Add skills validation harness and multi-harness packaging

.agents/plugins/marketplace.json

@@ -0,0 +1,20 @@
+{
+  "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

@@ -0,0 +1,16 @@
+{
+  "$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

@@ -0,0 +1,63 @@
+{
+  "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

@@ -0,0 +1,18 @@
+{
+  "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."
+    }
+  ]
+}

.github/workflows/prek.yml

@@ -0,0 +1,10 @@
+name: Prek checks
+
+on: [push, pull_request]
+
+jobs:
+  prek:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: j178/prek-action@v2

.markdownlint.json

@@ -0,0 +1,9 @@
+{
+  "default": true,
+  "MD013": false,
+  "MD024": {
+    "siblings_only": true
+  },
+  "MD033": false,
+  "MD041": false
+}

docs/AGENT_HOOKS.md

@@ -0,0 +1,23 @@
+# Agent hook provider notes
+
+This repo keeps nf-core validation policy provider-neutral in `scripts/agent_hooks/`.
+Provider-specific hook formats belong in adapter modules under
+`scripts/agent_hooks/providers/`.
+
+## Internal contract
+
+The internal interface is a phase report, not a provider wire format:
+
+```python
+report = run_phase("stop", files)
+```
+
+Provider adapters translate that report into each agent runtime's required stdout,
+stderr, and exit-code behavior.
+
+## Provider shape references
+
+- [Codex](agent-hooks/codex.md)
+- [Claude Code](agent-hooks/claude.md)
+- [Cursor](agent-hooks/cursor.md)
+- [Generic exit-code providers](agent-hooks/generic.md)

docs/agent-hooks/claude.md

@@ -0,0 +1,57 @@
+# Claude Code hook provider shape
+
+Claude Code uses JSON stdin for hook events and supports structured JSON stdout
+for decisions on blocking-capable events.
+
+## Stop input shape
+
+Claude Code `Stop` input is JSON on stdin. Relevant fields include:
+
+```json
+{
+  "hook_event_name": "Stop",
+  "session_id": "...",
+  "transcript_path": "/path/to/transcript.jsonl",
+  "cwd": "/path/to/project",
+  "stop_hook_active": false,
+  "last_assistant_message": "...",
+  "background_tasks": [],
+  "session_crons": []
+}
+```
+
+Important fields for this repo:
+
+- `cwd`
+- `hook_event_name`
+- `stop_hook_active`
+- `last_assistant_message`
+
+## Stop output shape
+
+For `Stop`, block with clean JSON on stdout:
+
+```json
+{
+  "decision": "block",
+  "reason": "Continue fixing before stopping."
+}
+```
+
+Allow stopping with:
+
+```json
+{
+  "decision": "approve",
+  "reason": "nf-core stop hook: checks passed"
+}
+```
+
+## Rules and gotchas
+
+- Use stdout for the structured response.
+- Keep stdout clean JSON; send harness logs to stderr.
+- The adapter should return exit code `0` when expressing a structured block.
+- If `stop_hook_active` is true, avoid recursive blocking.
+- `SessionEnd` is not a substitute for `Stop` because it does not provide the
+  same blocking control.

docs/agent-hooks/codex.md

@@ -0,0 +1,102 @@
+# Codex hook provider shape
+
+Source of truth: OpenAI Codex sources in `openai/codex`:
+
+- `docs/config.md`
+- `codex-rs/hooks/src/lib.rs`
+- `codex-rs/hooks/src/events/stop.rs`
+- `codex-rs/hooks/src/engine/output_parser.rs`
+- `codex-rs/hooks/schema/generated/stop.command.input.schema.json`
+- `codex-rs/hooks/schema/generated/stop.command.output.schema.json`
+- `codex-rs/config/src/hook_config.rs`
+
+## Events
+
+Codex hook events include:
+
+- `PreToolUse`
+- `PermissionRequest`
+- `PostToolUse`
+- `PreCompact`
+- `PostCompact`
+- `SessionStart`
+- `UserPromptSubmit`
+- `SubagentStart`
+- `SubagentStop`
+- `Stop`
+
+## nf-core hook manifest
+
+The Codex plugin manifest points at `plugins/nf-core-tools/hooks/codex.json`.
+That file uses Codex event names and nested command hook entries.
+
+## Hook config shape
+
+```json
+{
+  "hooks": {
+    "Stop": [
+      {
+        "matcher": null,
+        "hooks": [
+          {
+            "type": "command",
+            "command": "...",
+            "timeout": 600,
+            "statusMessage": "..."
+          }
+        ]
+      }
+    ]
+  }
+}
+```
+
+## Stop input shape
+
+Codex `Stop` input is JSON on stdin:
+
+```json
+{
+  "hook_event_name": "Stop",
+  "cwd": "/path/to/project",
+  "session_id": "...",
+  "turn_id": "...",
+  "transcript_path": null,
+  "model": "...",
+  "permission_mode": "default",
+  "stop_hook_active": false,
+  "last_assistant_message": null
+}
+```
+
+Important fields for this repo:
+
+- `cwd`
+- `hook_event_name`
+- `stop_hook_active`
+- `last_assistant_message`
+
+## Stop output shape
+
+Codex `Stop` output can block with clean JSON on stdout:
+
+```json
+{
+  "decision": "block",
+  "reason": "Continue fixing before stopping."
+}
+```
+
+A successful no-block response can be empty stdout or structured JSON without a
+block decision. This repo prefers structured JSON for provider adapters.
+
+## Rules and gotchas
+
+- `decision: "block"` requires a non-empty `reason`.
+- stdout must be valid hook JSON when using JSON output; route harness logs to stderr.
+- Exit code `2` plus stderr is also treated as a continuation/block prompt.
+- Other nonzero exits are hook failures, not normal block decisions.
+- If `stop_hook_active` is true, avoid blocking again to prevent recursive stop loops.
+- Keep a distinct Codex adapter even if it initially resembles Claude. Future
+  `PreToolUse`, `PermissionRequest`, and `PostToolUse` semantics differ.