Add multi-harness plugin manifests

.agents/plugins/marketplace.json

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+{
+  "name": "nf-core-agents",
+  "interface": {
+    "displayName": "nf-core Skills"
+  },
+  "plugins": [
+    {
+      "name": "nf-core-tools",
+      "source": {
+        "source": "local",
+        "path": "./plugins/nf-core-tools"
+      },
+      "policy": {
+        "installation": "AVAILABLE",
+        "authentication": "ON_INSTALL"
+      },
+      "category": "Developer Tools"
+    }
+  ]
+}

.claude-plugin/marketplace.json

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+{
+  "$schema": "https://json.schemastore.org/claude-code-marketplace.json",
+  "name": "nf-core-agents",
+  "owner": {
+    "name": "nf-core",
+    "url": "https://nf-co.re"
+  },
+  "plugins": [
+    {
+      "name": "nf-core-tools",
+      "source": "./plugins/nf-core-tools",
+      "description": "Cross-agent nf-core checks and workflow guardrails for nf-core projects",
+      "version": "0.1.0"
+    }
+  ]
+}

.claude/settings.json

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+{
+  "hooks": {
+    "PreToolUse": [
+      {
+        "matcher": "Edit|Write",
+        "hooks": [
+          {
+            "type": "command",
+            "command": "scripts/prek-hooks/claude/guard-nfcore-modules.sh"
+          }
+        ]
+      }
+    ],
+    "PostToolUse": [
+      {
+        "matcher": "Edit|Write",
+        "hooks": [
+          {
+            "type": "command",
+            "command": "scripts/prek-hooks/claude/lint-schema.sh"
+          }
+        ]
+      },
+      {
+        "matcher": "Edit|Write",
+        "hooks": [
+          {
+            "type": "command",
+            "command": "scripts/prek-hooks/claude/check-param-drift.sh"
+          }
+        ]
+      },
+      {
+        "matcher": "Edit|Write",
+        "hooks": [
+          {
+            "type": "command",
+            "command": "scripts/prek-hooks/claude/lint-local-module.sh"
+          }
+        ]
+      },
+      {
+        "matcher": "Edit|Write",
+        "hooks": [
+          {
+            "type": "command",
+            "command": "scripts/prek-hooks/claude/check-nftest-exists.sh"
+          }
+        ]
+      }
+    ],
+    "Stop": [
+      {
+        "hooks": [
+          {
+            "type": "command",
+            "command": "scripts/prek-hooks/check-changelog.sh"
+          }
+        ]
+      }
+    ]
+  }
+}

.cursor-plugin/marketplace.json

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+{
+  "name": "nf-core-agents",
+  "owner": {
+    "name": "nf-core",
+    "email": "infrastructure@nf-co.re"
+  },
+  "metadata": {
+    "description": "Agent skills and workflow guardrails for nf-core projects.",
+    "version": "0.1.0"
+  },
+  "plugins": [
+    {
+      "name": "nf-core-tools",
+      "source": "./plugins/nf-core-tools",
+      "description": "Cross-agent nf-core checks and workflow guardrails powered by shared prek hooks."
+    }
+  ]
+}

plugins/nf-core-tools/.app.json

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+{
+  "apps": []
+}

plugins/nf-core-tools/.claude-plugin/plugin.json

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+{
+  "$schema": "https://json.schemastore.org/claude-code-plugin-manifest.json",
+  "name": "nf-core-tools",
+  "version": "0.1.0",
+  "description": "Cross-agent nf-core checks and workflow guardrails for Nextflow pipelines, modules, subworkflows, and nf-core tools.",
+  "author": {
+    "name": "nf-core",
+    "url": "https://nf-co.re"
+  },
+  "repository": "https://github.com/nf-core/agents/tree/main/plugins/nf-core-tools",
+  "license": "MIT",
+  "keywords": [
+    "nf-core",
+    "nextflow",
+    "bioinformatics",
+    "pipelines",
+    "workflows",
+    "nf-test"
+  ]
+}

plugins/nf-core-tools/.codex-plugin/plugin.json

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+{
+  "name": "nf-core-tools",
+  "version": "0.1.0",
+  "description": "Cross-agent nf-core checks and workflow guardrails powered by shared prek hooks.",
+  "author": {
+    "name": "nf-core",
+    "email": "infrastructure@nf-co.re",
+    "url": "https://nf-co.re"
+  },
+  "homepage": "https://github.com/nf-core/agents/tree/main/plugins/nf-core-tools",
+  "repository": "https://github.com/nf-core/agents",
+  "license": "MIT",
+  "keywords": [
+    "nf-core",
+    "nextflow",
+    "lint",
+    "bioinformatics",
+    "workflows"
+  ],
+  "skills": "./skills/",
+  "hooks": "./hooks/codex.json",
+  "mcpServers": "./.mcp.json",
+  "apps": "./.app.json",
+  "interface": {
+    "displayName": "nf-core Tools",
+    "shortDescription": "Shared nf-core checks for Codex, Claude, Cursor.",
+    "longDescription": "Runs deterministic nf-core checks via shared prek hook IDs (schema lint, param drift, nf-test, changelog, and module guardrails).",
+    "developerName": "nf-core",
+    "category": "Developer Tools",
+    "capabilities": [
+      "Read",
+      "Write",
+      "Execute"
+    ],
+    "websiteURL": "https://github.com/nf-core/agents",
+    "privacyPolicyURL": "https://github.com/site/privacy",
+    "termsOfServiceURL": "https://docs.github.com/en/site-policy/github-terms/github-terms-of-service",
+    "defaultPrompt": [
+      "Run prek run --all-files and summarize failing nf-core hooks.",
+      "Run one failing hook by id and propose the smallest fix.",
+      "Check nextflow.config vs nextflow_schema.json drift and patch."
+    ],
+    "brandColor": "#0EA5A4",
+    "screenshots": []
+  }
+}

plugins/nf-core-tools/.cursor-plugin/plugin.json

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+{
+  "name": "nf-core-tools",
+  "displayName": "nf-core Tools",
+  "version": "0.1.0",
+  "description": "Cross-agent nf-core checks and workflow guardrails powered by shared prek hooks.",
+  "author": {
+    "name": "nf-core",
+    "email": "infrastructure@nf-co.re"
+  },
+  "publisher": "nf-core",
+  "homepage": "https://github.com/nf-core/agents/tree/main/plugins/nf-core-tools",
+  "repository": "https://github.com/nf-core/agents",
+  "license": "MIT",
+  "keywords": [
+    "nf-core",
+    "nextflow",
+    "lint",
+    "bioinformatics",
+    "workflows"
+  ],
+  "category": "Developer Tools",
+  "skills": "./skills/",
+  "hooks": "./hooks/cursor.json",
+  "mcpServers": "./.mcp.json"
+}

plugins/nf-core-tools/.mcp.json

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+{
+  "mcpServers": {}
+}

plugins/nf-core-tools/assets/README.md

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+# assets
+
+Place plugin icon/logo/screenshot files here if publishing to a marketplace UI.

plugins/nf-core-tools/hooks/README.md

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+# hooks
+
+Provider hook manifests live here.
+
+- `codex.json` uses Codex hook event names and nested command entries.
+- `cursor.json` uses Cursor hook event names and command entries.
+
+Both manifests adapt provider events to the shared internal phase runner instead
+of embedding nf-core validation policy directly in provider-specific JSON.

plugins/nf-core-tools/hooks/codex.json

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+{
+  "hooks": {
+    "Stop": [
+      {
+        "matcher": null,
+        "hooks": [
+          {
+            "type": "command",
+            "command": "./scripts/agent_hooks/run_phase.py stop --provider codex",
+            "timeout": 600,
+            "statusMessage": "Running nf-core stop checks"
+          }
+        ]
+      }
+    ]
+  }
+}

plugins/nf-core-tools/hooks/cursor.json

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+{
+  "hooks": {
+    "afterFileEdit": [
+      {
+        "command": "./scripts/agent_hooks/run_phase.py after-file-edit --provider cursor"
+      }
+    ],
+    "sessionEnd": [
+      {
+        "command": "./scripts/agent_hooks/run_phase.py stop --provider cursor"
+      }
+    ],
+    "stop": [
+      {
+        "command": "./scripts/agent_hooks/run_phase.py stop --provider cursor"
+      }
+    ]
+  }
+}

plugins/nf-core-tools/skills/nf-core-tools/SKILL.md

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+---
+name: nf-core-tools
+description: Run shared nf-core lint and policy checks via `prek run <hook-id>` or full `prek run --all-files` in this repo.
+license: MIT
+metadata:
+  author: nf-core
+  version: "0.1.0"
+  nf_core_tools_version: "4.0.2"
+---
+
+# nf-core tools
+
+## When to use
+
+- Need deterministic lint/policy checks across Codex, Claude, Cursor.
+- Need to run one specific hook fast.
+- Need strict nf-core guardrails for Nextflow edits.
+
+## Commands
+
+```sh
+prek run --all-files
+prek run nf-core-pipelines-lint --all-files
+prek run nf-core-component-lint --all-files
+prek run nf-core-schema-check --all-files
+prek run guard-nfcore-modules --all-files
+prek run lint-schema --all-files
+prek run check-param-drift --all-files
+prek run lint-local-module --all-files
+prek run check-nftest-exists --all-files
+prek run check-changelog --all-files
+```
+
+## Notes
+
+- `lint-schema` and `lint-local-module` require the `nf-core` CLI; target nf-core/tools 4.0.2 or newer when reproducing current docs behavior.
+- Hooks fail hard on violations (non-zero exit).