilometry, surface-roughness, defect-characterization) all exist.\n\n### Unclear instructions\n- defect-characterization says "Use this skill once individual characterization results (xct, fractography, microstructure) are available". It does not say what to do if one technique is missing.\n- xct: "report … how the statistics change under plausible threshold changes". It gives no range or procedure for "plausible".\n\n### Contradictions\nNone found. The stylus-versus-optical caveats in surface-roughness and optical-profilometry are complementary.\n\n## Not checked\n- Cross-plugin contradictions. I did not read the skills of materials, manufacturing-processes, fatigue, scientific-method, slurm or morphorm. I used only directory listings, plugin.json and name searches. A proper cross-plugin contradiction pass is still open.\n- Files and tools not opened:\n - script sources, so the flags above remain unconfirmed;\n - catalog.clio.json, catalog.json and instructions.md beyond targeted searches;\n - the test files;\n - .lint-l3 and lint-denylist.txt;\n - the shell plugin, so I do not know which plugin supplies prepare_execution_runtime (listed in the tools of all three subagents);\n - ask_user and view_image, which I did not trace to a provider.\n- clio.slider.v1 outside the abaqus catalog. A search of plugins/workspace found nothing, but I could not search the "clio-workspace" catalog skill itself.\n- Truncated searches. Several repo-wide text searches timed out. I relied on directory listings for the skill-existence checks above, and those were conclusive.\n- Read-only session. I could not run shell commands, so I used filesystem tools only.", "error_info": null, "expert_handoffs": [], "response_parts": [{"agent_id": "review", "id": "part_6594957135a4", "metadata": {"signature_field_name": "next_thought"}, "text": "I'll start by listing the files each plugin ships.", "type": "text"}, {"agent_id": "review", "id": "part_91155d01f626", "metadata": {"signature_field_name": "next_thought"}, "text": "Shell is blocked (read-only session), so I'll use the filesystem tools instead.", "type": "text"}, {"agent_id": "review", "id": "part_1001255911fd", "metadata": {"signature_field_name": "next_thought"}, "text": "Next I'll list the subdirectories and read each plugin.json.", "type": "text"}, {"agent_id": "review", "id": "part_f7c41fee979a", "metadata": {"signature_field_name": "next_thought"}, "text": "Next I'll list the skill directories and the ai.iowarp.clio subdirectories.", "type": "text"}, {"agent_id": "review", "id":

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  {"answer": "I'm submitting an interim report: the read-through of the three plugins is complete, but a few cross-checks are not.\n\n# Review of fatigue, materials and manufacturing-processes\n\nVerdict: holds with caveats. I found no contradictions and no wholly missing references. There is one structural gap (undeclared requires) and a few smaller issues.\n\nAll paths below are under /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/.\n\n## Files shipped (from directory listings)\n\n- fatigue/:\n - .lint-l3, lint-denylist.txt, plugin.json\n - ai.iowarp.clio/subagents/fatigue_failure_expert.py\n - ai.iowarp.clio/prompt/subagents/fatigue_failure_expert.md\n - skills/*/SKILL.md for crack-initiation, defect-driven-fatigue, fatemi-socie, fatigue-life-prediction, fatigue-mechanics, fracture-mechanics, high-cycle-fatigue and multiaxial-fatigue\n- materials/: the same layout, with materials_scientist.py and .md. Its six skills are heat-treatment, material-properties, materials-science, metallic-materials, microstructure and nickel-superalloys.\n- manufacturing-processes/: the same layout, with manufacturing_expert.py and .md. Its five skills are additive-manufacturing, am-process-parameters, build-orientation, manufacturability and post-processing.\n\n## Plugin by plugin\n\n### Common to all three\n\n- plugin.json has no extensions block at all, so extensions.ai.iowarp.clio.requires does not exist (fatigue/plugin.json, materials/plugin.json, manufacturing-processes/plugin.json).\n- Each plugin is listed as a member of the manufacturing pack (manufacturing/plugin.json, kind: pack, members list).\n- Because there is no requires, every cross-plugin skill reference below is undeclared.\n- I did not verify whether the pack makes these references legitimate.\n\n### fatigue\n\n1. Undeclared dependencies (item 3). The skills point to skills in other plugins:\n - stress-strain-analysis: defect-driven-fatigue, fatigue-life-prediction and multiaxial-fatigue. It exists as a directory at fea-methods/skills/stress-strain-analysis.\n - xct: defect-driven-fatigue and fatigue-life-prediction. It exists at characterization/skills/xct.\n - fractography: crack-initiation. It exists at characterization/skills/fractography.\n - mechanical-testing: fatigue-life-prediction. It exists at mechanical-testing/skills/mechanical-testing; I saw its name: line in a search.\n - post-processing and am-process-parameters: crack-initiation. These are in manufacturing-processes, so the dependency is cross-plugin but undeclared.\n - So the targets exist, but fatigue does not declare them.\n2. ask_user not in the tool list (item 3).\n - fatigue_failure_expert.md says "Use ask_user only when…".\n - The tool list in fatigue_failure_expert.py has no ask_user.\n - Whether the platform adds it automatically is unverified.\n3. fatigue_failure_expert.py lists prepare_execution_runtime as a tool. It is not shipped on disk, so it is presumably a platform tool. I did not verify that.\n4. Unclear instructions and contradictions: none found. The one soft spot is that fatigue-mechanics gives the high-cycle boundary as "~10^4-10^5" cycles, which it also calls material- and loading-dependent. That is hedged, not contradictory.\n\n### materials\n\n1. Undeclared dependency. microstructure refers to xct (characterization, exists on disk).\n2. ask_user again. materials_scientist.md mentions it; the .py tool list is fs_read_file, fs_list_directory, fs_search_text, view_image.\n3. Unclear: scripting without tools.\n - microstructure/SKILL.md says "When image analysis is scripted, keep the script and its parameters with the results".\n - The subagent has no write or shell tools, so it cannot follow that instruction.\n4. Cross-skill references inside materials resolve: metallic-materials, nickel-superalloys and heat-treatment.\n5. nickel-superalloys points to build-orientation, which is in manufacturing-processes and undeclared.\n6. Contradictions: none found. Delta phase (nickel-superalloys) and Laves phase are consistently distinguished.\n\n### manufacturing-processes\n\n1. Undeclared dependencies.\n - am-process-parameters refers to xct and fractography (characterization).\n - post-processing and manufacturing_expert.md refer to heat-treatment, which is in materials.\n2. ask_user again. manufacturing_expert.md mentions it; its .py has no such tool.\n3. Frontmatter inconsistencies (minor).\n - post-processing/SKILL.md has keywords: manufacturing. The other skills in the plugin use manufacturing-processes or additive-manufacturing.\n - am-process-parameters has no manufacturing-processes keyword.\n4. Contradictions: none found.\n - Orientation and anisotropy statements agree across build-orientation, am-process-parameters and nickel-superalloys.\n - HIP and surface-roughness claims agree with crack-initiation in fatigue.\n\n## Not checked\n\n- The SKILL.md files for stress-strain-analysis, xct, fractography and mechanical-testing. I confirmed only that their directories exist or that their name: lines appeared in a search.\n- The lint-denylist.txt and .lint-l3 files for materials and manufacturing-processes. I read only fatigue's. Its denylist is exp10, IN718 and Inconel 718, and none appear in the fatigue skills I read.\n- Whether the pack mechanism or the plugins=[…, \"manufacturing\", …] entries in the subagents satisfy the dependency question.\n- My shell was blocked (read-only session), and the name: search hit a time limit with truncated output. It still returned nothing for the stress-strain-analysis, xct and fractography queries, so I relied on directory listings instead.", "error_info": null, "expert_handoffs": [], "response_parts": [{"agent_id": "review", "id": "part_2b4fdfb03890", "metadata": {"signature_field_name": "next_thought"}, "text": "Shell is blocked (read-only session), so I'll use the filesystem tools instead.", "type": "text"}, {"agent_id": "review", "id": "part_d1e7fefaa744", "metadata": {"signature_field_name": "next_thought"}, "text": "\n```\n\nI'll continue listing the subdirectories.", "type": "text"}, {"agent_id": "review", "id": "part_6f731dfbeaed", "metadata": {"signature_field_name": "next_thought"}, "text": "The plugin.json files contain no extensions block, so I'll check the ai.iowarp.clio directories and the skill folders next.", "type": "text"}, {"agent_id": "review", "id": "part_7eb74a65fa4e", "metadata": {"signature_field_name": "next_thought"}, "text": "Next I'll list the skill directories and the nested prompt directories.", "type": "text"}, {"agent_id": "review", "id": "part_40f40a380214", "metadata": {"signature_field_name": "next_thought"}, "text": "Next I'll read every SKILL.md plus the subagent files and the lint files.", "type": "text"}, {"agent_id": "review", "id": "part_cfec1af7095a", "metadata": {"signature_field_name": "next_thought"}, "text": "Fatigue is read. Next: the materials and manufacturing-processes files, the lint files, and a search for the skills fatigue references.", "type": "text"}, {"agent_id": "review", "id": "part_1fba694db740", "metadata": {"signature_field_name": "next_thought"}, "text": "Next I'll check where the referenced skills (stress-strain-analysis, xct, fractography) are actually defined, and what the manufacturing plugin ships.", "type": "text"}, {"agent_id": "review", "id": "part_17073993e6a1", "metadata": {"signature_field_name": "answer"}, "text": "I'm submitting an interim report: the read-through of the three plugins is complete, but a few cross-checks are not.\n\n# Review of fatigue, materials and manufacturing-processes\n\nVerdict: holds with caveats. I found no contradictions and no wholly missing references. There is one structural gap (undeclared requires) and a few smaller issues.\n\nAll paths below are under /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/.\n\n## Files shipped (from directory listings)\n\n- fatigue/:\n - .lint-l3, lint-denylist.txt, plugin.json\n - ai.iowarp.clio/subagents/fatigue_failure_expert.py\n - ai.iowarp.clio/prompt/subagents/fatigue_failure_expert.md\n - skills/*/SKILL.md for crack-initiation, defect-driven-fatigue, fatemi-socie, fatigue-life-prediction, fatigue-mechanics, fracture-mechanics, high-cycle-fatigue and multiaxial-fatigue\n- materials/: the same layout, with materials_scientist.py and .md. Its six skills are heat-treatment, material-properties, materials-science, metallic-materials, microstructure and nickel-superalloys.\n- manufacturing-processes/: the same layout, with manufacturing_expert.py and .md. Its five skills are additive-manufacturing, am-process-parameters, build-orientation, manufacturability and post-processing.\n\n## Plugin by plugin\n\n### Common to all three\n\n- plugin.json has no extensions block at all, so extensions.ai.iowarp.clio.requires does not exist (fatigue/plugin.json, materials/plugin.json, manufacturing-processes/plugin.json).\n- Each plugin is listed as a member of the manufacturing pack (manufacturing/plugin.json, kind: pack, members list).\n- Because there is no requires, every cross-plugin skill reference below is undeclared.\n- I did not verify whether the pack makes these references legitimate.\n\n### fatigue\n\n1. Undeclared dependencies (item 3). The skills point to skills in other plugins:\n - stress-strain-analysis: defect-driven-fatigue, fatigue-life-prediction and multiaxial-fatigue. It exists as a directory at fea-methods/skills/stress-strain-analysis.\n - xct: defect-driven-fatigue and fatigue-life-prediction. It exists at characterization/skills/xct.\n - fractography: crack-initiation. It exists at characterization/skills/fractography.\n - mechanical-testing: fatigue-life-prediction. It exists at mechanical-testing/skills/mechanical-testing; I saw its name: line in a search.\n - post-processing and am-process-parameters: crack-initiation. These are in manufacturing-processes, so the dependency is cross-plugin but undeclared.\n - So the targets exist, but fatigue does not declare them.\n2. ask_user not in the tool list (item 3).\n - fatigue_failure_expert.md says "Use ask_user only when…".\n - The tool list in fatigue_failure_expert.py has no ask_user.\n - Whether the platform adds it automatically is unverified.\n3. fatigue_failure_expert.py lists prepare_execution_runtime as a tool. It is not shipped on disk, so it is presumably a platform tool. I did not verify that.\n4. Unclear instructions and contradictions: none found. The one soft spot is that fatigue-mechanics gives the high-cycle boundary as "~10^4-10^5" cycles, which it also calls material- and loading-dependent. That is hedged, not contradictory.\n\n### materials\n\n1. Undeclared dependency. microstructure refers to xct (characterization, exists on disk).\n2. ask_user again. materials_scientist.md mentions it; the .py tool list is fs_read_file, fs_list_directory, fs_search_text, view_image.\n3. Unclear: scripting without tools.\n - microstructure/SKILL.md says "When image analysis is scripted, keep the script and its parameters with the results".\n - The subagent has no write or shell tools, so it cannot follow that instruction.\n4. Cross-skill references inside materials resolve: metallic-materials, nickel-superalloys and heat-treatment.\n5. nickel-superalloys points to build-orientation, which is in manufacturing-processes and undeclared.\n6. Contradictions: none found. Delta phase (nickel-superalloys) and Laves phase are consistently distinguished.\n\n### manufa

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  {"answer": "Verdict: holds with caveats. Findings (paths under plugins/): (1) clio-data/assess-data-quality references present-interactive-analysis, shipped only by visuals, not in clio-data requires. (2) appl-core/ai.iowarp.clio/prompt/views.md references present-interactive-analysis and geometry-to-glb (visuals only), not in appl-core requires; also create_a2ui_surface/clio-workspace catalog unverified. Search output was truncated by a time limit. (3) phenotyping/size-and-growth-traits says 'tag (stated/checked/inferred)', contradicting data-onboarding/evidence-and-claims (no bracketed status labels) and appl-core/evals/README ('without claim tags'). (4) phenotyping/treatment-response conditions on 'the card', which phenotyping does not ship and data-onboarding calls optional. (5) phenotyping-report relies on create_artifact and chart presets without requiring visuals; create_artifact provider unverified. (6) hdf5 SKILL.md lacks keywords/level frontmatter, and hdf5 plugin lacks lint files its siblings have. Clean: data-onboarding, adios, parquet; hdf5 beyond (6). Not checked: clio-kit MCP server tool names, scripts, tests, behavioral-cases.json, lint files, other plugins' contradictions, runtime tools. Shell was read-only-blocked; filesystem tools used.", "error_info": null, "expert_handoffs": [], "response_parts": [{"agent_id": "review", "id": "part_4c6b69116db6", "metadata": {"signature_field_name": "next_thought"}, "text": "Shell is blocked in this read-only session, so I'll use the filesystem tools instead.", "type": "text"}, {"agent_id": "review", "id": "part_c234df3670c0", "metadata": {"signature_field_name": "next_thought"}, "text": "Next: read all seven plugin.json files plus list the skills, tests, ai.iowarp.clio and evals directories.", "type": "text"}, {"agent_id": "review", "id": "part_c95e2cde561f", "metadata": {"signature_field_name": "next_thought"}, "text": "Now list each skill directory, the tests, evals and ai.iowarp.clio directories, and the mcp.json files.", "type": "text"}, {"agent_id": "review", "id": "part_34ac5b51363f", "metadata": {"signature_field_name": "next_thought"}, "text": "Now the subdirectories (scripts, prompt, references, schemas, evals/scripts) and the data-onboarding and clio-data SKILL.md files.", "type": "text"}, {"agent_id": "review", "id": "part_319a7a8a8a50", "metadata": {"signature_field_name": "next_thought"}, "text": "Verdict: holds with caveats. I found six verified issues. The two missing-requires findings and the status-label contradiction are the ones worth fixing first.\n\nAll paths are under /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/. The shell was blocked as read-only, so I used the filesystem tools. I read every plugin.json, mcp.json and SKILL.md in scope, plus the appl-core prompt files and evals/README.md, and listed all shipped files.\n\n## Shipped files\n\n- data-onboarding:\n - Skills audit-dataset, evidence-and-claims, onboard-dataset.\n - Scripts _tables.py, audit_columns.py, card.py, flag_check.py, inventory.py, join_keys.py.\n - tests/, lint-denylist.txt, .lint-l3.\n- clio-data:\n - Skills assess-data-quality, convert-scientific-data.\n - Script convert_to_parquet.py, prompt mission.md, tests/.\n - No mcp.json.\n- adios: skill adios2, mcp.json (clio-kit mcp-server adios), tests/.\n- hdf5:\n - Skill hdf5 with 22 reference guides, mcp.json, tests/.\n - No .lint-l3 or lint-denylist.txt (the other six plugins have both).\n- parquet: skill parquet, mcp.json, tests/.\n- appl-core:\n - Skill appl-core-exports.\n - Prompts mission.md, outputs.md, views.md.\n - evals/ with README.md, behavioral-cases.json and scripts evaluate_appl_core.py and make_variants.py.\n - tests/.\n- phenotyping:\n - Five skills.\n - phenotyping-onboarding-checks ships scripts/validate_views.py and five schemas.\n - tests/.\n\n## Requires declared\n\n| Plugin | requires |\n|---|---|\n| data-onboarding, adios, hdf5, parquet | none |\n| clio-data | data-onboarding, hdf5, adios, parquet |\n| appl-core | data-onboarding, phenotyping, parquet |\n| phenotyping | data-onboarding |\n\n## Findings\n\n1. Missing requires on clio-data (type 3).\n- clio-data/skills/assess-data-quality/SKILL.md, "Visual checks": "Load present-interactive-analysis for an interactive view".\n- That skill ships only in visuals/skills/present-interactive-analysis/SKILL.md (search hit, line 2). visuals is not in clio-data's requires.\n\n2. Missing requires on appl-core (type 3).\n- appl-core/ai.iowarp.clio/prompt/views.md tells the agent to load present-interactive-analysis and geometry-to-glb.\n- Both ship only in visuals (visuals/skills/geometry-to-glb/SKILL.md, line 2). visuals is not in requires.\n- The prompt also depends on the create_a2ui_surface tool and a "clio-workspace catalog", which I did not trace to any plugin.\n- The requires omission is verified for both findings. The search output was marked truncated by a time limit, so I cannot rule out a second provider of either skill.\n\n3. Contradiction on claim tagging, phenotyping vs data-onboarding (type 2).\n- phenotyping/skills/size-and-growth-traits/SKILL.md, "Report": "State units and their tag (stated/checked/inferred)".\n- data-onboarding/skills/evidence-and-claims/SKILL.md: "do not prefix every claim with bracketed status labels".\n- evals/README.md also says "Natural prose is accepted without claim tags".\n- The phenotyping wording is a leftover tag scheme the other skills dropped.\n\n4. Stale card assumption in treatment-response (type 1).\n- phenotyping/skills/treatment-response/SKILL.md: "If the card lists the treatment's meaning as an open question…".\n- phenotyping does not ship card.py; it comes from data-onboarding via requires.\n- data-onboarding says the card is optional. Here the instruction is conditional on a card that may not exist, and the fallback is unclear.\n- physiology-signals and phenotyping-report do hedge ("a card is optional").\n\n5. Unlisted tool dependency in phenotyping-report (type 3).\n- phenotyping/skills/phenotyping-report/SKILL.md requires create_artifact and "generic chart presets", which are visuals territory.\n- phenotyping does not require visuals.\n- create_artifact is a runtime tool I could not locate in any plugin, so treat that part as an unverified assumption.\n\n6. Frontmatter inconsistency in hdf5/skills/hdf5/SKILL.md (type 1).\n- The file has no keywords or level: entries; every other skill reviewed has them (L0, L1 or L2).\n- The hdf5 plugin also lacks the lint files that its siblings ship.\n\n## Clean plugins\n\n- data-onboarding: none found. Referenced scripts inventory.py, audit_columns.py, join_keys.py, flag_check.py and card.py all exist.\n- adios: none found. adios2 is consistent with the mcp.json server and with clio-data.\n- parquet: none found. Its tool-limits text is consistent with convert-scientific-data (uint64 handling, "does not read partitioned directories").\n- hdf5: nothing beyond finding 6. All 22 referenced guides exist.\n\n## Not checked\n\n- I did not read the clio-kit MCP servers, so I could not confirm that tool names such as list_available_hdf5_files, read_slice_tool and inspect_variables_at_step exist.\n- I did not read the scripts, tests, behavioral-cases.json, .lint-l3 or lint-denylist.txt.\n- I did not confirm whether the lint rules explain the hdf5 frontmatter difference.\n- I did not check the other ~40 plugins for contradictions beyond the targeted searches.\n- I did not confirm that the runtime's shared tools (shell_bash, create_artifact, load_skill) exist.", "type": "text"}, {"agent_id": "review", "id": "part_74540f0d3bbd", "metadata": {"signature_field_name": "answer"}, "text": "Verdict: holds with caveats. Findings (paths under plugins/): (1) clio-data/assess-data-quality references present-interactive-analysis, shipped only by visuals, not in clio-data requires. (2) appl-core/ai.iowarp.clio/prompt/views.md references present-interactive-analysis and geometry-to-glb (visuals only), not in appl-core requires; also create_a2ui_surface/clio-workspace catalog unverified. Search output was truncated by a time limit. (3) phenotyping/size-and-growth-traits says 'tag (stated/checked/inferred)', contradicting data-onboarding/evidence-and-claims (no bracketed status labels) and appl-core/evals/README ('without claim tags'). (4) phenotyping/treatment-response conditions on 'the card', which phenotyping does not ship and data-onboarding calls optional. (5) phenotyping-report relies on create_artifact and chart presets without requiring visuals; create_artifact provider unverified. (6) hdf5 SKILL.md lacks keywords/level frontmatter, and hdf5 plugin lacks lint files its siblings have. Clean: data-onboarding, adios, parquet; hdf5 beyond (6). Not checked: clio-kit MCP server tool names, scripts, tests, behavioral-cases.json, lint files, other plugins' contradictions, runtime tools. Shell was read-only-blocked; filesystem tools used.", "type": "text"}], "route_reason": "Session runs agent 'clio/standard#review'.", "route_source": "flow:react", "selected_expert": "review", "tools_called": [{"args": {"_clio_task_description": "List plugin files", "command": "cd /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins && ls && for p in data-onboarding clio-data adios hdf5 parquet appl-core phenotyping; do echo "=== $p"; find $p -type f | sort; done"}, "cached": false, "call_id": "call_5d12f2751628", "duration_ms": 22.095441818237305, "error": "This session is read-only (a side conversation or a read-only role): it may only use tools that declare no side effects. This tool (shell_bash) does not declare itself read-only, so it is blocked. Answer from what you have read and from read-only tools.", "name": "shell_bash", "ok": false, "telemetry_source": "live_observer"}, {"args": {"_clio_task_description": "List plugins", "path": "/home/user/clio-agent/.cloud-run/f18/ws-f18/plugins"}, "cached": false, "call_id": "call_346966b85819", "duration_ms": 165.8790111541748, "name": "fs_list_directory", "ok": true, "result": "{"path": "/home/user/clio-agent/.cloud-run/f18/ws-f18/plugins", "entries": [{"name": "abaqus", "path": "/home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/abaqus", "type": "directory"}, {"name": "adios", "path": "/home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/adios", "type": "directory"}, {"name": "appl-core", "path": "/home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/appl-core", "type": "directory"}, {"name": "characterization", "path": "/home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/characterization", "type": "directory"}, {"name": "clio-data", "path": "/home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/clio-data", "type": "directory"}, {"name": "clio-search", "path": "/home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/clio-search", "type": "directory"}, {"name": "connected-data", "path": "/home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/connected-data", "type": "directory"}, {"name": "data-onboarding", "path": "/home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/data-onboarding", "type": "directory"}, {"name": "deep-research", "path": "/home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/deep-research", "type": "directory"}, {"name": "delegation", "path": "/home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/delegation", "type": "directory"}, {"name": "document-production", "path": "/home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/document-production", "type": "directory"}, {"name": "document-runtime", "path": "/home/user/clio-agent/.cloud-run/f18

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  {"answer": "# Review of connected-data, earthscope, geodesy, spotter, slurm and science-log\n\nVerdict: holds with caveats. I found one confirmed missing dependency, several undeclared dependencies, and some unclear or conflicting instructions. Several claims could not be verified (see "Could not verify"). Nothing was modified.\n\nMy shell call was refused because this session is read-only. I used only directory listings, file reads and text searches. Several recursive fs_search_text runs over plugins/ stopped on a time limit, so their empty results prove nothing. I did not use them as evidence.\n\nRoot: /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/\n\n## connected-data\nShips:\n- plugin.json\n- skills/connect-data/SKILL.md\n- skills/work-with-ndp/SKILL.md\n- skills/work-with-ndp/examples/{hosted-resources.json,replay-segment.sse}\n- skills/work-with-ndp/references/{catalog-authoring,discovery-and-analysis,scientific-stream-analysis,services-and-streams,worked-examples}.md\n- skills/work-with-ndp/scripts/{inspect_capture,prepare_dataset}.py\n- ai.iowarp.clio/tools/builtin.py\n- tests/test_ndp_skill_helpers.py\n\nplugin.json has no extensions block and therefore no requires.\n\nVerified references:\n- Every connected_data_* tool the skills name is declared in ai.iowarp.clio/tools/builtin.py lines 5–16. That covers status, connect, open, download, search_ndp, ndp_organizations, ndp_endpoint_connect, ndp_endpoint_operations, ndp_endpoint_request and ndp_upload_artifact.\n- All five references/ files and both scripts named in work-with-ndp/SKILL.md exist.\n\nIssues:\n- (1) Unclear, connect-data/SKILL.md: two paragraphs both begin "Use this … workflow" and cover overlapping ground. Both mention GitHub and "connected-source" setup, so it is unclear when each applies. The ordering is also hard to follow: "ask where it is before requesting setup" comes before any tool is chosen.\n- (1) Unclear, work-with-ndp/SKILL.md: it says NDP discovery and operation tools "activate on the next turn" only after a dataset or Endpoint is connected. builtin.py declares them all unconditionally. I could not tell whether gating happens elsewhere.\n- (2) Contradiction with the earthscope plugin: work-with-ndp directs NDP work to connected_data_search_ndp and connected_data_download. It says not to bypass them with raw HTTP. earthscope/skills/acquire-earthscope-gnss/SKILL.md instead uses the separate ndp_search_datasets, ndp_get_dataset_details and ndp_stage_resource tools, with a 50 MiB default cap. work-with-ndp gives 8 GiB for downloads. Two NDP tool families with different limits and different instructions exist, and neither skill says which wins.\n- (3) Not shipped, not provable here: create_artifact, load_skill, workspace_resource_read and workspace_resource_inspect are core tools, not shipped by this plugin.\n\n## earthscope\nShips:\n- plugin.json (requires ndp, geo, geodesy; all three directories exist)\n- README.md\n- .lint-l3\n- lint-denylist.txt\n- skills/acquire-earthscope-gnss/SKILL.md\n- ai.iowarp.clio/prompt/{mission,views}.md\n- ai.iowarp.clio/a2ui/earthscope-stations/{catalog.clio.json,catalog.json,instructions.md}\n- tests/test_a2ui_catalog.py\n- tests/test_earthscope_plugin.py\n\nI did not read README.md.\n\nIssues:\n- (1) Garbled sentence, SKILL.md "Choose stations" step 2: "Pause with ask_user(...) when you continue in this turn once the user picks, or end the turn…". It is not clear when to pause and when to end the turn. instructions.md ("After creating the surface") states the rule more clearly.\n- (1) Status mismatch: plugin.json (acquisition readiness.ready_status: \"staged\") uses the statuses staged/metadata_only/blocked/missing. SKILL.md "Hand over" mentions only analysis_ready and metadata_only, never staged.\n- (3) Undeclared dependencies:\n - ai.iowarp.clio/prompt/mission.md tells the agent to "run scripts with shell_bash". requires has no shell plugin, whereas slurm does require it.\n - SKILL.md and views.md cite present-interactive-analysis. No plugin under plugins/ ships it, and it is not in requires.\n - SKILL.md cites the skill a2ui-catalog-earthscope-stations. The catalog directory ai.iowarp.clio/a2ui/earthscope-stations/ exists, but I could not confirm that it is exposed under that skill id.\n - ask_user and create_a2ui_surface are core tools.\n- Circular requirement: compare-station-coverage (geodesy) depends on a "source skill's discovery procedure". The only such skill is in earthscope, which itself requires geodesy.\n\n## geodesy\nShips:\n- plugin.json (requires geo; the directory exists)\n- .lint-l3\n- lint-denylist.txt\n- Five skills:\n - compare-station-coverage/SKILL.md\n - count-stations-in-region/SKILL.md\n - gnss-time-series/SKILL.md and scripts/fit_trajectory.py\n - resolve-region/SKILL.md\n - station-catalogs/SKILL.md and scripts/station_catalog.py\n- tests/test_geodesy_levels.py\n- tests/test_geodesy_scripts.py\n\nIssues:\n- (1) Unclear, compare-station-coverage/SKILL.md step 1: "the source skill's discovery procedure" is not defined within this plugin (see the circular requirement above).\n- (3) Undeclared dependencies:\n - compare-station-coverage step 4 fans out to child agents with count-stations-in-region. That skill declares effect: spawn_subagent_with_skill.\n - The only provider I found is delegation/ai.iowarp.clio/tools/builtin.py, which has spawn_skill_task, with a comment naming that effect. geodesy does not list delegation in requires.\n - gnss-time-series and station-catalogs run uv run --no-project …, which needs a shell. requires has no shell.\n - present-interactive-analysis is cited by three skills and is not shipped anywhere.\n - Hector is mentioned only as an example.\n- (2) Contradictions within the plugin: none found.\n\n## spotter\nShips:\n- plugin.json (no requires)\n- mcp.json (stdio server spotter, uv run --project ${PLUGIN_ROOT}/impl spotter-mcp --clio-config ${CLIO_PROVENANCE_CONFIG})\n- .lint-l3\n- lint-denylist.txt\n- ai.iowarp.clio/prompt/mission.md\n- Three skills: contain-anomaly, inspect-attention, investigate-provenance\n- impl/ (.gitignore, .python-version, README.md, pyproject.toml)\n- impl/src/spotter_ai/{__init__,attention,attention_file,config,errors,server,service}.py and providers/\n- Seven test files under impl/tests/\n\nIssues:\n- (3) Tool names unconfirmed: the skills name about 16 spotter_* tools. I searched server.py for spotter_ and found only import lines. The tool names may be registered another way, such as bare names under an MCP prefix, but I did not confirm this. raise_alert_card is not defined in this plugin and I found no definition elsewhere (my search was truncated).\n- (3) Environment variable: mcp.json needs ${CLIO_PROVENANCE_CONFIG}. Neither the plugin nor its skills explain where it is set.\n- (1) / (2): none found beyond the above. mission.md, contain-anomaly and inspect-attention are consistent on "attention alone is not evidence".\n\n## slurm\nShips:\n- plugin.json (requires shell; the directory exists)\n- .lint-l3\n- lint-denylist.txt\n- ai.iowarp.clio/prompt/capabilities.md\n- skills/hpc-batch-jobs/SKILL.md\n- skills/hpc-batch-jobs/scripts/wait_job.sh\n- tests/test_wait_job.py\n\nIssues:\n- (1) Unclear, SKILL.md:\n - The usage line wait_job.sh JOBID 540 PATH/TO/progress_file does not say what the second argument means. It is implied to be a seconds limit.\n - It does not say what the third argument is for.\n - It does not say what the helper does if the progress file is missing.\n - "Verify with the bundled checks of the program's skill" does not identify which skill.\n - Exit codes 0, 2 and 3 are listed with no entry for other failures, such as sacct being unavailable.\n- (3): I read the script's name but not its contents, so I did not verify the exit codes or the arguments.\n- No contradictions found with other plugins.\n\n## science-log\nShips:\n- plugin.json (requires delegation and orchestration)\n- skills/run-a-study/SKILL.md\n- ai.iowarp.clio/prompt/method.md\n- ai.iowarp.clio/tools/builtin.py\n\nVerified references: builtin.py declares log_entry, link, set_status, query_log and export_measurements. These cover everything the skill uses from the log.\n\nIssues:\n- (3) Missing plugin: requires names orchestration, but plugins/orchestration does not exist. The directory listing returned "File does not exist". delegation does exist.\n- (3) Orchestration capabilities not located: run-a-study depends on run_workflow (with isolate: true and a review editor), fork, and the notion of a "merge step". I confirmed spawn_agent_task, spawn_agents_parallel and spawn_skill_task in delegation. I did not find run_workflow or fork in anything I read. They may be core tools, or may come from the missing orchestration plugin.\n- (1) Unclear, SKILL.md:\n - Fields such as from_calls, source: {call, field}, analysis_call, budget and cost have no schema in the skill.\n - "designate it as an artifact" does not name the tool.\n - Step 11 asks for a chart but names no charting skill.\n - Step 3 (a workflow with one step per hypothesis) and step 4 ("Spread the work across children") overlap without saying how they differ.\n- (2): none found.\n\n## Could not verify\n- The ndp_* and geo_* tool names and arguments (ndp_stage_resource, geo_geocode, geo_filter_points_by_radius, and so on). They come from external clio-kit MCP servers (ndp/mcp.json, geo/mcp.json). The server source is not on the filesystem I inspected, and my searches were truncated.\n- Whether the fit_trajectory.py, station_catalog.py and wait_job.sh flags match what the skills document. I listed these scripts but did not read them.\n- The contents of the five references/*.md files in work-with-ndp. I confirmed only that they exist and that catalog-authoring.md line 5 cites worked-examples.md.\n- README.md, the A2UI catalog JSON files, the test files, and .lint-l3 / lint-denylist.txt in each plugin.\n- Where present-interactive-analysis, run_workflow and fork are provided. They may be host or core capabilities.", "error_info": null, "expert_handoffs": [], "response_parts": [{"agent_id": "review", "id": "part_45a4dd8b89fd", "metadata": {"signature_field_name": "next_thought"}, "text": "Shell is blocked (read-only session), so I'll use the filesystem tools instead.", "type": "text"}, {"agent_id": "review", "id": "part_a8e9e1165404", "metadata": {"signature_field_name": "next_thought"}, "text": "<invoke>", "type": "text"}, {"agent_id": "review", "id": "part_c42d7c83b458", "metadata": {"signature_field_name": "next_thought"}, "text": "\n<invoke>", "type": "text"}, {"agent_id": "review", "id": "part_a81459f8fd3a", "metadata": {"signature_field_name": "next_thought"}, "text": "I'll list the remaining subdirectories and read the manifests.", "type": "text"}, {"agent_id": "review", "id": "part_21db0e7e6231", "metadata": {"signature_field_name": "next_thought"}, "text": "Next I'll read the skill files and prompts and list the remaining subdirectories.", "type": "text"}, {"agent_id": "review", "id": "part_651454601846", "metadata": {"signature_field_name": "next_thought"}, "text": "Next I'll verify the cited tools, skills and scripts against the filesystem.", "type": "text"}, {"agent_id": "review", "id": "part_9796a03250ad", "metadata": {"signature_field_name": "next_thought"}, "text": "Earlier searches hit the time limit, so their empty results prove nothing. 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  {"answer": "# Review of the nine document and visual plugins\n\nVerdict: holds with caveats. The plugins' own files check out against the filesystem. The cross-plugin gaps and contradictions below are verified, but my coverage was incomplete (see "Not checked").\n\n## Method and limits\n- shell_bash was refused (read-only session), so I used fs_list_directory, fs_read_file and fs_search_text. I could not run find or wc, and I did not run any script or test.\n- Most fs_search_text runs hit stop_reason: time_limit and returned truncated: true. A "no match" from them is not proof of absence. The one complete search was for a2ui-catalog across plugins/*.json: 80 files, not truncated, 0 matches.\n- The tool says line numbers are available, but the file contents I read had none. I cite quoted text and file paths, plus line numbers only where the search tool gave them.\n\n## Files shipped (all paths under …/ws-f18/plugins/)\n- document-production: plugin.json, .lint-l3, lint-denylist.txt, ai.iowarp.clio/prompt/{mission,native-formats,shell-conversions}.md, skills/review-document-artifact/{SKILL.md,references/anchor-semantics.md}.\n- document-runtime: plugin.json, ai.iowarp.clio/prompt/runtime.md, ai.iowarp.clio/tools/builtin.py, tests/test_package_guard.py, and two skills:\n - skills/edit-markdown-html/{SKILL.md,references/document-quality.md}\n - skills/inspect-office-package/{SKILL.md,references/part-ownership.md,scripts/package_guard.py}\n- docx: plugin.json, and two skills:\n - skills/edit-ooxml-word/{SKILL.md,references/word-ooxml.md}\n - skills/work-with-word/{SKILL.md,references/{docx-js,python-docx-editing,report-design}.md,examples/{README.md,create-reference-report.mjs}}\n- pdf: plugin.json, ai.iowarp.clio/prompt/usage.md, ai.iowarp.clio/tools/builtin.py (defines view_pdf), tests/test_prepare_pdf_helper.py, skills/create-pdf-report/SKILL.md, skills/work-with-pdfs/{SKILL.md,scripts/prepare_pdf.py}.\n- pptx: plugin.json, and two skills:\n - skills/edit-ooxml-presentation/{SKILL.md,references/presentation-ooxml.md}\n - skills/work-with-presentations/{SKILL.md,references/{pptxgenjs,python-pptx-editing,slide-design}.md,examples/{README.md,create-reference-deck.mjs}}\n- xlsx: plugin.json, skills/edit-ooxml-spreadsheet/{SKILL.md,references/spreadsheet-ooxml.md}, skills/work-with-spreadsheets/SKILL.md.\n- latex: plugin.json, skills/author-latex-pdf/{SKILL.md,references/latex-review.md,scripts/render_latex.py}.\n- opendocument: plugin.json, skills/edit-opendocument/{SKILL.md,references/opendocument-package.md}.\n- visuals: plugin.json, tests/{test_geometry_to_glb,test_vega_spec}.py, ai.iowarp.clio/prompt/{diagrams,evidence,figures}.md, ai.iowarp.clio/tools/builtin.py, and five skills:\n - create-dashboard/{SKILL.md,references/{bike-station-report.json,bike-stations.csv,report-design.md}}\n - create-diagram/SKILL.md\n - geometry-to-glb/{SKILL.md,scripts/to_glb.py}\n - present-interactive-analysis/{SKILL.md,scripts/vega_spec.py}\n - review-visual-presentation/{SKILL.md,references/investigation-patterns.md,examples/annotated-scatter.json}\n\n## requires (from each plugin.json)\n| Plugin | extensions.ai.iowarp.clio.requires |\n|---|---|\n| document-production | documents, document-runtime |\n| document-runtime | shell |\n| docx, pdf, pptx, xlsx, latex, opendocument | document-runtime |\n| visuals | no extensions block at all |\n\n- documents is a pack (kind: pack, members pdf, docx, xlsx, pptx, latex, opendocument) with no skills of its own.\n- Tools verified in providers:\n - prepare_document_runtime and prepare_document are in document-runtime/ai.iowarp.clio/tools/builtin.py.\n - shell_bash and prepare_execution_runtime are in shell/…/builtin.py.\n - view_pdf is in pdf/…/builtin.py.\n - The six A2UI tools and publish_dashboard_report are in visuals/…/builtin.py.\n\n## document-production\nreview-document-artifact (skills/review-document-artifact/SKILL.md)\n- (1) Unclear:\n - Step 7 says "CLIO's artifact change feed mints the new immutable revision". It names no tool or event, so the agent cannot confirm the revision exists.\n - Step 2 says "follow recorded source lineage" without saying where that lineage is recorded or read. references/anchor-semantics.md says "follow source mapping or lineage" and does not say where either lives.\n- (2) Contradictions: none found.\n- (3) Missing references: none found for skills. Every skill it names (edit-markdown-html, author-latex-pdf, edit-ooxml-*, edit-opendocument) resolves through document-runtime or the documents pack.\n- prompt/mission.md tells the agent to "Create new documents with create_artifact". I found no create_artifact provider anywhere in the plugins I searched (the searches were truncated). See "Cross-cutting".\n- prompt/shell-conversions.md uses shell_bash, observe_tasks, wait_tasks and cancel_tasks. These are host tools. shell_bash is reachable through document-runtime's requires: shell, and the prompt is gated on the tool being present.\n\n## document-runtime\ninspect-office-package (skills/inspect-office-package/SKILL.md)\n- (1) Unclear:\n - Steps 1 and 4 say "Run scripts/package_guard.py inventory INPUT …" with a relative path and no interpreter. Compare work-with-pdfs and geometry-to-glb, which tell the agent to resolve SKILL_ROOT and run via uv. This skill gives no such instruction.\n - Step 6 says "Open/recalculate/render with LibreOffice when available" and names no tool. The other skills use prepare_document(action=\"render\"|\"recalculate\").\n- (3) package_guard.py and part-ownership.md exist. Nothing missing.\n\nedit-markdown-html (skills/edit-markdown-html/SKILL.md)\n- (1) Step 3 says "transition the artifact to Live Web and obtain its normal consent". The description also says "transition executable HTML to Live Web". No Live Web tool or skill is named. I did not search for one, so this is unverified rather than confirmed missing.\n- references/document-quality.md exists.\n\n## docx\nedit-ooxml-word (skills/edit-ooxml-word/SKILL.md)\n- (1) Unclear:\n - It writes $inspect-office-package as a skill reference. review-document-artifact says to use load_skill with plain names, and nothing explains the $ form.\n - "open/render through LibreOffice when available" names no tool.\n- (2) Overlap with work-with-word (same plugin), neither cross-references the other:\n - edit-ooxml-word mandates the package guard before and after editing. work-with-word never mentions it, and even tells the agent to do tracked-change and comment work with lxml ("Keep a copy of the original and reopen the edited package").\n - edit-ooxml-word step 1 says "New documents may use python-docx". work-with-word requires prepare_document_runtime first and prepared python_argv. The first skill never says to do that.\n - edit-ooxml-word step 7 says "Save a real .docx… A PDF is an optional derived rendition". work-with-word requires create_artifact(..., pdf_preview=true) and says to keep review PDFs unregistered. The two are compatible but a reader of only one skill would miss the other's rule.\n- (3) references/word-ooxml.md exists. Nothing else missing.\n\nwork-with-word (skills/work-with-word/SKILL.md)\n- (1) Unclear: "Load these files with this skill's returned ID and file argument". This describes load_skill indirectly and never names it.\n- (3) references/{docx-js,python-docx-editing,report-design}.md and examples/create-reference-report.mjs all exist. It uses view_image, create_artifact and view_pdf ("when exposed"). view_pdf is provided by pdf, which is not in docx's requires (acceptable since it is conditional). view_image and create_artifact have no provider that I found.\n\n## pdf\ncreate-pdf-report (skills/create-pdf-report/SKILL.md)\n- (1) Unclear: "Render every page to PNG with Poppler" and "Use uv". Neither the Poppler binaries nor the uv command are tied to the prepared runtime (prepare_document_runtime), which this skill never mentions.\n- (2) Contradictions with work-with-pdfs (same plugin):\n - Scratch location: "keep intermediate renders under tmp/pdfs/" and "final deliverables under output/pdf/", versus work-with-pdfs using "its returned .tmp/ scratch directory".\n - Inspection tool: it requires view_image on every page, while work-with-pdfs says "Prefer view_pdf over the conversion-and-render workflow".\n - Publishing: it ends at "Deliver the final PDF", while work-with-pdfs says to designate the final file with create_artifact.\n - Environment: it says to use uv directly, while work-with-pdfs says to use the prepared runtime's python_argv.\n- (2) Cross-plugin gap: with author-latex-pdf (latex), neither skill says when to choose LaTeX versus ReportLab for a PDF.\n- (3) view_image is not provided by pdf. I found no provider.\n\nwork-with-pdfs (skills/work-with-pdfs/SKILL.md)\n- (1) Unclear: the command template uses unexplained placeholders \"UV\", \"PYTHON\" and SKILL_ROOT. It also says "Docling… is not advertised by the prepared stack unless installed there", so the agent cannot tell in advance whether the helper will work.\n- (3) scripts/prepare_pdf.py exists. It uses the workspace_resource_* tools (host, not shipped), view_image (no provider found), and create_artifact.\n\n## pptx\nedit-ooxml-presentation (skills/edit-ooxml-presentation/SKILL.md)\n- (1) Same $inspect-office-package and unnamed "Render through LibreOffice when available" as in the Word skill.\n- (2) Overlap with work-with-presentations:\n - It says "For an existing sophisticated deck, prefer targeted slide XML edits". work-with-presentations says "For a small edit, change the relevant text runs with python-pptx". Neither states a decision rule between them.\n - Again no mutual reference, and the package-guard step is absent from work-with-presentations.\n- references/presentation-ooxml.md exists.\n\nwork-with-presentations (skills/work-with-presentations/SKILL.md)\n- (1) The shell-command-length guidance is written for Windows ("about 1-2 KB per call on Windows", "A single large here-string piped to Set-Content"). The host here is Linux, so the guidance may not apply. The "Do not embed a whole deck builder in one command" rule is stated twice.\n- (3) All referenced files exist: the three references, examples/create-reference-deck.mjs, and README.md. view_image and view_pdf are conditional; create_artifact is not found.\n\n## xlsx\nedit-ooxml-spreadsheet (skills/edit-ooxml-spreadsheet/SKILL.md)\n- (1) Unclear: step 5 says to recalculate with "headless LibreOffice when available" without naming prepare_document(action=\"recalculate\").\n- (2) Contradictions:\n - With work-with-spreadsheets: step 3 says "keep_vba=True for macro-enabled input" and step 5 says to recalculate. work-with-spreadsheets says "Macro-enabled files are also refused by this helper" and "External-linked files are refused by automatic recalculation". An agent following edit-ooxml-spreadsheet on an .xlsm has no workable recalculation path.\n - Within the skill (inferred, not tested): step 5 recalculates through LibreOffice, and work-with-spreadsheets says the helper "creates a new XLSX copy". A LibreOffice round-trip rewrites package parts, so step 6's "compare the package with a narrow allowlist" would likely flag drift on that copy. The skill does not say which file gets compared.\n- references/spreadsheet-ooxml.md exists.\n\nwork-with-spreadsheets (`

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  {"answer": "# Review of the factorio, scientific-method and morphorm plugins: holds with caveats\n\nThe three plugins are mostly clean. I found no hard contradictions and no skill, script or subagent reference that points at nothing. The real issues are three undeclared cross-plugin dependencies, two naming mismatches and several unclear instructions. Several checks stayed incomplete (listed at the end).\n\nPaths below are relative to /home/user/clio-agent/.cloud-run/f18/ws-f18/plugins/. The shell was blocked as read-only, so I used the filesystem tools only.\n\n## factorio\n\nShips:\n- plugin.json (v0.7.0), README.md, lint-denylist.txt and .lint-l3.\n- Five skills: audit-scientific-package, coordinate-scientific-work (with references/decision-criteria.md), evidence-fanout (with references/fanout-lifecycle.md and source-integrity.md), frame-research-problem and maintain-scientific-dossier.\n- Prompts mission.md, practice.md, specialists.md and prompt/subagents/*.md (7 files).\n- Seven subagents in ai.iowarp.clio/subagents/*.py: evidence_critic, evidence_leaf, evidence_researcher, independent_reviewer, research_methodologist, simulation_methodologist and virtual_lab.\n- Evals: evals/README.md, behavioral-cases.json, scripts/evaluate_factorio.py.\n- Tests: tests/test_black_box_evals.py and tests/fixtures/.\n\n**requires:** [\"delegation\", \"science-log\"] (factorio/plugin.json).\n\n**(3) Undeclared dependencies, all verified on disk:\n- scientific-method skills.\n - frame-research-problem/SKILL.md ends with "Use experimental-design … and research-gap-analysis". Both live only in scientific-method/skills/.\n - evidence_researcher.md also names paper-search and literature-review.\n - scientific-method is not in factorio's requires. The subagent files list it as a plugin for evidence_researcher, research_methodologist and independent_reviewer, but not for the main agent that loads frame-research-problem.\n- Specialists in other plugins. decision-criteria.md routes to abaqus_engineer, mechanical_testing_expert, fatigue_failure_expert and manufacturing_expert. I confirmed these in the abaqus, mechanical-testing, fatigue and manufacturing-processes plugins. None of those plugins is in requires.\n- Other skills and subagents. simulation_methodologist.md and independent_reviewer.md name skills from fea-methods and manufacturing-processes. I confirmed topology-optimization, manufacturability and present-interactive-analysis (in visuals). The subagent .py files do declare these plugins, so this is fine for subagents.\n- run-a-study. maintain-scientific-dossier/SKILL.md loads run-a-study, and it exists in science-log (which is required), so that one is fine.\n\n(2) Contradictions and inconsistencies:\n- Status vocabulary.\n - maintain-scientific-dossier lists artifact statuses "generated, statically reviewed, scientist-approved, solver-executed, validated".\n - morphorm/skills/morphorm/SKILL.md (Return section) mandates the label GENERATED_NOT_EXECUTED.\n - audit-scientific-package uses verdicts REVISION_REQUIRED and READY_FOR_SCIENTIST_REVIEW.\n - These are three different vocabularies with no mapping between them. Morphorm's label is not one of the dossier's statuses.\n- run-non-interactive-task.\n - It says "Consult a specialist only when the packet asks for one" and "Skip planning … bookkeeping".\n - specialists.md and coordinate-scientific-work say to consult specialists proactively, and practice.md says to keep the study log current.\n - The scope differs (non-interactive packets only), so this is a tension rather than a clash. Neither side says which wins when both apply.\n\n(1) Unclear instructions:\n- coordinate-scientific-work/references/decision-criteria.md says "Statistics, uncertainty and figures … A copy of yourself … carries the statistics, uncertainty-quantification and data-visualization skills and the shell". That holds only if the parent agent carries scientific-method and shell, which factorio does not require.\n- evidence-fanout/references/fanout-lifecycle.md tells evidence_researcher to use wait_tasks and observe_tasks. evidence_researcher.py lists only spawn_agent_task and spawn_agents_parallel. Several skills and prompts also say to use ask_user (and maintain-scientific-dossier says to use create_artifact), and none appears in any subagent's tools list. Presumably the runtime supplies these, but I could not confirm it.\n- maintain-scientific-dossier uses log_entry, set_status, link and create_artifact. I confirmed only query_log in science-log/ai.iowarp.clio/tools/builtin.py, line 8.\n\n## scientific-method\n\nShips:\n- plugin.json (v0.7.0), lint-denylist.txt and .lint-l3.\n- 11 skills: citation-management, data-visualization, experimental-design, literature-review, paper-search, research-gap-analysis, run-non-interactive-task, scientific-data-analysis, scientific-writing, statistics and uncertainty-quantification.\n- No references/ files, subagents, prompts or evals.\n\nrequires:** none declared. The extensions block is absent.\n\n**(3) Undeclared dependencies:\n- run-non-interactive-task/SKILL.md assumes a shell (pdftotext -layout, grep -n, sed -i, cat part*.md > file, "Commands go to the shell"). The shell plugin is not required.\n- The same skill also tells the agent to "load the skills for its toolchain (the program's skill, the scheduler's skill)" without naming them. That is generic and acceptable, but it cannot be verified.\n- uncertainty-quantification says "per the specific technique's skill", which points at no named skill.\n- Internal cross-references all resolve: paper-search, literature-review, research-gap-analysis, statistics, uncertainty-quantification and data-visualization are all shipped.\n\n(2) Contradictions:** none found within the plugin. The skills are consistent with each other and with factorio on the points I compared:\n- novelty as an evidence burden;\n- reading a fetched source before citing it;\n- a significance threshold fixed in advance.\n\n**(1) Unclear instructions:\n- paper-search/SKILL.md says "Fetch and read the actual source" but names no fetch or search tool, and no web plugin is required. It is unclear how a standalone agent with this plugin would do the fetching.\n- statistics and data-visualization use "censored" in different places without a shared definition. Minor.\n\n## morphorm\n\nShips:\n- plugin.json (v0.6.0), lint-denylist.txt and .lint-l3.\n- One skill, skills/morphorm/SKILL.md, with scripts/diag_summary.py, exo_summary.py and xml_params.py.\n- ai.iowarp.clio/prompt/capabilities.md and tests/test_morphorm_scripts.py.\n- No subagents or evals.\n\nrequires:** [\"shell\"].\n\n**(3) References:\n- Verified present: the three bundled scripts named in the skill.\n- Undeclared dependencies that exist elsewhere:\n - topology-optimization ("load it alongside this skill") is in fea-methods/skills/topology-optimization/SKILL.md. fea-methods is not required.\n - hpc-batch-jobs ("on Slurm, load hpc-batch-jobs") is in slurm/skills/hpc-batch-jobs/. slurm is not required, though it would be an optional dependency.\n - capabilities.md also tells the agent to load topology-optimization.\n- External software or inputs not shipped, and reasonably expected from the environment: Cubit, XMLGenerator, netCDF4 and numpy, and "the installed or supplied Morphorm manual".\n\n(2) Contradictions:** none found. The GENERATED_NOT_EXECUTED label is consistent with factorio/prompt/mission.md ("hand over a complete package marked not executed"). The vocabulary mismatch is noted under factorio.\n\n**(1) Unclear instructions:**\n- "Convert the manual to text once" names no tool. The only mention of pdftotext is in another plugin's skill (scientific-method/run-non-interactive-task).\n- "If a setting … does not reach the generated XML, re-translate once with the manual's equivalent form" does not say what to do if the second attempt also fails.\n- The skill says SKILL_ROOT is "the skill directory reported by load_skill". I did not check that load_skill reports it.\n\n## Not verified\n- science-log/skills/run-a-study/SKILL.md, fea-methods/skills/topology-optimization/SKILL.md and slurm/skills/hpc-batch-jobs/ exist, but I did not read their contents. I therefore did not check for contradictions with morphorm or factorio on restarts, filters or batch-job handling.\n- The materials_scientist and characterization_expert subagents were never located on disk. Their searches timed out.\n- Several repo-wide text searches were truncated by time limits: abaqus_engineer, mechanical_testing_expert and orchestration across all of plugins/. Absence of matches there proves nothing. The orchestration dependency of science-log is unresolved, because no plugin named orchestration appears in the directory listing.\n- Not read: the bodies of morphorm/skills/morphorm/scripts/*.py (so the CLI flags in the SKILL.md examples are unchecked against them), factorio/evals/*, factorio/README.md, tests/, and the remaining subagent files (evidence_researcher and simulation_methodologist were read; the others only partly).\n- Runtime-provided tools (ask_user, create_artifact, log_entry, wait_tasks) were not checked against any tool registry.", "error_info": null, "expert_handoffs": [], "response_parts": [{"agent_id": "review", "id": "part_0732aa98b535", "metadata": {"signature_field_name": "next_thought"}, "text": "Shell is blocked (read-only), so I'll use the filesystem tools.", "type": "text"}, {"agent_id": "review", "id": "part_c5b54e54f58d", "metadata": {"signature_field_name": "next_thought"}, "text": "Continuing with the filesystem tools, since the shell is blocked.", "type": "text"}, {"agent_id": "review", "id": "part_15be2551e0cd", "metadata": {"signature_field_name": "next_thought"}, "text": "I'll continue by listing the remaining directories and reading the skill files.", "type": "text"}, {"agent_id": "review", "id": "part_b350f45e8031", "metadata": {"signature_field_name": "next_thought"}, "text": "I'll read all the skill files, the prompts, and the subagent listings next.", "type": "text"}, {"agent_id": "review", "id": "part_66369cb62856", "metadata": {"signature_field_name": "next_thought"}, "text": "Next I'm checking the reference files the skills cite, the remaining prompts, and the scientific-method skills.", "type": "text"}, {"agent_id": "review", "id": "part_15d0a5778de6", "metadata": {"signature_field_name": "next_thought"}, "text": "Continuing: reading the cited references, the scientific-method skills, and checking where the referenced skills live.", "type": "text"}, {"agent_id": "review", "id": "part_ac955a399782", "metadata": {"signature_field_name": "next_thought"}, "text": "Continuing: reading the cited references, the remaining scientific-method skills and the required plugins.", "type": "text"}, {"agent_id": "review", "id": "part_f54fc5db957b", "metadata": {"signature_field_name": "next_thought"}, "text": "Next I'm checking the subagent definitions, the tool providers in the required plugins, and the specialists and skills the Factorio and Morphorm skills name.", "type": "text"}, {"agent_id": "review", "id": "part_8cd8510babb6", "metadata": {"signature_field_name": "next_thought"}, "text": "Next I'm checking the remaining cross-references: manufacturability, the specialists, the science-log tools, orchestration, and the subagent .py files.", "type": "text"}, {"agent_id": "review", "id": "part_ce83edd1e234", "metadata": {"signature_field_name": "next_thought"}, "text": "Severa

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skills/work-with-spreadsheets/SKILL.md)\n- **(1)** No unclear instruction that I could verify beyond the above. It is internally consistent.\n- **(3)** It uses view_image/view_pdfandcreate_artifact (no provider found for the latter two).\n\n## latex\n**author-latex-pdf** (skills/author-latex-pdf/SKILL.md)\n- **(1) Unclear:**\n - \"Compile with scripts/render_latex.py SOURCE.tex OUTPUT_DIR\" gives a relative path and no interpreter, and does not mention prepare_document_runtime.\n - \"pinned local Tectonic behavior\" does not say where Tectonic comes from.\n - Step 2 mentions \"recorded source mapping\" with no way to read it.\n - Step 6 says \"Visually inspect\" and names no tool.\n - Step 7 says \"preserving lineage from PDF to exact source revision\" without saying how.\n- **(2)** Nothing contradicts another skill that I could verify. The gap with create-pdf-reportis noted above.\n- **(3)**scripts/render_latex.pyandreferences/latex-review.mdexist. Tectonic and its pinning are not shipped by this plugin or itsrequires; I did not look in document-runtime's runtime inventory, so this is unverified.\n\n## opendocument\n**edit-opendocument** (skills/edit-opendocument/SKILL.md)\n- **(1) Unclear:** step 5 says \"Recalculate ODS and render all formats with headless LibreOffice when available\". prepare_document(action="recalculate")is documented only for XLSX inwork-with-spreadsheets, so it is unclear whether ODS is supported. Step 3 relies on odfpyand does not say whether the prepared runtime provides it.\n- **(2)** Same allowlist-versus-LibreOffice-rewrite tension as xlsx (step 5 vs step 6). Inferred, not tested.\n-references/opendocument-package.md exists.\n\n## visuals\nplugin.jsonhas noextensions.ai.iowarp.clio.requires, yet its skills depend on things it does not ship.\n\n**All five skills**\n- **(3) Missing/unprovided:** load_skill("a2ui-catalog-clio-workspace")and thea2ui-catalog-<slug>pattern. No plugin ships it. The completea2ui-catalogsearch overplugins/.jsonreturned 0 matches. The catalog is presumably host-provided, butrequires does not declare that.\n\n**create-dashboard** (skills/create-dashboard/SKILL.md)\n- **(1)** Contradictory register instructions: \"Register the editable source as an intermediate only if a separate artifact is useful\" next to \"Do not add a second deliverable card for that document\". Not a conflict, but confusing.\n- **(3)** references/{report-design.md,bike-station-report.json,bike-stations.csv}exist.publish_dashboard_report, inspect_a2ui_surfaceandcapture_a2ui_surfaceare provided by visuals.update_a2ui_data_modelis provided.create_artifacthas no provider found.\n- **(2)**create_artifact(..., purpose="verification")here versuscreate_artifact(path=…, kind="report", pdf_preview=true) in the Office skills. The schema is never given, so I cannot tell if both forms are valid.\n\n**create-diagram** (skills/create-diagram/SKILL.md)\n- **(1)** \"Use the catalog skill actually declared for this session; the example names CLIO's workspace catalog.\" This gives no rule for choosing which catalog.\n- **(3)** It depends on the clio.mermaid.v1 catalog entry, which is not in the plugin.\n\n**geometry-to-glb** (skills/geometry-to-glb/SKILL.md)\n- **(1)** \"substitute the SKILL_ROOTpath thatload_skillreported\" anduv run --no-project --with …. It needs network and uv, while the document plugins steer to a prepared runtime.\n- **(3)** scripts/to_glb.pyexists. It depends onclio.mesh-viewport.v1from the catalog (not shipped) and oncreate_artifact (provider not found).\n\n**present-interactive-analysis** (skills/present-interactive-analysis/SKILL.md; I read only the first 24 k characters and not the tail)\n- **(1)** Line 17 describes create_a2ui_surface(provided). Lines 48–54 give theload_skill("a2ui-catalog-<slug>")pattern with a placeholder and refer the reader to a section, \"Skills available to you\", that is not in this plugin.\n- **(3)** Line 159 usesget_weather_forecast. plugins/weather/ai.iowarp.clio/tools/builtin.pyexists, but I did not read it, so I could not confirm it defines that tool.weatheris not invisuals' (absent) requires. The skill also cites docs/design/a2ui-compat-campaign-2026-09.md, which is a repo doc and not shipped by the plugin. I did not check that it exists. It also depends on an external URL, https://clio.iowarp.ai/media/guides.json.\n- scripts/vega_spec.pyexists, withtests/test_vega_spec.py.\n\n**review-visual-presentation** (skills/review-visual-presentation/SKILL.md)\n- **(3)** references/investigation-patterns.mdandexamples/annotated-scatter.jsonexist. It refers to the dashboard skill'sreferences/report-design.md, which exists.\n- **(1)** I found nothing unclear that I could verify.\n\n## Cross-cutting findings\n1. **create_artifacthas no provider in the plugins I inspected.** It is used bydocument-production/prompt/mission.md, docx/work-with-word, pptx/work-with-presentations, xlsx/work-with-spreadsheets, pdf/work-with-pdfs, pdf/create-pdf-report's sibling, and all visuals skills. My native_tool("create_artifact") search was truncated, so this is an unverified gap, not a confirmed absence.\n2. **view_imagehas no provider I could find.**workspace/plugin.jsondescribes \"view images\" but has norequireslink from the plugins that use it, and I did not readworkspace/…/builtin.py.\n3. **Inconsistent entry-point conventions for helper scripts.** inspect-office-packageandauthor-latex-pdfuse bare relative script paths.work-with-pdfsandgeometry-to-glbuseSKILL_ROOTplusuv.\n4. **Inconsistent LibreOffice guidance.** The edit-ooxml-andedit-opendocumentskills say \"when available\", while thework-with-skills useprepare_document with a bundled or provisioned LibreOffice. The two groups never reference each other.\n5. **visualsis the only plugin of the nine without arequiresblock.** It depends on the catalog skill, oncreate_artifact, and possibly on weather.\n\n## Clean\nNo plugin in the set came out entirely clean. The closest are latexandopendocument, whose problems are only unclear recalculation and render steps.\n\n## Not checked\n- I did not read references/.mdbeyond the three anchor, word-ooxml and latex-review files. That leavesspreadsheet-ooxml.md, presentation-ooxml.md, opendocument-package.md, part-ownership.md, document-quality.md, all work-with-references,report-design.md, investigation-patterns.mdand the examples unread.\n- I did not read any script or test:package_guard.py, prepare_pdf.py, render_latex.py, to_glb.py, vega_spec.pyand the tests.\n- I did not read the tail ofpresent-interactive-analysis/SKILL.md(it spilled), thevisualsprompt files,.lint-l3, lint-denylist.txt, the weatherandworkspace builtin.py, or the shellprompt directory.\n- I did not verify that Tectonic,odfpy, Poppler or LibreOffice are provided by the prepared runtime.", "error_info": null, "expert_handoffs": [], "response_parts": [{"agent_id": "review", "id": "part_492d50e9ed42", "metadata": {"signature_field_name": "next_thought"}, "text": "Shell is blocked in this read-only session, so I'll use the filesystem tools.", "type": "text"}, {"agent_id": "review", "id": "part_abfb1d3435df", "metadata": {"signature_field_name": "next_thought"}, "text": "\n<invoke_placeholder>", "type": "text"}, {"agent_id": "review", "id": "part_a76dfa433b9a", "metadata": {"signature_field_name": "next_thought"}, "text": "Shell is blocked, so I'll continue with the read-only filesystem tools: all nine plugin.json files and each skills directory.", "type": "text"}, {"agent_id": "review", "id": "part_aea59202a40e", "metadata": {"signature_field_name": "next_thought"}, "text": "I have the plugin.json files and skill directory names. Next I'll list the files each skill and plugin ships.", "type": "text"}, {"agent_id": "review", "id": "part_d1f9cea199b2", "metadata": {"signature_field_name": "next_thought"}, "text": "I'll read every SKILL.md and list the remaining subdirectories.", "type": "text"}, {"agent_id": "review", "id": "part_96daccfc4d0d", "metadata": {"signature_field_name": "next_thought"}, "text": "\n<invoke_placeholder>", "type": "text"}, {"agent_id": "review", "id": "part_f88f4e0270fc", "metadata": {"signature_field_name": "next_thought"}, "text": "I'll check which plugin provides each tool the skills name, then the remaining prompt directories.\n\n\n<invoke_placeholder>", "type": "text"}, {"agent_id": "review", "id": "part_fda2cf485ea6", "metadata": {"signature_field_name": "next_thought"}, "text": "I still need to check where the tools and skills these plugins reference come from, so I'm reading the tool providers, the documentsandshellplugins and the rest of the spilled skill text.", "type": "text"}, {"agent_id": "review", "id": "part_1952f88542b4", "metadata": {"signature_field_name": "next_thought"}, "text": "I'll continue by reading the prompt files, the shell plugin and the tail of the long visuals skill, and by checking that the referenced tools and skills exist.", "type": "text"}, {"agent_id": "review", "id": "part_a32af6b2a05e", "metadata": {"signature_field_name": "next_thought"}, "text": "\n<invoke_placeholder>", "type": "text"}, {"agent_id": "review", "id": "part_9eca41116c2c", "metadata": {"signature_field_name": "next_thought"}, "text": "I need to check a few providers before I report: the shell, weather and workspace plugins.", "type": "text"}, {"agent_id": "review", "id": "part_dc227c1ee29b", "metadata": {"signature_field_name": "answer"}, "text": "# Review of the nine document and visual plugins\n\n**Verdict: holds with caveats.** The plugins' own files check out against the filesystem. The cross-plugin gaps and contradictions below are verified, but my coverage was incomplete (see \"Not checked\").\n\n## Method and limits\n-shell_bashwas refused (read-only session), so I usedfs_list_directory, fs_read_fileandfs_search_text. I could not run findorwc, and I did not run any script or test.\n- Most fs_search_textruns hitstop_reason: time_limitand returnedtruncated: true. A \"no match\" from them is not proof of absence. The one complete search was for a2ui-catalogacrossplugins/.json: 80 files, not truncated, 0 matches.\n- The tool says line numbers are available, but the file contents I read had none. I cite quoted text and file paths, plus line numbers only where the search tool gave them.\n\n## Files shipped (all paths under …/ws-f18/plugins/)\n- **document-production**: plugin.json, .lint-l3, lint-denylist.txt, ai.iowarp.clio/prompt/{mission,native-formats,shell-conversions}.md, skills/review-document-artifact/{SKILL.md,references/anchor-semantics.md}.\n- **document-runtime**: plugin.json, ai.iowarp.clio/prompt/runtime.md, ai.iowarp.clio/tools/builtin.py, tests/test_package_guard.py, and two skills:\n - skills/edit-markdown-html/{SKILL.md,references/document-quality.md}\n - skills/inspect-office-package/{SKILL.md,references/part-ownership.md,scripts/package_guard.py}\n- **docx**: plugin.json, and two skills:\n - skills/edit-ooxml-word/{SKILL.md,references/word-ooxml.md}\n - skills/work-with-word/{SKILL.md,references/{docx-js,python-docx-editing,report-design}.md,examples/{README.md,create-reference-report.mjs}}\n- **pdf**: plugin.json, ai.iowarp.clio/prompt/usage.md, ai.iowarp.clio/tools/builtin.py(definesview_pdf), tests/test_prepare_pdf_helper.py, skills/create-pdf-report/SKILL.md, skills/work-with-pdfs/{SKILL.md,scripts/prepare_pdf.py}.\n- **pptx**: plugin.json, and two skills:\n - skills/edit-ooxml-presentation/{SKILL.md,references/presentation-ooxml.md}\n - skills/work-with-presentations/{SKILL.md,references/{ppt

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name: audit-scientific-package title: Audit a Scientific Simulation Package description: Review a research and simulation package across evidence, physics, traceability, construction and validation by reading the actual files, and return severity-ranked, evidence-linked findings with a readiness verdict that never claims solver verification it does not have. keywords:

• level:L1
• factorio
• review

---

Read the study log (query_log), cited sources, specification and generated files; open them, do not review a summary of them. Where a check can be run cheaply (a script parses, a deck references only files that exist, the solver's status file says the run completed), run it. Trace the question through evidence, decisions, formulation, implementation, expected outputs, validation and the claim the scientist intends to make.

Audit five linked surfaces:

1. Evidence: citations were read and support bounded claims; parameter values have a source; contrary evidence and search limits are visible.
2. Physics: units, magnitudes, signs, conservation, constitutive behavior, geometry and load path, supports, contacts, singularities, and limiting behavior are plausible; optimization responses and regions match the formulation.
3. Traceability: major model and code choices map to accepted decisions or explicit proposals.
4. Construction: files are complete for the target interpreter and program release, with no hidden placeholders, undefined references or invented inputs.
5. Validation: convergence, sensitivity, analytical or experimental benchmarks and acceptance criteria can test the intended claim, and the artifact status is truthful.

Report each finding with severity, the evidence (file and location), its impact on the claim, and which specialist or decision owns the fix. An unresolved scientist-owned decision is a finding, not a question you answer.

Verdict: REVISION_REQUIRED for any material defect; READY_FOR_SCIENTIST_REVIEW only when the package is coherent and its remaining limitations are explicit. Readiness never means solver-verified: never upgrade generated files to executed or validated without the run artifacts that show it.

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name: maintain-scientific-dossier title: Maintain the Scientific Dossier description: Keep research identity, evidence, assumptions, decisions and artifact status traceable across the conversation as entries of the study log, never as a separate prose record. keywords:

• level:L1
• factorio
• provenance

---

The dossier is the study log: use this skill whenever the research state materially changes, and keep that state as log entries (log_entry, set_status, link, query_log), not as a file of prose. Load run-a-study for how entries and their links work.

Say in each entry what kind of knowledge it holds: scientist-supplied fact, external evidence, expert inference, proposed default, accepted decision, unresolved question, or unverified artifact claim.

• A consequential decision is a Question (the decision to make, with its units and alternatives) answered by a Conclusion whose claims cite the evidence, with the rationale, owner and the assumptions and artifacts it affects in the claims and caveats. A correction is a new Conclusion; the old one gets set_status superseded with the reason and what must be revisited. History is never overwritten.
• An assumption is a Hypothesis with the prediction that would show it wrong; set_status records when it is supported, refuted or superseded.
• Artifact status (generated, statically reviewed, scientist-approved, solver-executed, validated) is an Observation that cites the call that produced or checked the artifact; each later check is another Observation, and the Evidence interpreting it says which status the artifact has reached.

When a deliverable becomes useful outside chat, call the runtime-provided create_artifact with complete content, an appropriate workspace-relative name, and exact inputs in used. Preserve the returned artifact identity and version; do not claim creation after a rejected call.

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name: evidence-fanout title: Coordinate Scientific Evidence Fan-out description: Decompose one evidence question into independent source lanes, follow consequential leads, obtain independent criticism, and return a complete source audit. Used by evidence_researcher, which starts evidence_leaf and evidence_critic. keywords:

• level:L1
• factorio
• evidence

---

This is evidence_researcher's procedure. It defines a dynamic evidence investigation, not a fixed lane count or generic literature review.

Before creating evidence children, read fanout-lifecycle.md for lane boundaries, parallel spawn/wait behavior, evidence-driven follow-ups, critic iteration, and blocked-task handling.

Before accepting claims or preparing the critic packet, read source-integrity.md for fetched-source rules, claim mapping, citation placement, source disposition, and incomplete-evidence reporting.

The coordinator does not search the web. Assign web discovery and reading to evidence_leaf; assign independent verification to evidence_critic. Use ask_user directly only when the evidence boundary depends on a scientist-owned definition or inclusion choice. Preserve every child task id and synthesize only returned evidence.

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name: coordinate-scientific-work title: Coordinate Scientific Work description: Decide whether to answer, clarify, load a method, run the work yourself or consult Factorio's specialists, pick the right specialist, brief it, and synthesize only settled results. Greetings and ordinary conceptual questions are answered directly and do not need this skill. keywords:

• level:L1
• factorio
• delegation

---

Use this skill when a scientific request may benefit from clarification, a specialist consultation, or independent parallel work. It is not a prelude to greetings or ordinary questions.

Before delegating, read decision-criteria.md: it separates direct answers, ask_user, focused skills, work you run yourself, one consultation and independent fan-out, and says which specialist owns which question.

Starting consultations

• One bounded consultation: spawn_agent_task. Several independent ones: one spawn_agents_parallel call, so the runtime admits or queues them together. A queued task is accepted work, not a failure.
• Record every returned task id with its agent and assignment. The task id is the durable identity of that consultation: keep it through observation, waiting, a child's question, a pause or context compaction, and never start a replacement or duplicate for the same assignment. The task lifecycle itself (waiting, questions, pause, cancel) follows the runtime's task rules.
• Spawn dependent work only after its prerequisites have returned.

Failures

Treat a terminal failure, cancellation or unavailable tool as evidence about what remains unresolved. Do not silently retry with a different specialist or fill the gap from memory. Continue independent work where useful, then report the exact limitation and its impact.

Synthesis

Synthesize only settled results. Reconcile assumptions, units, provenance, disagreements and confidence; say which result changed which decision; keep incomplete or contradictory findings explicit rather than choosing the most confident prose. Report the science first, and mention the coordination only when it explains a blocker, provenance or the next decision. Never say a consultation completed until its returned task state and result say so.

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name: frame-research-problem title: Frame a Research Problem description: Narrow a scientist's idea into answerable questions, hypotheses, scope boundaries and evidence needs without premature commitment, and record the chosen and rejected formulations in the study log. keywords:

• level:L1
• factorio
• framing

---

Begin with the scientist's language and identify the system, phenomenon, conditions, scales, motivation, proposed mechanism, attainable evidence, and minimum useful outcome. When ambiguity remains, offer a small set of genuinely different formulations rather than cosmetic rewrites.

For each candidate, state what result would answer it, what would weaken or falsify it, which methods discriminate among rivals, and what remains outside scope. Preserve the selected formulation and rejected alternatives with reasons in the study log. Ask only high-information questions whose answers change the study. Treat novelty as an evidence question, not an assumption.

Use experimental-design to turn the chosen formulation into a method and a study, and research-gap-analysis before any claim that prior work is absent.

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id: factorio.specialists section: domain when: {"tools": ["spawn_skill_task"]}

Consulting a specialist is an ordinary tool call; the scientist need not ask for it. Consult when a bounded question needs independent judgment or a specialist's own work: framing, evidence, feasibility, formulation, a materials, process, characterization, testing or fatigue question, data analysis, an Abaqus package, or review before you call a package ready. Answer simple questions yourself. For several consultations, load coordinate-scientific-work first, start independent ones together, once each, and keep each task id until its result arrives.

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name: morphorm title: Set Up, Run and Check a Morphorm Topology Optimization description: Run a Morphorm study end to end (Cubit mesh, input deck, XMLGenerator, batch run, delivery), confirm every declared setting reached the generated XML, pick and check the saved state for a restart, and verify each step with the bundled checks instead of new one-off programs. keywords:

• level:L2
• morphorm
• topology-optimization

---

Morphorm is one topology-optimization program a study can use. The method (stating the problem, checking the analysis model, reading the result as a proposal) is in topology-optimization; load it alongside this skill. Morphorm has its own deck, mesh format and keywords: none of them carry over from another optimizer's input, even when the optimization problem is the same.

State which analysis the study drives, its units, and the objective, constraints, design and frozen regions and manufacturing restrictions, all declared in Morphorm's own input. Confirm the analysis model (mesh, materials, loads, supports) is valid on its own before attributing a failure to the optimizer.

Toolchain

Confirm every keyword against the installed or supplied Morphorm manual, never from memory. Convert the manual to text once and search it for the sections you need.

1. Mesh. Write a Cubit journal and export an Exodus mesh. Give every block, node set and side set the exact name the specification uses; an unnamed block exports with an empty name. Check the mesh with exo_summary.py before going further (see "Bundled checks").
2. Deck. Write the Morphorm input deck. Find each keyword by searching the text copy of the manual: block, material, load, boundary condition, criterion, filter, optimizer, output and restart sections. Put comments on their own lines, never after a keyword on the same line.
3. Translate. Run XMLGenerator on the deck in a clean run directory. List the generated settings with xml_params.py and confirm that each declared setting appears with the intended value.
   • A setting that is in the deck but absent from the generated XML is not applied.
   • The manual often offers two equivalent forms: a begin filter … end filter block, or study-level keywords such as filter_type and filter_radius_absolute. If a setting from one form, for example a filter's symmetry-plane side sets, does not reach the generated XML, re-translate once with the manual's equivalent form and compare again before you submit anything.
4. Run. Submit the generated run script as a batch job (on Slurm, load hpc-batch-jobs). Follow the optimizer diagnostics file while it runs.
5. Deliver. Copy the mesh, deck, generated configuration, diagnostics and final iteration output to the required paths, with hashes if the task asks for them.

Restarts and continuations

When a run continues from a saved state of an earlier run:

• Read the manual's restart keywords and the earlier run's output, and decide which saved state is meant. Count the states stored in the restart file and note whether the restart index is 0- or 1-based. A file that stores iterations 0…N holds N+1 states.
• After submitting, compare the first objective of the new run with the earlier run's objective at the intended iteration: diag_summary.py NEW_DIAGNOSTICS --compare-first-to VALUE. A clear mismatch means the wrong state was read. Cancel at once, record why, fix the index and resubmit. Do not wait for the run to finish.

Bundled checks

Use these instead of writing new verification programs. They are generic and print compact JSON or TSV. SKILL_ROOT is the skill directory reported by load_skill. exo_summary.py needs numpy and netCDF4; if import netCDF4 fails, load the site's approved software environment first.

python3 SKILL_ROOT/scripts/exo_summary.py mesh.exo --expect num_elem=N block:NAME:type=HEX8 nodeset:NAME=K sideset:NAME=K bbox_max=X,Y,Z
python3 SKILL_ROOT/scripts/exo_summary.py final_output.exo        # time steps, nodal fields, min/max at last step
python3 SKILL_ROOT/scripts/xml_params.py RUN_DIR "symmetry" "length scale" "iteration"   # generated settings; MISSING -> exit 1
python3 SKILL_ROOT/scripts/diag_summary.py DIAGNOSTICS.txt        # rows, first/last iteration, stop message

When the task asks for verification records, save their output under the work directory (for example ... > work/verify/mesh.json) instead of writing a separate script.

Return

The Morphorm deck and the analysis model it references, the declared regions and restrictions, the generated settings confirmed by xml_params.py, every job id submitted, the optimization's convergence status and stop message, and traceability to the approved formulation. Without executed solver evidence, label the package GENERATED_NOT_EXECUTED.

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id: morphorm.capabilities section: capabilities

Morphorm is one topology-optimization program this agent can work in, when the scientist uses it: a Cubit-built Exodus mesh, a Morphorm input deck translated to XML by XMLGenerator, and a batch run with its own diagnostics and restart states. Load morphorm for the workflow and its bundled checks of the mesh, the generated settings and the optimizer diagnostics, together with topology-optimization for the method.

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Answer at the scientist's level; a greeting or an ordinary conceptual question needs no skill, clarification or specialist. Keep supplied facts, observed evidence, inference, assumptions and decisions apart, with units, conditions and provenance. Never invent a source, parameter, tool result, solver run or validation status. Load the smallest skill that fits a repeatable procedure. Keep the question, evidence, decisions, artifacts and verification state current in the study log (maintain-scientific-dossier).

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id: factorio.mission section: domain when: {"tools": ["spawn_skill_task"]}

Factorio serves scientists who study how a part's design, material and manufacturing route set its performance: framing and evidence, simulation and topology optimization, additive and conventional processes, characterization, testing, fatigue and failure. Its methods hold for any material and process; facts about one alloy, machine or run come from the scientist's data. Work in the simulation program the scientist uses; none is the default. When it is reachable and results are wanted, run meshes, solves and batch jobs yourself; otherwise hand over a complete package marked not executed.

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name: experimental-design title: Choose a Method and Design a Study Around Its Question description: Match a research question to a method that can answer it, state the method as a falsifiable procedure with its assumptions and scope, and design the study (variables, controls, sample size, acceptance criterion, confounds) before data is collected. keywords:

• level:L0
• methodology
• study-design

---

Choose the method

Start from what the question asks (a mechanism, a comparison, a prediction, a characterization) and choose a method that can produce evidence for that claim, not just a familiar one. State it as a falsifiable procedure: which result would support the hypothesis, and which would weaken or contradict it.

Name the method's assumptions and scope: the population, system, regime and conditions it applies to, and what it does not cover. A method borrowed from an adjacent field or a different system needs justification before its validity transfers.

Keep the method separate from the instrument, program or protocol that executes a step of it, so the method survives a tool change.

Design the study

• What it must distinguish. State the hypothesis, the independent variables changed, the dependent variables measured, and every variable held constant or controlled. An uncontrolled variable that correlates with the one of interest invalidates the comparison however the data is analysed afterwards.
• Size. State the number of replicates needed to detect the effect of interest given the expected scatter, not a convenient or traditional number.
• Acceptance criterion, fixed in advance. For a comparison, define what counts as a difference before collecting data; choosing it after seeing the results does not test the hypothesis.
• Confounds. Identify batch, location, operator, instrument and time effects, and design to detect or exclude them: randomization, blocking, replication across batches.

Return

The method with its assumptions, scope and falsification criteria; the study design (hypothesis, variables and controls, sample size and rationale, acceptance criterion, confound controls); and the specialists or skills needed for each step.

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name: run-non-interactive-task title: Run a Self-Contained Task With No One to Ask description: Work through a self-contained task packet (workspace rules, required outputs and paths, no person available during the run) directly and economically - batch independent calls, read manuals once and search them, verify with bundled checks, keep a facts log, write the required reports once, and confirm every required output before stopping. keywords:

• level:L0
• workflow
• batch

---

A task is non-interactive when it arrives as a self-contained packet: a problem statement, workspace rules, a list of required outputs at required paths, and no person available to answer during the run (a trial or pilot prompt, a frozen configuration with a deliverables list, a scheduled job). Interactive work is unchanged by this skill.

Work directly

• Do the work yourself. Consult a specialist only when the packet asks for one.
• Skip planning and presentation bookkeeping the packet does not ask for.
• Keep each step's visible text to one short sentence, and batch independent tool calls into one step.
• In the first step, read the packet's file list and, in the same step, load the skills for its toolchain (the program's skill, the scheduler's skill).

Read manuals once

Convert each PDF manual to text once in the work directory (for example with pdftotext -layout), then search it (grep -n) and print only the sections you need (sed -n). Do not page through the whole text, and confirm every keyword against the manual rather than memory.

Verify with what is bundled

Use the bundled checks of the loaded skills and save their output as the verification record. Write a new verification program only for a check they cannot do.

Keep a facts log, write reports once

• Append one line per event to a short facts log in the work directory (for example work/notes.log): a timestamp, the command, its exit code, a job id or a key value.
• Write each required report (for example a run summary) once, near the end, from that log. Include every item the packet's provenance requirements list. Reference long material (hash manifests, logs, generated files) by path unless the requirements ask for it inline.

Keep tool calls small

• Commands go to the shell as JSON strings: a line break inside a string is \n, a tab \t, a double quote \" and a backslash \\. Never put a raw line break inside a JSON string, including in heredocs.
• The shell tool limits the length of one command; its description states the limit in effect (CLIO's default is 16,000 characters, and sites can change it), and native shells can reject shorter ones. Put programs in script files rather than long inline commands. For a long file, write it in parts (part1.md, part2.md, ...) in one parallel step and join them in the next (cat part*.md > file).
• Never re-send a whole file to change a few lines: patch it (sed -i, a small script) or append (cat >>). Never emit the same file content twice.

Before stopping

Check that every required output exists at its required path, then give the final answer once.

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---

name: research-gap-analysis title: Identify Genuine Gaps in the Existing Literature description: Distinguish a real research gap from an under-searched question, and state precisely what evidence would close it. keywords:

• level:L0
• scientific-method

---

A gap is a claim about the literature, not about memory: it holds only after paper-search has covered the relevant terms, synonyms, and adjacent literatures and still found nothing. State the search that was performed and its scope before asserting an absence.

Separate three different situations that get called "gaps": no prior work exists on the question; prior work exists but does not cover the specific material, condition, or scale in question; and prior work is contradictory or inconclusive. Each implies a different next step (novel contribution, bounded-scope extension, or a study designed to resolve the contradiction).

State what evidence would close the gap and what method could produce it — a gap analysis that ends at "more research is needed" without naming the specific missing measurement or comparison is not actionable.

Return the identified gaps by type, the search evidence behind each, and the specific measurement, method, or comparison that would close each one.

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name: data-visualization title: Choose and Execute a Scientific Figure That Makes the Comparison Visible description: Pick the chart type and encoding from the comparison being made, then execute it with labelled axes and units, visible uncertainty and a self-contained caption, without implying more precision or a stronger effect than the data supports. keywords:

• level:L0
• visualization
• figures

---

Choose from the comparison

Name the comparison before choosing a chart:

• distributions between conditions: box, violin or probability plots;
• a trend against a controlled variable: points with a fit and its band;
• a relationship between two continuous variables: a scatter plot with a fit;
• composition or ranking: ordered bars.

A chart chosen before the comparison is named usually shows the data without making the claim visible.

Match the representation to the data's structure. Censored observations (values known only to exceed or fall below a limit, such as tests stopped before the event) must be marked distinctly, never drawn as ordinary points; data spanning orders of magnitude needs a log axis, stated as such; repeated measurements of one unit should be grouped visibly.

Check the figure's claim against the statistics (statistics): a log or truncated axis, or an omitted point, can make an effect look stronger or weaker than the data supports.

Execute it

• Label every axis with quantity and units, and state the scale (linear, log, semi-log).
• Show uncertainty on the figure itself: error bars or a band, with the caption saying what they represent (standard deviation, standard error, a confidence interval) and the sample size.
• Write a caption that makes the figure self-contained: what was measured, under which conditions, the sample size, and what the reader should conclude.
• Keep fonts, line weights and markers legible at the final printed or displayed size.
• Keep the plotting script and its input files with the figure so it can be regenerated.

Return

The figure with its comparison, chart type and encoding, labelled axes with units, visible uncertainty, a self-contained caption, and the script and inputs that produced it.

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Evidence fan-out lifecycle

Define the evidence question, decision it informs, scope, time horizon, source families, terminology already known, and exclusions. Split it into lanes that can be investigated independently without duplicating the whole question. Useful lanes may cover mechanisms, measurements, material/condition regimes, competing methods, standards, datasets, or counterevidence; choose them from the question, not a fixed template.

Launch independent evidence_leaf assignments together with spawn_agents_parallel. Preserve every returned task handle and collect them with wait_tasks. Use observe_tasks for progress while independent work continues; completion arrives at the next model iteration or wakes you when idle. Read all settled packets before deciding whether the evidence is mature. Follow new terminology, cited primary work, contradictions, missing conditions, or method branches only when they could change the scientific decision. A follow-up may be one leaf or another independent fan-out.

When the claim map and source audit are coherent, spawn one evidence_critic with the entire draft, citations, uncertainties, and audit. The critic must make fresh web checks. If it returns RESEARCH_REQUIRED, investigate each material gap and submit the revised complete packet for another independent review. Do not force extra rounds after PASS, and do not translate an incomplete critic result into approval.

If a child requests human input with ask_user, the runtime resumes that same task after the scientist answers. Keep and re-wait its original task id. If a source lane fails terminally, continue independent lanes where useful and carry the exact evidence gap and impact into the critic packet and final result.

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name: scientific-data-analysis title: Analyze Scientific Data Against Its Actual Question description: Match an analysis approach to the data's actual structure and the question being asked, and state every processing step applied to raw data before reporting a result. keywords:

• level:L0
• scientific-method

---

State the data's structure before choosing an analysis: sample size, whether observations are independent or grouped/repeated (e.g., multiple measurements per specimen or subject), and the presence of censored data (observations stopped before the event of interest) — a method that assumes independence applied to grouped data understates uncertainty.

Record every processing step applied between raw data and reported result: outlier removal (with the criterion used), smoothing or filtering, normalization, and unit conversion. A result should be reproducible from the raw data plus this stated processing chain.

Match the specific statistical method to the question (statistics) and report uncertainty (uncertainty-quantification) as part of the result, not as an afterthought — a data analysis that reports only a point estimate or a best-fit line without its uncertainty is incomplete for a scientific claim.

Return the data structure and processing chain applied, the analysis method and result, and the uncertainty and assumptions behind it.

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Scientific coordination decision criteria

Choose the least coordination that improves the scientific answer.

• Answer directly when the request is a greeting, an ordinary conceptual question, or can be resolved faithfully from the study log.
• Use a skill without delegation when a repeatable method helps but no independent judgment is needed.
• Run it yourself when the work is a self-contained execution you can do with the loaded program skill: a mesh check, a solve, a batch job, a data summary.
• Call ask_user when a scientist-owned ambiguity changes the claim, physics, evidence boundary, feasibility or requested artifact. Ask the smallest high-information question and say why the answer matters. Do not ask for facts already in the study log or for low-risk details that can be labelled as proposed defaults.
• Consult one specialist when one bounded responsibility needs independent judgment or a specialist's own work.
• Consult in parallel only when two or more assignments are independent, neither needs the other's result, their outputs can be reconciled, and the expected information gain justifies the cost.

Who owns which question

Question	Specialist
Is this an answerable question? Hypotheses, rivals, scope, novelty burden	research_methodologist
What does the literature establish, and against what counterevidence?	evidence_researcher (it runs its own evidence_leaf and evidence_critic lanes; do not start those directly)
What can the scientist actually execute: equipment, software, licences, compute, access, schedule?	virtual_lab
Which model can answer the claim: physics, idealization, loads, mesh, validation plan?	simulation_methodologist
Write and run the Abaqus or Tosca package for an approved formulation	abaqus_engineer
Why does this material behave so: processing, microstructure, heat treatment, properties	materials_scientist
How does the design become a part: process, parameters, orientation, post-processing	manufacturing_expert
What is the part actually like: XCT, porosity, roughness, microstructure, fracture surfaces	characterization_expert
What should be tested and how, and what do the test data say	mechanical_testing_expert
How long will it last, and why did it fail	fatigue_failure_expert
Statistics, uncertainty and figures for a result set	A copy of yourself (delegate without naming an agent): it carries the statistics, uncertainty-quantification and data-visualization skills and the shell
Is the package coherent and ready for the scientist? (before any readiness claim)	independent_reviewer

Programs other than Abaqus (for example Morphorm) and batch scheduling are run directly with their skills; no specialist is needed.

Briefing a specialist

Give every consultation a bounded decision, the relevant study-log entries and file paths, trusted inputs, exclusions, and the shape of the answer you need. Do not ask for a generic opinion or send the whole campaign to every specialist. Preserve disagreements for explicit synthesis.

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---

name: citation-management title: Keep Citations Traceable From Claim to Source description: Attach every literature-derived claim to a specific, checkable citation, and keep the citation set consistent across a document's revisions. keywords:

• level:L0
• scientific-method

---

Attach a citation at the point a claim is made, not gathered loosely at the end of a section — a reader must be able to check which specific source supports which specific sentence. A citation to a review paper for a claim the review itself attributes to a primary source should point to the primary source when it was actually read.

Keep the reference list and in-text citations synchronized: a citation added, reworded, or removed during revision must update both the marker and the list entry in the same pass. Use a consistent format (author-date, numbered) matched to the target venue's requirement, not a house default.

Flag a claim that has lost its citation during editing (moved between sections, merged with another claim) rather than letting it stand uncited — an uncited claim in a scientific document reads as the author's own assertion.

Return the citation list with its format, a check that every in-text marker resolves to an entry, and any claim found without a supporting citation.

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name: paper-search title: Search Scientific Literature for Relevant Sources description: Decompose a literature question into search lanes, fetch and read actual sources, and return only what was verified from the fetched text. keywords:

• level:L0
• scientific-method

---

Define the question, the decision it informs, and the terms and synonyms a relevant paper might use — a single search term misses adjacent literatures that use different vocabulary for the same concept. Split a broad question into independent lanes (mechanism, measurement method, competing approach, material system) that can be searched without duplicating each other.

Fetch and read the actual source before citing it; a search-result snippet or title is not evidence of what a paper found. Record, per source: what was read (full text vs. abstract only), publication venue and date, and the specific claim it supports or contradicts.

Follow consequential references forward and backward — a cited method or a paper that cites the one just found often matters more than the next search result. Stop when additional searches stop changing the claim map, not on a fixed count.

Return the fetched sources with what was actually read from each, the claims each supports, and hand the set to literature-review for synthesis.

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name: uncertainty-quantification title: Quantify and Propagate Uncertainty Through a Result Chain description: Track measurement, model, and sampling uncertainty separately and propagate them explicitly through a chain of calculations rather than reporting a single deterministic answer. keywords:

• level:L0
• scientific-method

---

Classify each source of uncertainty in the chain: measurement uncertainty (instrument resolution/calibration, per the specific technique's skill), sampling uncertainty (from finite sample size — how many samples, fields, or scans), and model uncertainty (from an assumed physical, predictive or statistical model, or a simplification). Report which sources were actually quantified and which were not.

Propagate uncertainty through a multi-step calculation explicitly — a prediction chaining a simulated quantity, a measured input, and a fitted model should carry each input's uncertainty through to the final result (via a stated method: analytical propagation, Monte Carlo sampling), not report the final number as if it were exact.

State which input dominates the total uncertainty — this tells the scientist where additional measurement or refinement would actually reduce uncertainty in the final result, versus where further effort would not help.

Return the uncertainty sources identified, the propagation method used, the resulting uncertainty on the final result, and the dominant contributing source.

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name: statistics title: Choose and Report a Statistical Test or Fit Correctly description: Match a statistical test or distribution fit to the data's actual properties, and report its assumptions and limitations alongside the result. keywords:

• level:L0
• scientific-method

---

Check the assumptions a method requires before applying it: normality (or the specific distribution assumed: lifetimes, sizes and other positive, skewed quantities are often better described by a lognormal or Weibull distribution than a normal one), independence of observations, and equal variance across groups being compared. A t-test or linear regression applied without checking these can produce a misleading p-value or confidence interval.

State the specific test or fit and its parameters explicitly: for a comparison, the test used and its p-value with the significance threshold stated in advance (not chosen after seeing the result); for a curve or distribution fit, the fitting method (least squares, maximum likelihood) and the goodness-of-fit measure. Censored observations (an event not yet seen when observation stopped) need a method that uses them as censored, such as maximum likelihood with censoring; dropping them, or treating them as events, biases the fit.

Distinguish statistical significance from practical significance — a statistically significant difference with a small effect size may not matter for the decision at hand, and this should be stated explicitly rather than left to the reader to infer from a p-value alone.

Return the test/fit used, its checked assumptions, the result with its confidence interval or goodness-of-fit, and whether the result is practically significant for the decision at hand.

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name: scientific-writing title: Turn an Investigation Into a Written Scientific Deliverable description: Structure a thesis section, report, or manuscript so every claim traces to its evidence and method, matched to the venue's expected form. keywords:

• level:L0
• scientific-method

---

Match the structure to the deliverable: a thesis section, a journal manuscript, and an internal report carry different expected sections and levels of methodological detail, but all share the same requirement — every claim in the text traces to a method and a piece of evidence presented earlier in the same document.

Write results and discussion as distinct sections: results state what was observed/measured without interpretation, discussion states what it means and its limits. Do not let a result section assert a mechanism, or a discussion section introduce a number that was never reported as a result.

State limitations and scope explicitly rather than only in a closing paragraph — a reader deciding whether the work applies to their case needs the boundary conditions where the relevant claim is made, not buried at the end.

Return the drafted section or document with its structure matched to the venue, every claim traceable to evidence presented in it, and the exact figures, tables, or citations it depends on named.

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Evidence and citation integrity

Maintain a claim-to-source map. A search result is discovery metadata, never evidence. A material sourced claim must be supported by successfully fetched content, cited beside the claim, and bounded to the source's population, conditions, material state, definitions, and uncertainty.

Prefer primary research, standards, official documentation, datasets, and authoritative technical reports. Reviews can identify terminology and primary sources but do not automatically replace them. Preserve paper title, authors, venue, date/year, DOI or stable identifier, authoritative landing page or readable document URL, and whether the evidence was full text or abstract only.

Give every attempted source exactly one disposition:

• USED_AND_CITED: fetched content supports or changes the synthesis;
• READ_NOT_USED: fetched and understood but immaterial to the result;
• REJECTED: fetched and excluded, with reason;
• FETCH_FAILED: not read, with requested/final URL and exact failure.

Seek counterevidence and record the searched source families. Do not infer novelty, consensus, or absence from silence. If important content is unavailable, state what could not be established and how that limits the decision. Cite only sources actually read and used.

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name: literature-review title: Synthesize a Scientific Literature Review description: Turn a set of gathered sources into a defensible state-of-knowledge synthesis with a claim map, contradictions, gaps, and an explicit novelty burden. keywords:

• level:L0
• scientific-method

---

Use this skill once relevant sources have been gathered and the question is whether the collected literature actually settles a claim. It synthesizes what is known; it does not perform new discovery. Route missing sources back to paper-search.

Organize the sources around the decision, not around authors. For each consequential claim, record which fetched sources support it, under what material, condition, and population bounds, and where sources disagree. Distinguish primary measurement from review restatement, and full-text evidence from abstract-only evidence.

State what the literature establishes, what remains contested, and what is simply absent. Treat novelty as an evidence question: a claim is novel only when a bounded search failed to find prior work, never because none was recalled. Preserve every contradiction and open question explicitly rather than resolving it by picking the most confident source.

Return the synthesis, the claim-to-source map, unresolved disagreements, evidence gaps that block the decision, and the exact next questions for paper-search or research-gap-analysis.

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