molecule-core/CLAUDE.md

CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

Molecule AI is a platform for orchestrating AI agent workspaces that form an organizational hierarchy. Workspaces register with a central platform, communicate via A2A protocol, and are visualized on a drag-and-drop canvas.

Ecosystem Context

Before research, strategy, or design work, skim docs/ecosystem-watch.md — it catalogs adjacent agent projects (Holaboss, Hermes, gstack, …) with overlap / differentiation / terminology-collision notes. Cross-referenced from PLAN.md and README.md; it's the canonical starting point for "what else is out there."

Architecture

Canvas (Next.js :3000) ←WebSocket→ Platform (Go :8080) ←HTTP→ Postgres + Redis
                                                                  ↑
                                   Workspace A ←──A2A──→ Workspace B
                                   (Python agents)
                                        ↑ register/heartbeat ↑
                                        └───── Platform ─────┘

Four main components:

• Platform (platform/): Go/Gin control plane — workspace CRUD, registry, discovery, WebSocket hub, liveness monitoring
• Canvas (canvas/): Next.js 15 + React Flow (@xyflow/react v12) + Zustand + Tailwind — visual workspace graph
• Workspace Runtime (workspace-template/): Unified Docker image with pluggable adapter system — supports LangGraph, Claude Code, OpenClaw, DeepAgents, CrewAI, AutoGen. Adapters in workspace-template/adapters/. Deps installed at startup via entrypoint.sh.
• molecli (platform/cmd/cli/): Go TUI dashboard (Bubbletea + Lipgloss) — real-time workspace monitoring, event log, health overview, delete/filter operations

Build & Run Commands

Infrastructure

./infra/scripts/setup.sh    # Start Postgres, Redis, Langfuse; run migrations
./infra/scripts/nuke.sh     # Tear down everything, remove volumes

Platform (Go)

cd platform
go build ./cmd/server       # Build server
go run ./cmd/server          # Run server (requires Postgres + Redis running)
go build -o molecli ./cmd/cli  # Build TUI dashboard
./molecli                    # Run TUI dashboard (requires platform running)

Must run from platform/ directory (not repo root). Env vars: DATABASE_URL, REDIS_URL, PORT, PLATFORM_URL (default http://host.docker.internal:PORT — passed to agent containers so they can reach the platform), SECRETS_ENCRYPTION_KEY (optional AES-256, 32 bytes), CONFIGS_DIR (auto-discovered), PLUGINS_DIR (deprecated — plugins are now installed per-workspace via API; the plugins/ registry at repo root is auto-discovered), ACTIVITY_RETENTION_DAYS (default 7), ACTIVITY_CLEANUP_INTERVAL_HOURS (default 6), CORS_ORIGINS (comma-separated, default http://localhost:3000,http://localhost:3001), RATE_LIMIT (requests/min, default 600), WORKSPACE_DIR (optional — global fallback host path for /workspace bind-mount; overridden by per-workspace workspace_dir column in DB; if neither is set, each workspace gets an isolated Docker named volume), AWARENESS_URL (optional — if set, injected into workspace containers along with a deterministic AWARENESS_NAMESPACE derived from workspace ID), MOLECULE_IN_DOCKER (optional — set to 1 when the platform itself runs inside Docker so the A2A proxy rewrites 127.0.0.1:<port> URLs to container hostnames; auto-detected via /.dockerenv).

Plugin install safeguards (bound the cost of a single POST /workspaces/:id/plugins install so a slow/malicious source can't tie up a handler):

• PLUGIN_INSTALL_BODY_MAX_BYTES — max request body size (default 65536 = 64 KiB)
• PLUGIN_INSTALL_FETCH_TIMEOUT — duration string; whole fetch+copy deadline (default 5m)
• PLUGIN_INSTALL_MAX_DIR_BYTES — max staged-tree size (default 104857600 = 100 MiB)

See docs/plugins/sources.md for the two-axis source/shape plugin model.

molecli reads MOLECLI_URL (default http://localhost:8080) to locate the platform. Logs are written to molecli.log in the working directory (already covered by *.log in .gitignore).

Canvas (Next.js)

cd canvas
npm install
npm run dev                  # Dev server on :3000
npm run build && npm start   # Production

Env vars: NEXT_PUBLIC_PLATFORM_URL (default http://localhost:8080), NEXT_PUBLIC_WS_URL (default ws://localhost:8080/ws).

Workspace Images

bash workspace-template/build-all.sh                   # Build base + ALL runtime images
bash workspace-template/build-all.sh claude-code       # Build base + specific runtime only

Each runtime has its own Docker image extending workspace-template:base, with deps pre-installed for fast startup. The base Dockerfile (workspace-template/Dockerfile) builds :base, then each adapters/*/Dockerfile extends it (e.g. claude_code/Dockerfile installs the claude CLI). Always use build-all.sh — it builds base first, then all runtimes in order. No :latest tag — each runtime uses its own tag to avoid confusion.

Runtime	Image Tag	Key Deps
langgraph	workspace-template:langgraph	langchain-anthropic, langgraph
claude-code	workspace-template:claude-code	claude-agent-sdk (pip), @anthropic-ai/claude-code (npm)
openclaw	workspace-template:openclaw	openclaw deps
crewai	workspace-template:crewai	crewai
autogen	workspace-template:autogen	autogen
deepagents	workspace-template:deepagents	deepagents

Templates are framework presets in workspace-configs-templates/: claude-code-default, langgraph, openclaw, deepagents. Agent roles are configured after deployment via Config tab or API.

For Claude Code runtime, write your OAuth token to workspace-configs-templates/claude-code-default/.auth-token.

Pre-commit Hook

git config core.hooksPath .githooks            # Install hooks (agents do this via initial_prompt)

Enforces: 'use client' on hook-using .tsx files, dark theme (no white/light), no SQL injection (fmt.Sprintf with SQL), no leaked secrets (sk-ant-, ghp_, AKIA). Commit is rejected until violations are fixed — agents cannot bypass this.

Plugins

Shared plugins in plugins/ are auto-loaded by every workspace:

• molecule-dev: Codebase conventions (rules injected into CLAUDE.md) + review-loop skill for multi-round QA cycles
• superpowers: verification-before-completion, test-driven-development, systematic-debugging, writing-plans
• ecc: General Claude Code guardrails

Scripts

bash scripts/setup-default-org.sh              # Create PM + 3 teams (Marketing/Research/Dev) via API
OPENAI_API_KEY=... bash scripts/test-a2a-cross-runtime.sh  # E2E: Claude Code ↔ OpenClaw A2A test
OPENAI_API_KEY=... bash scripts/test-team-e2e.sh           # E2E: Multi-template team + A2A

Unit Tests

cd platform && go test -race ./...               # 487 Go tests (handlers, registry, provisioner, CLI, delegation, org, channels, wsauth — sqlmock + miniredis)
cd canvas && npm test                            # 352 Vitest tests (store, components, hydration, buildTree, secrets API, org template import)
cd workspace-template && python -m pytest -v     # 1078 pytest tests (adds platform_auth token store for Phase 30.1)
cd sdk/python && python -m pytest -v              # 87 SDK tests (agentskills.io spec validator, CLI, AgentskillsAdaptor round-trip, workspace/org/channel validators)

Integration Tests

bash tests/e2e/test_api.sh             # 62 API tests against localhost:8080
bash tests/e2e/test_a2a_e2e.sh         # 22 A2A end-to-end tests (requires 2 online agents)
bash tests/e2e/test_activity_e2e.sh    # 25 activity/task E2E tests (requires 1 online agent)
bash tests/e2e/test_comprehensive_e2e.sh # 68 checks — ALL endpoints, memory, runtime, bundles, approvals

test_api.sh requires platform running. Tests full CRUD, registry, heartbeat, discovery, peers, access control, events, degraded/recovery lifecycle, activity logging, current task tracking, bundle round-trip (export → delete → import → verify).

test_a2a_e2e.sh requires platform + two provisioned agents (Echo Agent, SEO Agent) running with a valid OPENROUTER_API_KEY. Tests message/send, JSON-RPC wrapping, error handling, peer discovery, agent cards, heartbeat. Timeout configurable via A2A_TIMEOUT env var (default 120s).

test_activity_e2e.sh requires platform + one online agent. Tests A2A communication logging (request/response capture, duration, method), agent self-reported activity, type filtering, current task visibility via heartbeat, cross-workspace activity isolation, edge cases.

MCP Server

cd mcp-server
npm install && npm run build   # Build MCP server
node dist/index.js             # Run (stdio transport)

Exposes 87 tools for managing Molecule AI from Claude Code, Cursor, Codex, or any MCP client. Includes workspace CRUD, async delegation, plugins (install/uninstall/list), global secrets, pause/resume, org import, A2A chat, approvals, memory, files, config, discovery, bundles, templates, traces, activity logs, and social channels (add/update/remove/send/test). Configured in .mcp.json. Env: MOLECULE_URL (default http://localhost:8080).

CI Pipeline

GitHub Actions (.github/workflows/ci.yml) runs on push to main and PRs:

• platform-build: Go build, vet, go test -race with coverage profiling (25% baseline threshold)
• canvas-build: npm build, vitest run (no --passWithNoTests -- tests must exist and pass)
• mcp-server-build: npm build
• python-lint: pytest --cov=. --cov-report=term-missing (pytest-cov enabled)

Docker Compose

docker compose -f docker-compose.infra.yml up -d    # Infra only
docker compose up                                     # Full stack

Key Architectural Patterns

Import Cycle Prevention

The platform uses function injection to avoid Go import cycles between ws, registry, and events packages:

• ws.NewHub(canCommunicate AccessChecker) — Hub accepts registry.CanCommunicate as a function
• registry.StartLivenessMonitor(ctx, onOffline OfflineHandler) — Liveness accepts broadcaster callback
• registry.StartHealthSweep(ctx, checker ContainerChecker, interval, onOffline) — Health sweep accepts Docker checker interface
• Wiring happens in platform/cmd/server/main.go — init order: wh → onWorkspaceOffline → liveness/healthSweep → router

Container Health Detection

Three layers detect dead containers (e.g. Docker Desktop crash):

1. Passive (Redis TTL): 60s heartbeat key expires → liveness monitor → auto-restart
2. Proactive (Health Sweep): registry.StartHealthSweep polls Docker API every 15s → catches dead containers faster
3. Reactive (A2A Proxy): On connection error, checks provisioner.IsRunning() → immediate offline + restart

All three call onWorkspaceOffline which broadcasts WORKSPACE_OFFLINE + go wh.RestartByID(). Redis cleanup uses shared db.ClearWorkspaceKeys().

Template Resolution (Create)

Runtime detection happens before DB insert: if payload.Runtime is empty and a template is specified, the handler reads runtime: from configsDir/template/config.yaml first. If still empty, defaults to "langgraph". This ensures the correct runtime (e.g. claude-code) is persisted in the DB and used for container image selection.

When a workspace specifies a template that doesn't exist, the Create handler falls back:

1. Check os.Stat(configsDir/template) — use if exists
2. Try {runtime}-default template (e.g. claude-code-default/)
3. Generate default config via ensureDefaultConfig() (includes .auth-token copy for CLI runtimes)

Communication Rules (registry/access.go)

CanCommunicate(callerID, targetID) determines if two workspaces can talk:

• Same workspace → allowed
• Siblings (same parent_id) → allowed
• Root-level siblings (both parent_id IS NULL) → allowed
• Parent ↔ child → allowed
• Everything else → denied

The A2A proxy (POST /workspaces/:id/a2a) enforces this for agent-to-agent calls. Canvas requests (no X-Workspace-ID), self-calls, and system callers (webhook:*, system:*, test:* prefixes via isSystemCaller() in a2a_proxy.go) bypass the check.

JSONB Gotcha

When inserting Go []byte (from json.Marshal) into Postgres JSONB columns, you must:

1. Convert to string() first
2. Use ::jsonb cast in SQL

lib/pq treats []byte as bytea, not JSONB.

WebSocket Events Flow

1. Action occurs (register, heartbeat, etc.)
2. broadcaster.RecordAndBroadcast() inserts into structure_events table + publishes to Redis pub/sub
3. Redis subscriber relays to WebSocket hub
4. Hub broadcasts to canvas clients (all events) and workspace clients (filtered by CanCommunicate)

Canvas State Management

• Initial load: HTTP fetch from GET /workspaces → Zustand hydrate
• Real-time updates: WebSocket events → applyEvent() in Zustand store
• Position persistence: onNodeDragStop → PATCH /workspaces/:id with {x, y}
• Embedded sub-workspaces: nestNode sets hidden: !!targetId on child nodes; children render as recursive TeamMemberChip components inside parent (up to 3 levels), not as separate canvas nodes. Use n.data.parentId (not React Flow's n.parentId) for hierarchy lookups.
• Chat: two sub-tabs — "My Chat" (user↔agent, source=canvas) and "Agent Comms" (agent↔agent A2A traffic, source=agent). History loaded from GET /activity with source filter. Real-time via A2A_RESPONSE + AGENT_MESSAGE WebSocket events. Conversation history (last 20 messages) sent via params.metadata.history in A2A message/send requests.
• Config save: "Save & Restart" writes config.yaml and auto-restarts the workspace. "Save" writes only (shows restart banner). Secrets POST/DELETE auto-restart on the platform side.

Initial Prompt

Agents can auto-execute a prompt on startup before any user interaction. Configure via initial_prompt (inline string) or initial_prompt_file (path relative to config dir) in config.yaml. After the A2A server is ready, main.py sends the prompt as a message/send to self. A .initial_prompt_done marker file prevents re-execution on restart. Org templates support initial_prompt on both defaults (all agents) and per-workspace (overrides default).

Important: Initial prompts must NOT send A2A messages (delegate_task, send_message_to_user) — other agents may not be ready. Keep them local: clone repo, read docs, save to memory, wait for tasks.

Workspace Lifecycle

provisioning → online (on register) → degraded (error_rate > 0.5) → online (recovered) → offline (Redis TTL expired OR health sweep detects dead container) → auto-restart → provisioning → ... → removed (deleted). Any state → paused (user pauses) → provisioning (user resumes). Paused workspaces skip health sweep, liveness monitor, and auto-restart.

Platform API Routes

Method	Path	Handler
GET	/health	inline
GET	/metrics	metrics.Handler() — Prometheus text format (v0.0.4); no auth, scrape-safe
POST/GET/PATCH/DELETE	/workspaces[/:id]	workspace.go
GET/PATCH	/workspaces/:id/config	workspace.go
GET/POST	/workspaces/:id/memory	workspace.go
DELETE	/workspaces/:id/memory/:key	workspace.go
POST/PATCH/DELETE	/workspaces/:id/agent	agent.go
POST	/workspaces/:id/agent/move	agent.go
GET/POST/PUT	/workspaces/:id/secrets	secrets.go (POST/PUT auto-restarts workspace)
DELETE	/workspaces/:id/secrets/:key	secrets.go (DELETE auto-restarts workspace)
GET	/workspaces/:id/model	secrets.go
GET	/settings/secrets	secrets.go — list global secrets (keys only, values masked)
PUT/POST	/settings/secrets	secrets.go — set a global secret {key, value}
DELETE	/settings/secrets/:key	secrets.go — delete a global secret
GET/POST/DELETE	/admin/secrets[/:key]	secrets.go — legacy aliases for /settings/secrets
WS	/workspaces/:id/terminal	terminal.go
POST	/workspaces/:id/expand	team.go
POST	/workspaces/:id/collapse	team.go
POST/GET	/workspaces/:id/approvals	approvals.go
POST	/workspaces/:id/approvals/:id/decide	approvals.go
GET	/approvals/pending	approvals.go
POST/GET	/workspaces/:id/memories	memories.go
DELETE	/workspaces/:id/memories/:id	memories.go
GET	/workspaces/:id/traces	traces.go
GET/POST	/workspaces/:id/activity	activity.go
POST	/workspaces/:id/notify	activity.go (agent→user push message via WS)
POST	/workspaces/:id/restart	workspace.go
POST	/workspaces/:id/pause	workspace.go (stops container, status→paused)
POST	/workspaces/:id/resume	workspace.go (re-provisions paused workspace)
POST	/workspaces/:id/a2a	workspace.go
POST	/workspaces/:id/delegate	delegation.go (async fire-and-forget)
GET	/workspaces/:id/delegations	delegation.go (list delegation status)
GET/POST	/workspaces/:id/schedules	schedules.go (cron CRUD)
PATCH/DELETE	/workspaces/:id/schedules/:scheduleId	schedules.go
POST	/workspaces/:id/schedules/:scheduleId/run	schedules.go (manual trigger)
GET	/workspaces/:id/schedules/:scheduleId/history	schedules.go (past runs)
GET/POST	/workspaces/:id/channels	channels.go (social channel CRUD)
PATCH/DELETE	/workspaces/:id/channels/:channelId	channels.go
POST	/workspaces/:id/channels/:channelId/send	channels.go (outbound message)
POST	/workspaces/:id/channels/:channelId/test	channels.go (test connection)
GET	/channels/adapters	channels.go (list available platforms)
POST	/channels/discover	channels.go (auto-detect chats for a bot token)
POST	/webhooks/:type	channels.go (incoming social webhook)
GET	/workspaces/:id/shared-context	templates.go
GET/PUT/DELETE	/workspaces/:id/files[/*path]	templates.go
GET/PUT	/canvas/viewport	viewport.go
GET	/templates	templates.go
POST	/templates/import	templates.go
POST	/registry/register	registry.go
POST	/registry/heartbeat	registry.go
POST	/registry/update-card	registry.go
GET	/registry/discover/:id	discovery.go
GET	/registry/:id/peers	discovery.go
POST	/registry/check-access	discovery.go
GET	/plugins	plugins.go (list registry; supports ?runtime= filter)
GET	/plugins/sources	plugins.go (list registered install-source schemes)
GET/POST/DELETE	/workspaces/:id/plugins[/:name]	plugins.go — list, install ({"source":"scheme://spec"}), uninstall per-workspace
GET	/workspaces/:id/plugins/available	plugins.go (filtered by workspace runtime)
GET	/workspaces/:id/plugins/compatibility?runtime=X	plugins.go (preflight runtime-change check)
GET	/bundles/export/:id	bundle.go
POST	/bundles/import	bundle.go
GET	/org/templates	org.go (list available org templates)
POST	/org/import	org.go (import entire org hierarchy from YAML)
GET	/ws	socket.go

Database

16 migration files in platform/migrations/. Key tables: workspaces (core entity with status, runtime, agent_card JSONB, heartbeat columns, current_task, awareness_namespace, workspace_dir), canvas_layouts (x/y position), structure_events (append-only event log), activity_logs (A2A communications, task updates, agent logs, errors), workspace_schedules (cron tasks with expression, timezone, prompt, run history), workspace_channels (social channel integrations — Telegram, Slack, etc., with JSONB config and allowlist), agents, workspace_secrets, global_secrets, agent_memories (HMA scoped memory), approvals.

The platform auto-discovers and runs migrations on startup from several candidate paths.

Project Memory (Awareness MCP)

IMPORTANT: These instructions override default behavior. You must follow them exactly.

Awareness Memory Integration (MANDATORY)

awareness_* = cross-session persistent memory (past decisions, knowledge, tasks). Other tools = current codebase navigation (file search, code index). Use BOTH - they serve different purposes.

STEP 1 - SESSION START: Call awareness_init(source="claude-code") -> get session_id, review context. If active_skills[] is returned: skill = reusable procedure done 2+ times; summary = injectable instruction, methods = steps. Apply matching skills to tasks.

STEP 2 - RECALL BEFORE WORK (progressive disclosure):

1. awareness_recall(semantic_query=..., keyword_query=..., detail='summary') → lightweight index.
2. Review summaries/scores, pick relevant IDs.
3. awareness_recall(detail='full', ids=[...]) → expand only what you need.

STEP 3 - RECORD EVERY CHANGE: After EVERY code edit, decision, or bug fix: awareness_record(content=, insights={knowledge_cards:[...], action_items:[...], risks:[...]}) Content should be RICH and DETAILED — include reasoning, key code snippets, user quotes, alternatives considered, and files changed. Do NOT compress into a single-line summary. The content IS the memory — more detail = better recall. Include insights to create searchable knowledge in ONE step (recommended). Skipping = permanent data loss.

STEP 4 - CATEGORY GUIDE (for insights.knowledge_cards):

• decision = choice made between alternatives.
• problem_solution = bug/problem plus the fix that resolved it.
• workflow = process, setup, or configuration steps only.
• pitfall = blocker, warning, or limitation without a fix yet.
• insight = reusable pattern or general learning.
• skill = reusable procedure done 2+ times; summary = injectable instruction, methods = steps.
• key_point = important technical fact when nothing else fits. Never default everything to workflow.

STEP 5 - SESSION END: awareness_record(content=[step1, step2, ...], insights={...}) with final summary.

BACKFILL (if applicable): If MCP connected late: awareness_record(content=)

RULES VERSION: Pass rules_version="2" to awareness_init so the server knows you have these rules. If the server returns _setup_action, the rules have been updated — follow the instruction to re-sync.

NOTE: memory_id from X-Awareness-Memory-Id header. source/actor/event_type auto-inferred.

Compliance Check

Before responding to ANY user request:

1. Have you called awareness_init yet this session? If not, call it NOW.

2. Did you just edit a file? Call awareness_record(content=, insights={...}) IMMEDIATELY.

3. Is the user asking about past work? Call awareness_recall FIRST.