molecule-core/docs/plugins/agentskills-compat.md
Hongming Wang 479a027e4b chore: open-source restructure — rename dirs, remove internal files, scrub secrets
Renames:
- platform/ → workspace-server/ (Go module path stays as "platform" for
  external dep compat — will update after plugin module republish)
- workspace-template/ → workspace/

Removed (moved to separate repos or deleted):
- PLAN.md — internal roadmap (move to private project board)
- HANDOFF.md, AGENTS.md — one-time internal session docs
- .claude/ — gitignored entirely (local agent config)
- infra/cloudflare-worker/ → Molecule-AI/molecule-tenant-proxy
- org-templates/molecule-dev/ → standalone template repo
- .mcp-eval/ → molecule-mcp-server repo
- test-results/ — ephemeral, gitignored

Security scrubbing:
- Cloudflare account/zone/KV IDs → placeholders
- Real EC2 IPs → <EC2_IP> in all docs
- CF token prefix, Neon project ID, Fly app names → redacted
- Langfuse dev credentials → parameterized
- Personal runner username/machine name → generic

Community files:
- CONTRIBUTING.md — build, test, branch conventions
- CODE_OF_CONDUCT.md — Contributor Covenant 2.1

All Dockerfiles, CI workflows, docker-compose, railway.toml, render.yaml,
README, CLAUDE.md updated for new directory names.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
2026-04-18 00:24:44 -07:00

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# Molecule AI plugins and the agentskills.io standard
> **TL;DR** — every skill inside a Molecule AI plugin is a spec-compliant
> [agentskills.io](https://agentskills.io) skill, which means the same
> skill directory is installable in **Claude Code, Cursor, GitHub Copilot,
> VS Code, OpenAI Codex, Gemini CLI, Amp, OpenCode, OpenHands, Letta,
> Goose, Roo Code, Kiro, Factory, Ona, Junie**, and ~20 other agent
> products that ship the standard today. Molecule AI adds a *plugin*
> superset on top: a bundle of skills + rules + per-runtime adapters,
> so the same plugin can orchestrate across a team of agents running on
> different LLM runtimes.
## The two layers
```
plugins/my-plugin/ ← Molecule AI bundle (our layer)
├── plugin.yaml ← Molecule AI manifest: name, version,
│ runtimes, adapters, description
├── rules/*.md ← Molecule AI-only: always-on prose
│ appended to the runtime memory file
├── skills/ ← agentskills.io layer starts here
│ ├── <skill-name-1>/
│ │ ├── SKILL.md ← agentskills spec: frontmatter + body
│ │ ├── scripts/ ← optional, executable code
│ │ ├── references/ ← optional, deep-dive docs
│ │ └── assets/ ← optional, templates/data
│ └── <skill-name-2>/
│ └── SKILL.md
└── adapters/ ← Molecule AI-only: per-runtime installers
├── claude_code.py
└── deepagents.py
```
The boundary is clean:
- **Everything under `skills/<name>/`** follows the spec. A skill-aware
tool that doesn't know what Molecule AI is can consume it as-is.
- **Everything above `skills/`** is our superset — bundle metadata,
cross-runtime install logic, always-on rules.
## What the spec defines (and what we follow exactly)
Per [agentskills.io/specification](https://agentskills.io/specification):
| Spec requirement | How Molecule AI enforces it |
|---|---|
| Skill is a directory with `SKILL.md` at the root | `skills/<name>/SKILL.md` |
| Directory name matches frontmatter `name` | Enforced by `molecule_plugin validate` |
| `name`: 164 chars, lowercase + hyphens, no consecutive or edge hyphens | Regex-validated |
| `description`: 11024 chars, covers what+when | Length-validated |
| `license`, `compatibility`, `metadata`, `allowed-tools` optional | Passed through unchanged |
| `scripts/`, `references/`, `assets/` optional dirs | Skill loader reads all three |
| Progressive disclosure (metadata → body → sub-files) | Claude Code reads it natively; other runtimes load via plugin adaptor |
## Where we extend the spec (bundle layer)
The spec doesn't address bundling, cross-runtime installation, or
always-on rules. That's what `plugin.yaml` adds:
```yaml
# plugins/my-plugin/plugin.yaml
name: my-plugin
version: 1.0.0
description: Bundle of related skills + rules for <use case>.
author: your-name
tags: [example]
# Declared supported workspace runtimes — each must have a matching
# adapters/<runtime>.py file, or the install falls through to raw-drop.
runtimes:
- claude_code
- deepagents
# Optional — these are document hints, not enforced by the spec.
# The skills list is informational; the skill loader discovers everything
# under skills/ regardless.
skills:
- my-skill-a
- my-skill-b
# Optional — always-on markdown files appended to the runtime memory file
# (CLAUDE.md on Claude Code and DeepAgents). The spec has no always-on tier.
rules:
- rules/conventions.md
```
### Rules vs skills
- **A skill** is activated on demand — the agent reads its `name` and
`description` at startup, then loads the body when the task matches.
- **A rule** is always-on — its text is appended to the runtime's
memory file (CLAUDE.md) so the agent sees it on every turn.
Rules are a Molecule AI-specific extension. If we ever need to represent a
rule as a spec-compliant skill (e.g. for distribution to a non-Molecule AI
tool), write it as a skill whose `description` explicitly says "apply
continuously in this codebase" — the tool will decide whether to honor it.
### Per-runtime adapters
The spec leaves install semantics to the host tool. Molecule AI's plugin
adapters (`plugins/<name>/adapters/<runtime>.py`) bridge the gap for
runtimes that don't read `SKILL.md` natively. For most plugins the
built-in `AgentskillsAdaptor` covers the common shape (copy skills to
`/configs/skills/`, append rules to CLAUDE.md). See
[plugins_registry](../../workspace/plugins_registry/__init__.py)
for the resolution order.
## Validator
Run before publishing a plugin:
```bash
python -m molecule_plugin validate plugins/my-plugin
```
Checks:
1. `plugin.yaml` parses and declares known runtimes.
2. Every `skills/<name>/SKILL.md`:
- has valid frontmatter
- `name` matches the directory name
- `name` matches the spec regex (lowercase, hyphens, length)
- `description` is 11024 chars
- optional fields (`license`, `compatibility`, `metadata`,
`allowed-tools`) conform to spec types
CI runs this against every first-party plugin on every PR, so spec drift
is caught before merge.
## Publishing a skill to agentskills-compatible tools
Any `skills/<name>/` directory from a Molecule AI plugin is a valid standalone
skill. To publish it for Cursor / Codex / Goose / etc. users:
1. Copy `plugins/my-plugin/skills/<name>/` into a new repo.
2. Validate: `python -m molecule_plugin validate .` (or `skills-ref validate`
from the upstream [agentskills/agentskills](https://github.com/agentskills/agentskills) repo).
3. Publish the repo; users install according to their tool's docs.
The skill will use default activation semantics in each tool. Molecule AI's
plugin bundle (runtimes, adapters, rules) is not needed — it only matters
if the skill is installed inside Molecule AI.
## Hermes runtime compatibility (issue #852)
As of 2026-04-18, `hermes` has been added to the `runtimes:` field in
the five SKILL.md-only first-party plugins. agentskills.io v0.8.0
confirmed that SKILL.md-only plugins are natively hermes-compatible via
**raw-drop** (no adapter file required). Hook-based plugins remain
`claude_code`-only — they rely on harness-level hooks that hermes does
not expose.
| Plugin | Before | After |
|---|---|---|
| `ecc` | `[claude_code, deepagents]` | `[claude_code, deepagents, hermes]` |
| `superpowers` | `[claude_code, deepagents]` | `[claude_code, deepagents, hermes]` |
| `molecule-dev` | `[claude_code, deepagents]` | `[claude_code, deepagents, hermes]` |
| `molecule-skill-cron-learnings` | `[claude_code]` | `[claude_code, hermes]` |
| `molecule-skill-update-docs` | `[claude_code]` | `[claude_code, hermes]` |
Companion PRs:
- [molecule-ai-plugin-ecc#2](https://github.com/Molecule-AI/molecule-ai-plugin-ecc/pull/2)
- [molecule-ai-plugin-superpowers#2](https://github.com/Molecule-AI/molecule-ai-plugin-superpowers/pull/2)
- [molecule-ai-plugin-molecule-dev#2](https://github.com/Molecule-AI/molecule-ai-plugin-molecule-dev/pull/2)
- [molecule-ai-plugin-molecule-skill-cron-learnings#2](https://github.com/Molecule-AI/molecule-ai-plugin-molecule-skill-cron-learnings/pull/2)
- [molecule-ai-plugin-molecule-skill-update-docs#2](https://github.com/Molecule-AI/molecule-ai-plugin-molecule-skill-update-docs/pull/2)
Security note: Security Auditor was offline at time of change. Self-assessed
as non-security-impacting — adding `hermes` to a string list in `plugin.yaml`
creates no new tool surface or execution path.
## Why this matters strategically
- **Zero-cost distribution.** Every skill we ship to Molecule AI users is
automatically installable in ~35 other agent products, no rewrite.
- **We're visible in the spec ecosystem.** Our plugin directory becomes
discoverable alongside Anthropic's own example skills. If the spec
adds new fields, we inherit them for free.
- **Our moat stays intact.** Multi-agent orchestration, A2A, per-runtime
adapters, and the visual canvas — none of this is in scope for the
spec and is unlikely to be. That's where Molecule AI differentiates.