molecule-core/docs/glossary.md

Glossary — Molecule AI terminology vs. ecosystem neighbors

The agent-infra ecosystem has coalesced around a common vocabulary that nevertheless means different things in different projects. This page defines how Molecule AI uses each term and flags the conflicts you're most likely to hit when reading adjacent documentation.

Cross-referenced from docs/ecosystem-watch.md — when a new project lands in the watch list with a colliding term, add a row here.

Core terms

Term	What we mean	What others mean
harness	The Claude Code execution environment: ~/.claude/settings.json, hooks, skills, MCP servers, the surrounding CLI. The layer around the agent that enforces behavior before tool calls fire.	OpenHarness (HKUDS/OpenHarness): a research framework wrapper for studying agent internals — closer to a probe than an enforcement layer.
workspace	An isolated Docker container running one agent with a role, git state, hook pipeline, runtime image, and per-workspace bearer token. Long-lived — a workspace is provisioned once and stays up.	Paperclip: closer to "employee" (a persona with memory). Hermes: closer to "project" (a unit of work scoped by time). In Molecule, persona = role, unit of work = task/delegation.
plugin	A directory under plugins/ packaging one or more skills or an MCP server wrapper, installable per-workspace via POST /workspaces/:id/plugins. Governed by plugin.yaml.	Langflow: a visual UI node / component in a flowchart. CrewAI: a Python-importable callable registered as a capability.
agent	A persistent containerized workspace running continuously — an identity with memory, a role, and a schedule. Not a one-shot invocation.	Most frameworks (AutoGPT, LangChain agents, OpenAI Assistants): a stateless function-call loop. No persistence between invocations unless explicitly checkpointed.
flow	A task execution within a workspace — a request enters, the agent runs tools, emits a response, logs activity. No explicit graph abstraction.	Langflow: a directed graph of nodes you author visually. LangGraph: a stateful graph of callable nodes. Our "flow" is an imperative timeline, not a graph.
team	A named cluster of workspaces under a PM (org template expand_team). Used for role grouping in Canvas.	CrewAI: a "crew" is a sequence of agents that pass a task through a declared order. Our "team" is an org-chart abstraction, not an execution order.
skill	A directory with SKILL.md that an agent invokes via the Skill tool. Skills are documentation + optional scripts that teach an agent a recipe.	Anthropic Skills API: nearly identical. CrewAI tool: closer to our plugin's MCP tool, not our skill.
channel	An outbound/inbound social integration (Telegram, Slack, …) per-workspace, wired in workspace_channels.	Slack's "channel": the container for messages. We use "channel" for the adapter + credentials, not the conversation itself.
runtime	The execution engine image tag for a workspace: one of langgraph, claude-code, openclaw, crewai, autogen, deepagents, hermes.	LangGraph runtime: the Python process running the graph. We use "runtime" for the Docker image + adapter pairing, not the inner process.

Near-miss terms

These don't appear in the table above because we don't use them in the same sense as the reference project — flagged so you don't confuse the two:

• crew (CrewAI) — we don't use this term; the analogue is team.
• tool — a LangChain @tool-decorated callable, shared vocabulary with most frameworks. No conflict, but "skill" is the user-facing abstraction an agent picks up from SKILL.md; "tool" is the thing under the hood.
• component (Langflow) — no analogue. We have plugin (role-level), skill (agent-recipe-level), and adapter (runtime-level). A Langflow "component" is visual; ours is structural.
• pipeline — overloaded in our repo: CI pipeline, ingestion pipeline, etc. Always use the qualifier.

When to update this file

• A project enters docs/ecosystem-watch.md with a term that collides with ours → add a row.
• We rename an internal term (e.g., "workspace" to "agent") → update every row that references it, update CLAUDE.md, update README.md, update docs/architecture.md.
• A user reports confusion reading a cross-project tutorial → add a row with the confusing term.

Cross-references

• README.md — top-level stack description.
• CLAUDE.md — operational vocabulary for agents in this repo.
• docs/ecosystem-watch.md — source of truth for adjacent-project claims.
• docs/architecture.md — deeper definitions for workspace, canvas, platform.