docs: update clone URLs after molecule-core repo split (quickstart + self-hosting)

docs(arch): correct staging DNS — per-tenant CNAME, no wildcard

app/(home)/page.tsx

@@ -1,29 +1,100 @@
 import Link from 'next/link';
 
+// Three quick-start lanes — keeps the home page from being a wall of text
+// and lets builders, operators, and integrators each find their entry
+// point in one click.
+const lanes = [
+  {
+    kicker: '01',
+    title: 'Build a workspace',
+    body: 'Pick a runtime template (Claude Code, LangGraph, CrewAI, Hermes, …), wire your tools, and ship.',
+    href: '/docs/workspace',
+    cta: 'Workspace guide →',
+  },
+  {
+    kicker: '02',
+    title: 'Run an organisation',
+    body: 'Topology, A2A, three-tier memory, governance — the platform layer that ties multi-agent teams together.',
+    href: '/docs/platform',
+    cta: 'Platform reference →',
+  },
+  {
+    kicker: '03',
+    title: 'Publish to the Marketplace',
+    body: 'Plugins, agents, and org bundles ship as signed manifests. Authors keep 80%, paid via Stripe Connect.',
+    href: '/docs/marketplace',
+    cta: 'Author guide →',
+  },
+];
+
 export default function HomePage() {
   return (
-    <main className="flex flex-1 flex-col items-center justify-center px-6 py-24 text-center">
+    <main className="flex flex-1 flex-col">
-      <h1 className="mb-4 text-5xl font-bold tracking-tight sm:text-6xl">
+      {/* Statusbar — mirrors the landing's "All systems · status.* · phase" strip */}
-        Molecule AI
+      <div className="border-b border-fd-border bg-fd-muted px-6 py-1.5 text-[11px] font-mono text-fd-muted-foreground flex flex-wrap justify-between gap-4">
-      </h1>
+        <span>
-      <p className="mb-8 max-w-2xl text-lg text-fd-muted-foreground">
+          <span className="inline-block size-1.5 rounded-full bg-[#2f7a4d] align-middle mr-1.5" />
-        Build and run multi-agent organisations. Templates, plugins, channels,
+          All systems · status.moleculesai.app
-        and the runtime that ties them together — documented end to end.
+        </span>
-      </p>
+        <span>Phase 33 shipped · Phase 35 Marketplace public beta</span>
-      <div className="flex flex-wrap items-center justify-center gap-3">
-        <Link
-          href="/docs"
-          className="rounded-md bg-fd-primary px-5 py-2.5 text-sm font-medium text-fd-primary-foreground transition-colors hover:opacity-90"
-        >
-          Read the docs
-        </Link>
-        <Link
-          href="https://github.com/Molecule-AI/molecule-monorepo"
-          className="rounded-md border border-fd-border px-5 py-2.5 text-sm font-medium transition-colors hover:bg-fd-muted"
-        >
-          View on GitHub
-        </Link>
       </div>
+
+      {/* Hero */}
+      <section className="px-6 py-20 sm:py-28 max-w-6xl mx-auto w-full">
+        <div className="text-[11px] font-mono uppercase tracking-[0.08em] text-fd-muted-foreground mb-4 flex items-center gap-2">
+          <span className="inline-block size-1.5 rounded-full bg-[#c0532b]" />
+          Documentation
+        </div>
+        <h1 className="text-5xl sm:text-6xl font-semibold tracking-tight leading-[1.05] mb-5 max-w-3xl">
+          The operating system for{' '}
+          <span className="text-[#3b5bdb]">AI agent organizations.</span>
+        </h1>
+        <p className="text-lg text-fd-muted-foreground max-w-2xl leading-relaxed mb-8">
+          Build and run multi-agent organisations the way you'd staff a company.
+          Templates, plugins, channels, runtimes, governance — documented end
+          to end.
+        </p>
+        <div className="flex flex-wrap items-center gap-3">
+          <Link
+            href="/docs"
+            className="rounded-md bg-fd-primary px-5 py-2.5 text-sm font-medium text-fd-primary-foreground transition hover:opacity-90"
+          >
+            Read the docs
+          </Link>
+          <Link
+            href="https://github.com/Molecule-AI"
+            target="_blank"
+            rel="noopener noreferrer"
+            className="rounded-md border border-fd-border px-5 py-2.5 text-sm font-medium transition hover:bg-fd-muted"
+          >
+            View on GitHub
+          </Link>
+        </div>
+      </section>
+
+      {/* Three lanes */}
+      <section className="px-6 pb-24 max-w-6xl mx-auto w-full">
+        <div className="grid grid-cols-1 md:grid-cols-3 gap-4">
+          {lanes.map((lane) => (
+            <Link
+              key={lane.kicker}
+              href={lane.href}
+              className="group rounded-lg border border-fd-border bg-fd-card p-6 transition hover:border-fd-foreground hover:-translate-y-0.5"
+            >
+              <div className="text-[11px] font-mono text-[#3b5bdb] mb-3 tracking-[0.08em]">
+                {lane.kicker}
+              </div>
+              <h3 className="text-base font-semibold mb-2">{lane.title}</h3>
+              <p className="text-sm text-fd-muted-foreground leading-relaxed mb-4">
+                {lane.body}
+              </p>
+              <div className="text-xs font-mono text-fd-foreground group-hover:text-[#3b5bdb] transition">
+                {lane.cta}
+              </div>
+            </Link>
+          ))}
+        </div>
+      </section>
     </main>
   );
 }

app/global.css

@@ -1,3 +1,32 @@
 @import 'tailwindcss';
 @import 'fumadocs-ui/css/neutral.css';
 @import 'fumadocs-ui/css/preset.css';
+
+/* Warm-paper light theme — aligned with the landing page (moleculesai.app).
+   Tokens map fumadocs' @theme variables onto our brand palette so docs,
+   marketing, and the canvas read as one product. */
+@theme {
+  --font-sans: var(--font-geist), ui-sans-serif, system-ui, sans-serif;
+  --font-mono: var(--font-mono), ui-monospace, SFMono-Regular, monospace;
+
+  --color-fd-background: #fafaf7;
+  --color-fd-foreground: #15181c;
+  --color-fd-muted: #f3f1ec;
+  --color-fd-muted-foreground: #5a5e66;
+  --color-fd-popover: #ffffff;
+  --color-fd-popover-foreground: #15181c;
+  --color-fd-card: #ffffff;
+  --color-fd-card-foreground: #15181c;
+  --color-fd-border: #e6e2d8;
+  --color-fd-primary: #3b5bdb;
+  --color-fd-primary-foreground: #ffffff;
+  --color-fd-secondary: #efece4;
+  --color-fd-secondary-foreground: #15181c;
+  --color-fd-accent: #efece4;
+  --color-fd-accent-foreground: #15181c;
+  --color-fd-ring: #3b5bdb;
+  --color-fd-overlay: hsla(0, 0%, 0%, 0.18);
+}
+
+/* Dark mode keeps fumadocs' neutral defaults — readers expect docs sites
+   to honor their system preference, and our landing only ships light. */

app/layout.config.tsx

@@ -1,7 +1,50 @@
 import type { BaseLayoutProps } from 'fumadocs-ui/layouts/shared';
 
+// Molecule logo — the same triangle-of-nodes mark used on moleculesai.app.
+// Inlined as a JSX element so fumadocs renders it in the topbar without a
+// separate asset request.
+const MoleculeLogo = (
+  <svg
+    width="22"
+    height="22"
+    viewBox="0 0 28 28"
+    fill="none"
+    aria-hidden="true"
+  >
+    <circle cx="14" cy="6" r="2.5" fill="currentColor" />
+    <circle cx="6" cy="20" r="2.5" fill="currentColor" />
+    <circle cx="22" cy="20" r="2.5" fill="currentColor" />
+    <circle
+      cx="14"
+      cy="14"
+      r="1.6"
+      fill="none"
+      stroke="currentColor"
+      strokeWidth="1.2"
+    />
+    <line x1="14" y1="8.5" x2="14" y2="12.6" stroke="currentColor" strokeWidth="1.2" />
+    <line x1="8" y1="18.5" x2="12.7" y2="14.8" stroke="currentColor" strokeWidth="1.2" />
+    <line x1="20" y1="18.5" x2="15.3" y2="14.8" stroke="currentColor" strokeWidth="1.2" />
+  </svg>
+);
+
 export const baseOptions: BaseLayoutProps = {
   nav: {
-    title: 'Molecule AI',
+    title: (
+      <span className="flex items-center gap-2 font-semibold tracking-tight">
+        {MoleculeLogo}
+        <span>Molecule AI</span>
+        <span className="text-xs uppercase tracking-[0.08em] text-fd-muted-foreground font-mono">
+          Docs
+        </span>
+      </span>
+    ),
+    url: 'https://doc.moleculesai.app',
   },
+  links: [
+    { text: 'Platform', url: 'https://app.moleculesai.app', external: true },
+    { text: 'Marketplace', url: 'https://market.moleculesai.app', external: true },
+    { text: 'Landing', url: 'https://www.moleculesai.app', external: true },
+  ],
+  githubUrl: 'https://github.com/Molecule-AI',
 };

app/layout.tsx

@@ -1,10 +1,16 @@
 import './global.css';
 import { RootProvider } from 'fumadocs-ui/provider/next';
-import { Inter } from 'next/font/google';
+import { Geist, JetBrains_Mono } from 'next/font/google';
 import type { ReactNode } from 'react';
 
-const inter = Inter({
+const geist = Geist({
   subsets: ['latin'],
+  variable: '--font-geist',
+});
+
+const jetbrains = JetBrains_Mono({
+  subsets: ['latin'],
+  variable: '--font-mono',
 });
 
 export const metadata = {
@@ -19,8 +25,12 @@ export const metadata = {
 
 export default function Layout({ children }: { children: ReactNode }) {
   return (
-    <html lang="en" className={inter.className} suppressHydrationWarning>
+    <html
-      <body className="flex flex-col min-h-screen">
+      lang="en"
+      className={`${geist.variable} ${jetbrains.variable}`}
+      suppressHydrationWarning
+    >
+      <body className="flex flex-col min-h-screen font-sans">
         <RootProvider>{children}</RootProvider>
       </body>
     </html>

content/docs/agent-runtime/workspace-runtime.md

@@ -73,6 +73,72 @@ At a high level, `workspace/main.py` does this:
 10. Start the skill watcher when skills are configured.
 11. Serve the A2A app through Uvicorn.
 
+## Boot-Smoke Contract (`MOLECULE_SMOKE_MODE`)
+
+The image-publish CI pipeline runs each template's image with `MOLECULE_SMOKE_MODE=1` to exercise lazy imports inside `executor.execute()` against stub credentials and no network. The runtime detects the env var, invokes `executor.execute()` once with a stubbed `RequestContext` and a short timeout, then exits — registration, heartbeats, and the A2A server are skipped.
+
+This catches lazy imports that pure `python3 -c "import adapter"` smokes miss: imports nested inside `if`-branches, deferred until first call, or behind `importlib.import_module()`.
+
+### What adapter authors need to do
+
+**Most adapters need to do nothing.** If `setup()` only writes files, parses config, or instantiates Python objects, the smoke gate just works.
+
+**Adapters whose `setup()` does real I/O must opt out of that I/O under smoke mode.** This applies to:
+
+- spawning subprocesses that require valid credentials (e.g. a gateway daemon)
+- making real network calls
+- writing to filesystem locations that need a specific uid/gid the smoke harness can't guarantee
+
+The contract:
+
+```python
+async def setup(self, config: AdapterConfig) -> None:
+    if os.environ.get("MOLECULE_SMOKE_MODE") == "1":
+        return  # skip real I/O; runtime's smoke short-circuit handles the rest
+    # ... real setup ...
+```
+
+For shell entrypoints that wrap `molecule-runtime`:
+
+```bash
+if [ "${MOLECULE_SMOKE_MODE:-0}" = "1" ]; then
+  exec molecule-runtime
+fi
+```
+
+### What gets exercised under smoke mode
+
+- All `/app/*.py` modules import cleanly (covered by a separate static-import smoke step)
+- `adapter.setup()` runs (with the opt-out above for I/O-heavy adapters)
+- `adapter.create_executor()` runs
+- `executor.execute()` is invoked once against a stub `RequestContext`/`EventQueue` with `MOLECULE_SMOKE_TIMEOUT_SECS` (default 5s); a clean timeout exits 0, an import error exits non-zero
+
+### What the gate does NOT prove
+
+A green gate means **"imports are healthy enough that `executor.execute()` reaches its body"** — that's the regression class the gate exists to catch (lazy `from x import y` inside an `if`-branch, or `importlib.import_module()` on a path that breaks after a wheel bump).
+
+It does **not** prove that `execute()` produces the right output for real input. The harness reports PASS in three distinct cases:
+
+1. **Clean return** — execute() ran to completion within the timeout.
+2. **Timeout** — execute() was still running when the timer fired (typical for adapters that do real I/O inside execute(): subprocess to a gateway, httpx call to an upstream LLM).
+3. **Any non-import exception** — execute() raised `RuntimeError`, auth errors, validation errors, etc. The harness only fails on `ImportError`/`ModuleNotFoundError`.
+
+The stub `RequestContext` carries a non-empty `"smoke test"` text message (so adapters relying on `extract_message_text(ctx)` returning input still work), and the harness never drains the `EventQueue` — what `execute()` writes back is ignored.
+
+If you need correctness coverage, write a separate integration test that runs the workspace against real or mocked infrastructure — the smoke gate is a strict subset.
+
+### Stub env the smoke harness sets
+
+| Var | Value |
+|---|---|
+| `MOLECULE_SMOKE_MODE` | `1` |
+| `MOLECULE_SMOKE_TIMEOUT_SECS` | `10` (CI default) |
+| `WORKSPACE_ID` | `fake-smoke` |
+| `PYTHONPATH` | `/app` (mirrors the platform provisioner) |
+| `CLAUDE_CODE_OAUTH_TOKEN`, `ANTHROPIC_API_KEY`, `GEMINI_API_KEY`, `OPENAI_API_KEY` | `sk-fake-smoke-*` |
+
+A `config.yaml` from the template repo's root is mounted at `/configs/config.yaml`.
+
 ## Core Runtime Pieces
 
 | File | Responsibility |

content/docs/architecture/staging-environment.md

@@ -27,7 +27,8 @@ CP (Railway):       staging service                 production service
                     staging.api.moleculesai.app     api.moleculesai.app
 
 Tenant EC2s:        staging EC2 instances            production EC2 instances
-                    *.staging.moleculesai.app        *.moleculesai.app
+                    <slug>.staging.moleculesai.app   <slug>.moleculesai.app
+                    (per-tenant CNAME, no wildcard)  (per-tenant CNAME, no wildcard)
 
 App (Vercel):       staging.app.moleculesai.app     app.moleculesai.app
                     (Vercel preview)                 (Vercel production)
@@ -38,8 +39,10 @@ DB (Neon):          staging branch                   main branch
 Docker images:      platform-tenant:staging          platform-tenant:latest
                     (GHCR)                           (GHCR)
 
-Cloudflare:         *.staging.moleculesai.app        *.moleculesai.app
+Cloudflare:         per-tenant CNAMEs under          per-tenant CNAMEs under
-                    (separate tunnel/worker)         (tunnel per tenant)
+                    staging.moleculesai.app          moleculesai.app
+                    (one CNAME + one tunnel          (one CNAME + one tunnel
+                     per provisioned tenant)          per provisioned tenant)
 ```
 
 ## Deploy flow
@@ -115,15 +118,35 @@ platform-tenant:sha-xxxxx  — immutable, pinned to specific commit
 #       pushes :latest only on manual promote
 ```
 
-### 5. Cloudflare: staging subdomain
+### 5. Cloudflare: per-tenant CNAMEs (no wildcard)
 
-Option A (simple): `*.staging.moleculesai.app` with its own tunnel/worker
+There is **no `*.staging.moleculesai.app` wildcard record** and there is no
-Option B (full): separate Cloudflare zone for staging (overkill)
+`*.moleculesai.app` wildcard either. The control plane writes a per-tenant
+CNAME at provision time, pointing `<slug>.<env-domain>` at that tenant's
+Cloudflare tunnel (`<tunnel-id>.cfargotunnel.com`).
 
-Recommend Option A:
+Verified in `molecule-controlplane/internal/provisioner/ec2.go` — the
-- Add `staging.moleculesai.app` DNS records
+provisioner calls `Tunnel.CreateTunnelDNS(ctx, slug, domain, tunnelID)`
-- Staging tenants get `slug.staging.moleculesai.app` subdomains
+during workspace provision, then records a `cf_dns` row in
-- Production tenants get `slug.moleculesai.app` (unchanged)
+`tenant_resources` with `type=CNAME` for symmetric create/delete audit.
+
+Implications for staging:
+
+- Staging tenants get `<slug>.staging.moleculesai.app` only **after** they
+  are provisioned through the staging control plane. The CNAME is
+  written as part of `Provision()`.
+- Production tenants get `<slug>.moleculesai.app` the same way, against
+  the production CP.
+- Pre-provision, an unknown slug returns **NXDOMAIN**. This is correct
+  behavior, not a regression — there is no wildcard to catch the lookup.
+- Tests that hit a staging slug they have not provisioned themselves
+  will fail with `getaddrinfo ENOTFOUND` (Node) or `Name or service not
+  known` (curl). The fix is to provision your own slug against the
+  staging CP first; do not file this as an infrastructure bug.
+
+The same model applies to both environments — the only difference is
+the parent zone (`staging.moleculesai.app` vs `moleculesai.app`) and the
+CP that writes the records.
 
 ### 6. EC2: staging tag
 

content/docs/external-agents.mdx

@@ -21,6 +21,17 @@ register and heartbeat by hand. Use it when your agent can't run an MCP
 stdio server.
 </Callout>
 
+## Pick the right path
+
+| Your agent runs as | Best path | Why |
+|---|---|---|
+| **An MCP-aware runtime** (Claude Code, Hermes, OpenCode, Cursor, Cline) | [Bring Your Own Runtime (MCP)](/docs/runtime-mcp) | Universal `molecule-mcp` wheel — no HTTP server, no tunnel. |
+| **A Claude Code session on your laptop** | [Claude Code Channel Plugin](/docs/guides/claude-code-channel-plugin) | Polling-based; no tunnel/public URL needed. Set up in under a minute. |
+| Any HTTP server with a public URL | The flow on this page (or the [Python SDK guide](/docs/guides/external-agent-registration)) | Push-based; lower latency; works for any A2A-compatible HTTP endpoint. |
+| A custom A2A server you wrote yourself | The flow on this page | Direct register + heartbeat + handler. |
+
+The rest of this doc covers the third + fourth rows. For Claude Code or other MCP runtimes, follow the linked guides.
+
 ## Prerequisites
 
 - A running Molecule AI platform (default `http://localhost:8080`)

content/docs/guides/claude-code-channel-plugin.md

@@ -0,0 +1,222 @@
+---
+title: "Claude Code Channel Plugin — Connect a Claude Code Session as an External Workspace"
+description: "Bridge Molecule A2A traffic into a running Claude Code session via MCP. Polling-based, no tunnel required. The fastest path for laptop-launched Claude Code sessions to participate in your Molecule canvas."
+---
+
+# Claude Code Channel Plugin
+
+Run [Claude Code](https://claude.com/claude-code) on your laptop and have it appear on the Molecule AI canvas as a first-class external workspace. Inbound A2A messages from peer workspaces surface as conversation turns; replies route back through Molecule's A2A endpoints.
+
+> **What this is:** [`Molecule-AI/molecule-mcp-claude-channel`](https://github.com/Molecule-AI/molecule-mcp-claude-channel) — an MCP-based "channel plugin" that turns a Claude Code session into a Molecule workspace.
+
+> **What this is NOT:** the [Python SDK / curl register flow](/docs/guides/external-agent-registration) for arbitrary HTTP-speaking agents. That flow needs a public URL the platform can POST to. This one polls — runs on any laptop behind any NAT.
+
+---
+
+## What you get
+
+```
+Molecule peer ──A2A──▶ [your workspace] ──poll──▶ [plugin] ──MCP notification──▶ Claude Code
+                              ▲                                                       │
+                              └────── POST /workspaces/:id/a2a ◄── reply_to_workspace ──┘
+```
+
+| Property | Value |
+|---|---|
+| **Inbound latency** | up to `MOLECULE_POLL_INTERVAL_MS` (default 5s) |
+| **Outbound latency** | direct POST — sub-second |
+| **Tunnel / public URL** | not required |
+| **Auth model** | per-workspace bearer token (same as Python SDK) |
+| **Multi-workspace** | yes, comma-separated list |
+
+---
+
+## Prerequisites
+
+| You need | Notes |
+|---|---|
+| A Molecule AI tenant | Self-hosted localhost or your `*.staging.moleculesai.app` SaaS tenant |
+| One or more workspace IDs | Created via canvas or `POST /workspaces` (see [External Agent Registration](/docs/guides/external-agent-registration)) |
+| The workspace bearer token | Shown once when the workspace is created — save it from the canvas modal |
+| Claude Code | `claude` CLI ≥ the version that supports `--channels` |
+| `bun` | The plugin runs under bun for fast startup; `bun install` is invoked automatically by `start` |
+
+> **Note:** The platform must be running molecule-core ≥ PR #2300, which shipped the `?since_secs=` query parameter on `GET /workspaces/:id/activity`. Available on all staging-onward and self-hosted main builds after 2026-04-29.
+
+---
+
+## Step 1 — Create the workspace
+
+In your Molecule canvas:
+
+1. Click **+ New workspace**
+2. Choose **External** runtime
+3. Set tier as needed; click **Create**
+4. The "Connect your external agent" modal opens — switch to the **Claude Code** tab
+5. Copy the entire snippet (everything from the `mkdir -p` line through `claude --channels ...`)
+
+Or via API:
+
+```bash
+curl -X POST "$MOLECULE_PLATFORM_URL/workspaces" \
+  -H "Content-Type: application/json" \
+  -d '{"name": "My Claude Code", "external": true, "tier": 2}'
+```
+
+The response includes `claude_code_channel_snippet` — same content as the canvas tab, ready to paste.
+
+## Step 2 — Set up the channel config
+
+Run the snippet from Step 1. It does two things:
+
+```bash
+mkdir -p ~/.claude/channels/molecule
+cat > ~/.claude/channels/molecule/.env <<'EOF'
+MOLECULE_PLATFORM_URL=https://your-tenant.staging.moleculesai.app
+MOLECULE_WORKSPACE_IDS=ws-uuid-1
+MOLECULE_WORKSPACE_TOKENS=<paste auth_token from create response>
+EOF
+chmod 600 ~/.claude/channels/molecule/.env
+```
+
+Replace the token placeholder with the workspace bearer from Step 1.
+
+## Step 3 — Launch Claude Code
+
+```bash
+claude --channels plugin:molecule@Molecule-AI/molecule-mcp-claude-channel
+```
+
+You should see on stderr (use `--debug` to surface):
+
+```
+molecule channel: connected — watching 1 workspace(s) at https://your-tenant.staging.moleculesai.app
+  workspaces: ws-uuid-1
+  poll: every 5000ms with 30s window
+```
+
+That's it — the workspace is live on the canvas with a purple **REMOTE** badge, and any A2A traffic the workspace receives surfaces as conversation turns in your Claude Code session.
+
+---
+
+## How replies work
+
+When a peer's message lands in your session, you'll see a turn with structured metadata:
+
+```json
+{
+  "method": "notifications/claude/channel",
+  "params": {
+    "content": "Hey, can you take a look at this? <issue body>",
+    "meta": {
+      "source": "molecule",
+      "workspace_id": "ws-uuid-1",
+      "peer_id": "ws-uuid-pm-coordinator",
+      "method": "user_message",
+      "activity_id": "act-...",
+      "ts": "2026-04-29T..."
+    }
+  }
+}
+```
+
+Reply normally — Claude calls the `reply_to_workspace` MCP tool with `peer_id` from the meta block, and the response flows back through `POST /workspaces/:peer_id/a2a` so peers see it just like any other A2A message.
+
+---
+
+## Multi-workspace setup
+
+Watch multiple workspaces from a single Claude Code session by comma-separating the lists. Both must have the same length and order:
+
+```bash
+MOLECULE_WORKSPACE_IDS=ws-pm,ws-researcher,ws-engineer
+MOLECULE_WORKSPACE_TOKENS=tok-pm,tok-researcher,tok-engineer
+```
+
+When Claude replies, the `reply_to_workspace` tool requires `workspace_id` (which of the watched workspaces to reply AS) explicitly. With a single workspace it's implicit.
+
+---
+
+## Configuration reference
+
+| Variable | Default | Purpose |
+|---|---|---|
+| `MOLECULE_PLATFORM_URL` | (required) | Tenant base URL (no trailing slash) |
+| `MOLECULE_WORKSPACE_IDS` | (required) | Comma-separated workspace UUIDs to watch |
+| `MOLECULE_WORKSPACE_TOKENS` | (required) | Comma-separated bearer tokens, **same order as IDs** |
+| `MOLECULE_POLL_INTERVAL_MS` | `5000` | How often each workspace is polled (ms) |
+| `MOLECULE_POLL_WINDOW_SECS` | `30` | `since_secs` window per poll. Wider than interval to recover from missed ticks |
+| `MOLECULE_STATE_DIR` | `~/.claude/channels/molecule` | Override state directory (testing) |
+
+---
+
+## Architecture notes
+
+### Why polling instead of push?
+
+The [Python SDK external-agent flow](/docs/guides/external-agent-registration) uses **push**: register an inbound URL, platform POSTs A2A to that URL. Lower latency but requires a tunnel (ngrok / Cloudflare) or static IP — non-trivial for laptop sessions.
+
+This plugin uses **polling** as the default because it works through every NAT/firewall with zero infra. Cost: up to `MOLECULE_POLL_INTERVAL_MS` of inbound latency. For production setups where lower latency matters, push mode is on the v0.2 roadmap.
+
+### Why the 30s window over a 5s interval?
+
+A single missed tick (transient network blip, GC pause, laptop sleep) shouldn't lose messages. The plugin re-fetches the last 30 seconds on every poll and dedups by `activity_id`, so 25 seconds of overlap is the recovery margin. Increase `MOLECULE_POLL_WINDOW_SECS` for noisier networks.
+
+### Singleton lock
+
+Only one channel server runs per host — multiple instances would race the dedup state and double-deliver. The plugin maintains a PID file at `~/.claude/channels/molecule/bot.pid` and on startup kills any stale predecessor. This mirrors the [`@claude-plugins-official/telegram`](https://github.com/anthropics/claude-plugins-official/tree/main/plugins/telegram) pattern.
+
+---
+
+## Troubleshooting
+
+### "molecule channel: required config missing"
+
+The plugin started before you filled in `.env`. Re-run the snippet from Step 2, then re-launch Claude Code.
+
+### "molecule channel: poll `<ws-id>` returned 401"
+
+Bearer token mismatch. Two common causes:
+
+- The token in `MOLECULE_WORKSPACE_TOKENS` doesn't match the workspace whose ID is in the corresponding position of `MOLECULE_WORKSPACE_IDS`. Verify same-order pairing.
+- The workspace was rotated and the token was revoked. Generate a new token from the canvas Settings tab (or `POST /admin/workspaces/:id/tokens`).
+
+### "molecule channel: poll `<ws-id>` returned 404"
+
+Either the workspace doesn't exist or the `MOLECULE_PLATFORM_URL` is wrong. Confirm:
+
+```bash
+curl -fsS "$MOLECULE_PLATFORM_URL/workspaces/$WS_ID" \
+  -H "Authorization: Bearer $WS_TOKEN" | jq '.workspace.id'
+```
+
+### A2A messages aren't surfacing
+
+Check that the watched workspace is actually receiving them — the plugin only pulls `activity_logs` rows whose `activity_type = a2a_receive`. If peers aren't sending to this workspace, there's nothing to surface. Verify with:
+
+```bash
+curl -fsS "$MOLECULE_PLATFORM_URL/workspaces/$WS_ID/activity?type=a2a_receive&limit=10" \
+  -H "Authorization: Bearer $WS_TOKEN" | jq
+```
+
+If that returns events but Claude doesn't see them, file an issue at [`Molecule-AI/molecule-mcp-claude-channel`](https://github.com/Molecule-AI/molecule-mcp-claude-channel/issues) with the workspace_id + sample event.
+
+---
+
+## Limitations (v0.1)
+
+- **Polling-only inbound.** No push mode yet; latency floor is `MOLECULE_POLL_INTERVAL_MS`.
+- **No pairing flow.** Tokens are configured manually via `.env`; no canvas-side approval handshake.
+- **No file-attachment download.** URLs surface in the meta block; the host fetches on-demand.
+- **No outbound channel-init.** The plugin only sends replies (in response to inbound A2A); starting a fresh A2A conversation initiated FROM the Claude Code side requires a future `start_workspace_chat` tool.
+
+Track the v0.2 roadmap on the [plugin repo's README](https://github.com/Molecule-AI/molecule-mcp-claude-channel#limitations-v01).
+
+---
+
+## See also
+
+- [External Agent Registration](/docs/guides/external-agent-registration) — full A2A wire-shape reference + Python SDK + curl flow
+- [External Workspace Quickstart](/docs/guides/external-workspace-quickstart) — 5-min guide for any HTTP-speaking agent
+- [Remote Workspaces FAQ](/docs/guides/remote-workspaces-faq) — production hardening notes
+- [`Molecule-AI/molecule-mcp-claude-channel`](https://github.com/Molecule-AI/molecule-mcp-claude-channel) — plugin source code, issues, v0.2 roadmap

content/docs/guides/external-workspace-quickstart.md

@@ -9,6 +9,8 @@ Run an agent on your laptop, a home server, a cloud VM, or any machine with inte
 
 > **Looking for the operator-focused reference?** See [External Agent Registration](/docs/guides/external-agent-registration) for full capability + auth details, or [Remote Workspaces FAQ](/docs/guides/remote-workspaces-faq) for hardening + production notes. This doc is the fast path.
 
+> **Running Claude Code on your laptop?** Skip this guide — use the [Claude Code Channel Plugin](/docs/guides/claude-code-channel-plugin) instead. It's polling-based and needs no tunnel, so your laptop session shows up on the canvas in under a minute.
+
 ---
 
 ## What is an "external workspace"?

content/docs/marketplace.mdx

@@ -0,0 +1,166 @@
+---
+title: Marketplace
+description: A tiered library of plugins, agents, and bundles you can mount into any Molecule workspace.
+---
+
+## Overview
+
+The Molecule **Marketplace** is the distribution surface for reusable agent
+infrastructure. It surfaces three tiers of artifacts — from a single MCP
+plugin to a full team topology — and the same governance, memory, and audit
+substrate runs underneath each one.
+
+You browse and install via the Marketplace UI at
+[`https://moleculesai.app`](https://moleculesai.app), or pin entries from
+your `workspace.yaml` for reproducible deployments.
+
+---
+
+## Three Tiers
+
+| Tier | Name | Granularity | Mount as |
+|------|------|-------------|----------|
+| **L1** | Plugins | A single MCP server / tool pack | Tool capability on an agent or workspace |
+| **L2** | Agents | A prebuilt single-agent skill (prompts + tools + policy) | Workspace member |
+| **L3** | Bundles | A full team topology (root + children with their own scopes) | Workspace |
+
+The tier model is intentionally additive — an L3 Bundle is composed of L2
+Agents, which in turn use L1 Plugins. Forking a Bundle gives you the lineage
+to swap any constituent piece without rewiring the operating model.
+
+### L1 — Plugins
+
+Plugins are MCP servers or agentskills.io packs. Examples:
+
+- `postgres` — read/write Postgres with role-scoped credentials
+- `slack` — post and search Slack with workspace-scoped tokens
+- `linear` — create / triage / comment on Linear issues
+- `gh-actions` — query and dispatch GitHub Actions runs
+- `sentry` — read incident timeline, ack alerts
+
+Plugins follow the [two-axis source/shape model](/docs/plugins) and install
+from either a curated `local://` source or a pinned `github://owner/repo#tag`.
+
+### L2 — Agents
+
+Agents are single-purpose skills mounted as a workspace member. They ship with:
+
+- A **system prompt** baked in
+- A **tool manifest** specifying which L1 plugins they require
+- A **policy** declaring scope reads/writes and approval requirements
+
+Examples:
+
+- `code-reviewer` — five-axis review, posts inline comments via `gh-actions`
+- `oncall-triager` — reads Sentry, drafts a runbook step, requests approval before paging
+- `churn-analyst` — periodic Postgres + Stripe rollup, posts a weekly Slack summary
+
+Mount an agent via the workspace UI or `workspace.yaml`:
+
+```yaml
+members:
+  - kind: agent
+    source: marketplace://l2/code-reviewer
+    version: ^1.2.0
+    scopes:
+      - read: pull_requests
+      - write: pull_request_comments
+```
+
+### L3 — Bundles
+
+Bundles are complete team topologies. A bundle ships:
+
+- A **root agent** that coordinates the team
+- One or more **child agents**, each with its own scope, memory, and tool
+  list
+- A **policy graph** declaring which scopes the root can write through and
+  which approvals route to humans
+
+Examples:
+
+- `growth-team` — root strategist + content-writer + analytics-rollup +
+  experiment-designer
+- `platform-ops` — root SRE + on-call triager + change-reviewer +
+  incident-scribe
+- `revenue-pod` — root commercial lead + churn-analyst + cs-summarizer +
+  expansion-prospector
+
+Mount a bundle as a workspace:
+
+```yaml
+workspace:
+  bundle: marketplace://l3/platform-ops
+  bundle_version: ^0.4.0
+  overrides:
+    members:
+      change-reviewer:
+        scopes:
+          - read: ["github:Molecule-AI/*", "linear:eng"]
+```
+
+Forking is encouraged — the bundle author publishes the operating model;
+your team tunes it for your processes without rebuilding the substrate.
+
+---
+
+## Trust Tiers
+
+Every Marketplace entry carries a **trust tier** that signals review depth
+and supply-chain provenance:
+
+| Trust | Vetting | Provenance |
+|-------|---------|------------|
+| **Verified** | Reviewed by Molecule for safety, prompt-injection resistance, and policy correctness | Published from a Molecule-controlled identity |
+| **Partner** | Reviewed by a Marketplace partner; carries the partner's identity badge | Published from a verified partner account |
+| **Community** | Self-published; static analysis + sandbox runtime; no human review | Pinned to a specific commit SHA |
+
+The trust tier is shown on every listing card and gated by enterprise
+policy: organizations on the Enterprise plan can restrict installs to
+Verified-only via `policy.marketplace.min_trust = verified`.
+
+---
+
+## Installing from the Marketplace
+
+Browse listings at [`https://moleculesai.app`](https://moleculesai.app).
+Each card shows tier (L1/L2/L3), trust badge, runtime compatibility, and
+required scopes. The "Install" flow:
+
+1. Picks a workspace (or creates a new one) to mount into.
+2. Surfaces required scopes for review and approval.
+3. Pins to a specific version (semver range, exact tag, or commit SHA).
+4. Writes the entry into your `workspace.yaml` and triggers a workspace
+   redeploy.
+
+You can also install non-interactively:
+
+```bash
+curl -X POST https://app.moleculesai.app/cp/orgs/$ORG/marketplace/install \
+  -H "Authorization: Bearer $CP_ADMIN_API_TOKEN" \
+  -H "Content-Type: application/json" \
+  -d '{
+    "tier": "l2",
+    "slug": "code-reviewer",
+    "version": "^1.2.0",
+    "workspace_id": "ws_abc123"
+  }'
+```
+
+---
+
+## Listing on the Marketplace
+
+If you have built reusable agent infrastructure — a plugin, agent, or
+bundle — you can list it on the Marketplace and reach every Molecule
+organization. See [Listing on the Marketplace](/docs/marketplace/creators)
+for the full builder workflow.
+
+---
+
+## See also
+
+- [Plugins](/docs/plugins) — L1 source/shape model and install mechanics
+- [External Agents](/docs/external-agents) — bringing a non-Molecule agent runtime
+- [Workspace Configuration](/docs/workspace-config) — `workspace.yaml` reference
+- [Listing on the Marketplace](/docs/marketplace/creators) — builder workflow

content/docs/marketplace/creators.mdx

@@ -0,0 +1,164 @@
+---
+title: Listing on the Marketplace
+description: How builders ship plugins, agents, and bundles to every Molecule organization.
+---
+
+## Overview
+
+The Marketplace is open to external builders. If you have authored reusable
+agent infrastructure — an MCP plugin, a single-agent skill, or a full team
+bundle — you can list it and reach every Molecule organization. We handle
+distribution, billing, and policy; you keep the IP and the upgrade cadence.
+
+This page walks through the three-step workflow: **Build · List · Earn**.
+
+---
+
+## 1. Build
+
+You author your artifact against the open Molecule SDK. The same primitives
+we use internally are available to you:
+
+- **Workspace** — the durable boundary for memory, members, and policy
+- **A2A** — agent-to-agent messaging, used to talk to runtimes you don't
+  own (LangGraph, CrewAI, etc.)
+- **Memory scopes** — hierarchical, governance-aware persistence
+- **Audit** — every action is captured at the orchestration layer
+
+Pick the tier that matches your artifact's granularity:
+
+### L1 — Plugins
+
+A plugin is an MCP server (or an agentskills.io pack). The
+[two-axis source/shape model](/docs/plugins) describes how the workspace
+runtime loads it. Authoring requirements:
+
+- A `plugin.yaml` manifest declaring tools, required scopes, and runtime
+  compatibility.
+- A README documenting the tool surface and side effects.
+- For MCP plugins: an HTTP or stdio MCP server pinned to a tagged commit.
+
+A reference plugin lives at
+[`Molecule-AI/molecule-ai-plugin-template`](https://github.com/Molecule-AI/molecule-ai-plugin-template).
+
+### L2 — Agents
+
+An agent is a single workspace member with a baked-in prompt + tools +
+policy. Authoring requirements:
+
+- An `agent.yaml` manifest declaring system prompt, required L1 plugins,
+  scope reads/writes, and approval triggers.
+- A `prompts/` directory with the system prompt and any reusable templates.
+- A `tests/` directory exercising the prompt against canned scenarios.
+
+Reference: [`Molecule-AI/molecule-ai-agent-template`](https://github.com/Molecule-AI/molecule-ai-agent-template).
+
+### L3 — Bundles
+
+A bundle ships a complete team topology — a root agent plus children, each
+with its own scope and memory. Authoring requirements:
+
+- A `bundle.yaml` declaring members, their scopes, and the policy graph
+  (which scopes the root can write through, which approvals route to
+  humans).
+- A `members/` directory containing member-specific overrides if any
+  member is a fork of an L2 agent.
+- A `topology.svg` diagram (auto-rendered from `bundle.yaml`, but you can
+  override).
+
+Reference: [`Molecule-AI/molecule-ai-bundle-template`](https://github.com/Molecule-AI/molecule-ai-bundle-template).
+
+---
+
+## 2. List
+
+Submit through the **Creator Portal** at
+[`https://moleculesai.app/creators`](https://moleculesai.app/creators).
+The submission flow:
+
+1. **Connect** — link the GitHub repository hosting your artifact. We pull
+   from tagged releases; we never re-tag or modify your code.
+2. **Manifest check** — we validate `plugin.yaml` / `agent.yaml` /
+   `bundle.yaml` against the schema for your tier and surface any gaps.
+3. **Static analysis** — credential-shape scan, prompt-injection-pattern
+   scan, and dependency vulnerability check on every tagged release.
+4. **Sandbox boot** — your artifact is mounted into a throwaway workspace
+   to verify it boots, declares its scopes correctly, and surfaces a
+   reasonable error path.
+5. **Trust tier** — every artifact starts at **Community**. Apply for
+   **Partner** or **Verified** review once you have a couple of releases
+   under your belt.
+
+Pricing is configured at submission:
+
+- **Free** — no charge to install.
+- **Per-seat** — a flat monthly amount per workspace member that mounts
+  the artifact.
+- **Per-use** — metered against a unit you define (token calls, runs,
+  alerts handled).
+- **Hybrid** — base seat fee plus metered overages.
+
+You can change pricing on subsequent releases; existing installs are
+grandfathered to the version they pinned.
+
+---
+
+## 3. Earn
+
+Once your listing is live, you receive:
+
+- **Distribution** — every Molecule organization sees your listing in the
+  Marketplace UI, gated only by their policy (`min_trust`, region, etc.).
+- **Billing** — Molecule handles the charge to the installing
+  organization, deducts the platform fee (15% as of writing; check the
+  current rate in the Creator Portal), and pays out monthly.
+- **Audit visibility** — you see install counts, version distribution,
+  and aggregated usage metrics in the Creator Portal. You do **not** see
+  per-organization data.
+- **Upgrade cadence** — semver: bump tags, organizations on a `^range`
+  pin pull updates on their next workspace redeploy. Major bumps require
+  re-approval of any new scopes.
+
+---
+
+## Policy & Safety
+
+By listing, you agree to:
+
+- **No exfiltration** — your code does not transmit organization data
+  outside the scopes it declares.
+- **Pinned releases** — every version is pinned to an immutable commit;
+  retagging is not permitted.
+- **Disclose model usage** — if your agent calls an LLM API, declare the
+  provider and model so enterprise plans can route through their own
+  keys.
+- **Respect approval triggers** — if your `agent.yaml` declares a scope
+  that requires human approval (e.g. `write: pull_request_merge`), you
+  must call the approval API before acting.
+
+Listings that violate these terms are de-listed; refunds for affected
+installs are paid from your account.
+
+---
+
+## Maintenance
+
+Once a listing is live, you can:
+
+- Push new tagged releases — they enter the static-analysis + sandbox
+  flow automatically.
+- Mark older versions as **deprecated** to nudge installs to upgrade.
+- File **security advisories** that surface to every organization on a
+  vulnerable pinned version.
+- Yank a release in the rare case of a critical bug; organizations
+  pinned to the yanked tag are notified and offered the next safe version.
+
+---
+
+## See also
+
+- [Marketplace](/docs/marketplace) — tier model and installation overview
+- [Plugins](/docs/plugins) — L1 plugin source/shape mechanics
+- [Workspace Configuration](/docs/workspace-config) — pinning marketplace
+  entries in `workspace.yaml`
+- [Security » OWASP Agentic Top 10](/docs/security/owasp-agentic-top-10) — supply-chain considerations relevant to bundle authors

content/docs/meta.json

@@ -20,6 +20,9 @@
     "self-hosting/admin-token",
     "observability",
     "troubleshooting",
+    "---Marketplace---",
+    "marketplace",
+    "marketplace/creators",
     "---Security---",
     "security/index",
     "security/safe-mcp-advisory",

content/docs/quickstart.md

@@ -11,8 +11,8 @@ Get a Molecule AI workspace running in under five minutes.
 ## 1. Install Molecule AI
 
 ```bash
-git clone https://github.com/Molecule-AI/molecule-core.git
+git clone https://github.com/Molecule-AI/molecule-monorepo.git
-cd molecule-core
+cd molecule-monorepo
 docker compose up -d
 ```
 
@@ -78,4 +78,4 @@ Or type `/ask what's our deployment status?` in your connected Discord channel.
 - [Review the REST API reference](/docs/guides/org-api-keys)
 - [Browse all guides](/docs/guides)
 
-Explore the [GitHub repo](https://github.com/Molecule-AI/molecule-core) for self-hosting options, or visit [moleculesai.app](https://moleculesai.app) for the hosted platform.
+Explore the [GitHub repo](https://github.com/Molecule-AI/molecule-monorepo) for self-hosting options, or visit [moleculesai.app](https://moleculesai.app) for the hosted platform.

content/docs/runtime-mcp.mdx

@@ -52,14 +52,54 @@ set.
 
 ### Claude Code
 
+Two equivalent paths — pick whichever your version supports.
+
+**CLI (Claude Code 2.1+):** pass each env var with `-e`, scope with
+`-s user` so the server is available in every project, and put the
+command after `--`:
+
 ```bash
-claude mcp add molecule -s user -- env \
+claude mcp add molecule -s user \
-  WORKSPACE_ID=<your-workspace-uuid> \
+  -e WORKSPACE_ID=<your-workspace-uuid> \
-  PLATFORM_URL=https://<your-tenant>.moleculesai.app \
+  -e PLATFORM_URL=https://<your-tenant>.moleculesai.app \
-  MOLECULE_WORKSPACE_TOKEN=<your-token> \
+  -e MOLECULE_WORKSPACE_TOKEN=<your-token> \
-  molecule-mcp
+  -- molecule-mcp
 ```
 
+<Callout type="info">
+Older docs used a `-- env VAR=val ... molecule-mcp` shell trick (with
+`env` as the command). It still works but produces a less idiomatic
+`~/.claude.json` entry and trips up the post-2.1 flag parser if you
+forget the `--`. Prefer the `-e` form above.
+</Callout>
+
+**Direct edit of `~/.claude.json`:** add the entry under the **top-level
+`mcpServers` key** (this is the user-scope location — available in
+every project). If you'd rather scope it to a single project, use a
+`.mcp.json` file in that project's root with the same `mcpServers`
+shape.
+
+```json
+{
+  "mcpServers": {
+    "molecule": {
+      "type": "stdio",
+      "command": "molecule-mcp",
+      "args": [],
+      "env": {
+        "WORKSPACE_ID": "<your-workspace-uuid>",
+        "PLATFORM_URL": "https://<your-tenant>.moleculesai.app",
+        "MOLECULE_WORKSPACE_TOKEN": "<your-token>"
+      }
+    }
+  }
+}
+```
+
+If `molecule-mcp` isn't on the PATH that Claude Code sees (common on
+macOS — see [Troubleshooting](#command-not-found-molecule-mcp-from-inside-the-runtime)),
+replace `"command": "molecule-mcp"` with the absolute path from `which molecule-mcp`.
+
 Reconnect with `/mcp` (or restart the Claude Code session) and the tools
 appear in the next turn.
 
@@ -104,31 +144,53 @@ Cline) and restart the client.
 
 ## Optional — declare your identity & capabilities
 
-Three additional env vars control how your workspace appears on the
+Four additional env vars control how your workspace appears on the
-canvas and to peer agents calling `list_peers`:
+canvas and how the wheel's inbound-delivery contract behaves:
 
 | Env var | What it sets | Default |
 |---|---|---|
 | `MOLECULE_AGENT_NAME` | Display name on the canvas card | `molecule-mcp-{id[:8]}` |
 | `MOLECULE_AGENT_DESCRIPTION` | One-line description in Details/Skills tabs | empty |
 | `MOLECULE_AGENT_SKILLS` | Comma-separated skill names — e.g. `research,code-review,memory-curation` | `[]` |
+| `MOLECULE_MCP_POLL_TIMEOUT_SECS` | How long the agent blocks on `wait_for_message` per turn (the universal poll path). `0` disables polling for push-only mode (Claude Code launched with `--dangerously-load-development-channels server:molecule`). Above 60 clamps to 60. | `2` |
 
 Skills are surfaced two places:
 
 1. **Canvas Skills tab** — each skill renders as a chip with the name
 2. **Peer agents calling `list_peers`** — they see `{name, skills: [...]}` for each peer, so other agents can route delegations to the right specialist instead of guessing from name alone
 
-Example with all three set:
+Example with all three set (Claude Code 2.1+ CLI form):
 
 ```bash
-claude mcp add molecule -s user -- env \
+claude mcp add molecule -s user \
-  WORKSPACE_ID=<uuid> \
+  -e WORKSPACE_ID=<uuid> \
-  PLATFORM_URL=https://<tenant>.moleculesai.app \
+  -e PLATFORM_URL=https://<tenant>.moleculesai.app \
-  MOLECULE_WORKSPACE_TOKEN=<token> \
+  -e MOLECULE_WORKSPACE_TOKEN=<token> \
-  MOLECULE_AGENT_NAME='Research Assistant' \
+  -e MOLECULE_AGENT_NAME='Research Assistant' \
-  MOLECULE_AGENT_DESCRIPTION='Reads, summarises, cites.' \
+  -e MOLECULE_AGENT_DESCRIPTION='Reads, summarises, cites.' \
-  MOLECULE_AGENT_SKILLS=research,summarisation,citations \
+  -e MOLECULE_AGENT_SKILLS=research,summarisation,citations \
-  molecule-mcp
+  -- molecule-mcp
+```
+
+Or as the equivalent `~/.claude.json` entry:
+
+```json
+{
+  "mcpServers": {
+    "molecule": {
+      "type": "stdio",
+      "command": "molecule-mcp",
+      "env": {
+        "WORKSPACE_ID": "<uuid>",
+        "PLATFORM_URL": "https://<tenant>.moleculesai.app",
+        "MOLECULE_WORKSPACE_TOKEN": "<token>",
+        "MOLECULE_AGENT_NAME": "Research Assistant",
+        "MOLECULE_AGENT_DESCRIPTION": "Reads, summarises, cites.",
+        "MOLECULE_AGENT_SKILLS": "research,summarisation,citations"
+      }
+    }
+  }
+}
 ```
 
 A peer agent's `list_peers()` call would then surface this workspace
@@ -158,7 +220,7 @@ status. If the workspace is still offline after ~30s, check
 | `delegate_task` | Send a task to a peer and wait for the reply |
 | `delegate_task_async` | Fire-and-forget delegation; result lands in inbox |
 | `check_task_status` | Poll an async delegation |
-| `wait_for_message` | Block until the next inbound A2A message arrives |
+| `wait_for_message` | Block until the next inbound A2A message arrives — the universal inbound-delivery primitive (see [Inbound delivery](#inbound-delivery-universal-poll-optional-push)) |
 | `inbox_peek` / `inbox_pop` | Inspect / acknowledge queued inbound messages |
 | `send_message_to_user` | Push a chat bubble to the user's canvas |
 | `commit_memory` / `recall_memory` | Persistent KV (local / team / global scope) |
@@ -168,29 +230,125 @@ External runtimes can't accept inbound HTTP, so the wheel polls
 through `wait_for_message` + `inbox_peek` / `inbox_pop`. Use those
 instead of waiting for an HTTP webhook — there isn't one.
 
-### Push-UX for notification-capable hosts
+### Inbound delivery: universal poll, optional push
 
-On top of the polling tools, the wheel emits a JSON-RPC notification
+Inbound messages reach the agent via one of two paths. The wheel
-(`notifications/claude/channel`) on every new inbound message. Hosts
+exposes both; which one fires depends on the host's capabilities.
-that recognise that method (Claude Code today; any compliant client
+Both paths converge on the same `inbox_pop` ack so dedup is automatic.
-tomorrow) treat the notification as a conversation interrupt — the
-message text becomes the next agent turn without the agent having to
-call `wait_for_message` first.
 
-Hosts that don't recognise the method silently ignore it, so the same
+**Poll path (universal default — works on every spec-compliant MCP
-wheel works for both push-capable and poll-only runtimes. There is no
+client).** The wheel's `initialize` handshake includes an `instructions`
-config flag to toggle: pollers keep polling, notification-capable hosts
+field telling the agent: *"At the start of every turn, before producing
-get push automatically.
+your final response, call `wait_for_message(timeout_secs=N)` to check
+for inbound messages."* Every MCP client surfaces `instructions` to
+the agent's system prompt automatically, so Claude Code, Cursor, Cline,
+OpenCode, hermes-agent, and codex all receive the polling contract
+without any per-client wiring. The 2-second default is tuned for the
+"peer A2A landed seconds before my turn started" common case; tune
+via the `MOLECULE_MCP_POLL_TIMEOUT_SECS` env var
+(see "Optional — declare your identity & capabilities" above).
+
+**Push path (Claude Code with channel push enabled — strictly
+better when available).** On top of the poll path, the wheel emits a
+JSON-RPC notification (`notifications/claude/channel`) on every new
+inbound message and declares the matching `experimental.claude/channel`
+capability in `initialize`. Claude Code with channel push enabled
+turns the notification into an inline `<channel source="molecule"
+...>` synthetic user turn — zero agent-side polling cost, zero
+per-turn stall.
+
+**Today (research preview), Claude Code's channel push requires
+either the `--dangerously-load-development-channels` launch flag OR
+an entry on Claude Code's approved channel-server allowlist.** The
+wheel ships the wire shape correctly, but a standard `claude` launch
+without the flag silently drops the notification — which is why the
+poll path has to be the floor.
+
+Since Claude Code 2.1.x the flag takes a tagged allowlist, not a bare
+switch. Pass each MCP server you want to push from as `server:<name>`
+(matching the name you registered the server under in Claude Code's
+config — `molecule` if you followed [Step 2](#claude-code) above):
+
+```bash
+claude --dangerously-load-development-channels server:molecule
+```
+
+Multiple entries are space-separated:
+`server:molecule server:telegram`. A bare
+`--dangerously-load-development-channels` (no value) is rejected with
+`argument missing`; an untagged value (`molecule`) is rejected with
+`entries must be tagged`. Easy way to confirm push is live: the
+session header prints `Listening for channel messages from:
+server:molecule`, and inbound canvas messages render inline as
+`← molecule: <text>` instead of arriving via `inbox_peek`.
+
+Set `MOLECULE_MCP_POLL_TIMEOUT_SECS=0` to disable polling entirely
+when you're running Claude Code with the dev-channels flag and don't
+want the per-turn stall. The instructions adapt automatically: with
+polling disabled, the agent is told push is the only delivery path.
+
+#### `<channel>` envelope attributes
+
+Every inbound message — push or poll — carries the same metadata
+shape. On the push path, attributes render inline as XML-style attrs
+on the `<channel>` tag; on the poll path, the same fields appear in
+the JSON returned by `inbox_peek` / `wait_for_message`. Either way,
+the agent sees a consistent view.
+
+| Attribute | When present | Description |
+|---|---|---|
+| `source` | always | Always `molecule` — distinguishes our channel from other registered servers (`telegram`, etc.). |
+| `kind` | always | `canvas_user` (a human in the canvas chat) or `peer_agent` (another workspace's agent). Drives reply routing. |
+| `peer_id` | always | Empty for `canvas_user`; the sender's workspace UUID for `peer_agent`. Use as `workspace_id` when calling `delegate_task` to reply. |
+| `peer_name` | `peer_agent` only | The peer's display name (e.g. `ops-agent`) resolved from the platform registry. Absent on registry-lookup failure — the push still delivers. |
+| `peer_role` | `peer_agent` only | The peer's declared role (e.g. `sre`, `coordinator`). Same registry source as `peer_name`; same graceful-degrade rule. |
+| `agent_card_url` | `peer_agent` only | URL of the platform's discover endpoint for this peer. Fetch it if you need the peer's full capability list (skills, runtime, etc.). |
+| `activity_id` | always | The inbox row ID. **Pass it to `inbox_pop` after handling** so the message isn't re-delivered on the next push or poll cycle. |
+| `ts` | always | ISO-8601 timestamp of when the message landed in the platform's activity log. |
+
+`peer_name` and `peer_role` are added by the wheel via a TTL'd
+registry lookup keyed on `peer_id`. Cache TTL is 5 minutes — long
+enough that a busy multi-peer chat doesn't hit the registry on every
+push, short enough that role/name renames propagate within a single
+agent session. Lookup failure is silent: the attributes are simply
+absent and the push delivers anyway, so a registry stall can never
+block inbound messages.
+
+`agent_card_url` is constructed deterministically from `peer_id`, so
+it's present even if the registry is down. The agent can hit it
+later to enumerate the sender's capabilities once the registry is
+back up.
+
+Worked push example for a `peer_agent` arrival:
+
+```
+<channel source="molecule" kind="peer_agent"
+         peer_id="11111111-2222-3333-4444-555555555555"
+         peer_name="ops-agent" peer_role="sre"
+         agent_card_url="https://platform.example.com/registry/discover/11111111-2222-3333-4444-555555555555"
+         activity_id="act-742" ts="2026-05-01T12:34:56Z">
+  Can you check the deploy status for the canary?
+</channel>
+```
+
+| Client | Push path | Poll path |
+|---|---|---|
+| Claude Code with `--dangerously-load-development-channels server:molecule` | ✅ inline `← molecule:` tag | ✅ also works |
+| Claude Code (standard launch) | ❌ silently dropped | ✅ via instructions |
+| Cursor / Cline / OpenCode / codex | ❌ method ignored | ✅ via instructions |
+| hermes-agent | ❌ method ignored | ✅ naturally polls every cycle |
 
 ### MCP spec compliance
 
 The wheel speaks MCP protocol version **2024-11-05** over stdio
-JSON-RPC, declaring only the `tools` capability. It implements the
+JSON-RPC. It declares the standard `tools` capability plus the
-standard request methods and nothing client-specific:
+`experimental.claude/channel` capability for the optional push path
+(see [Inbound delivery](#inbound-delivery-universal-poll-optional-push)).
+It implements the standard request methods and nothing client-specific:
 
 | MCP method | Behavior |
 |---|---|
-| `initialize` | Echoes `protocolVersion: "2024-11-05"`, `serverInfo`, declares `tools` capability |
+| `initialize` | Echoes `protocolVersion: "2024-11-05"`, `serverInfo`, declares `tools` + `experimental.claude/channel` capabilities, returns the dual-path delivery `instructions` |
 | `notifications/initialized` | No-op (no response — per spec) |
 | `tools/list` | Returns all exposed tools in one response (no pagination cursor — surface is small) |
 | `tools/call` | Dispatches by name, returns `content: [{ type: "text", text: ... }]` |
@@ -198,8 +356,10 @@ standard request methods and nothing client-specific:
 
 The push-UX notification (`notifications/claude/channel`) is the only
 non-standard method emitted, and it's a one-way notification — clients
-that don't handle it discard it per JSON-RPC semantics. No part of the
+that don't handle it discard it per JSON-RPC semantics. The poll path
-wheel's tool surface depends on a client recognizing it.
+(via the standard `instructions` field) carries delivery for those
+clients, so no part of the wheel's tool surface depends on a client
+recognizing the notification.
 
 This means **any spec-compliant MCP client** can drive the wheel:
 Claude Code, Cursor, Cline, OpenCode, hermes-agent, or anything else
@@ -305,6 +465,21 @@ A quick way to confirm: `ps aux | grep molecule-mcp` and check the
 PID hasn't changed across `/mcp` reconnects. If the same PID stays
 alive, the runtime is still using the old config.
 
+### `claude mcp add` rejects the install command on Claude Code 2.1+
+
+Two common shapes from older docs trip the 2.1+ parser:
+
+- `claude mcp add molecule -s user -- env VAR=val molecule-mcp` — works
+  but lands as `command: "env"` with positional args, which surprises
+  some MCP clients on older 2.1.x patch builds.
+- `claude mcp add molecule -e VAR=val molecule-mcp` (missing `--`) — the
+  CLI parses `molecule-mcp` as a flag value, not a command, and either
+  errors or silently registers nothing.
+
+Use the `-e` form **with** `--` (see [Step 2](#claude-code)), or skip the
+CLI entirely and write the JSON shape into `~/.claude.json` directly.
+The on-disk shape is the source of truth and not version-sensitive.
+
 ### `command not found: molecule-mcp` from inside the runtime
 
 The runtime's `PATH` may differ from your interactive shell — common
@@ -319,6 +494,44 @@ which molecule-mcp
 Then point `command` at that absolute path in `claude mcp add` /
 `.cursor/mcp.json` / `mcp_servers.yaml`.
 
+### `error: option '--dangerously-load-development-channels <servers...>' argument missing`
+
+You're on Claude Code 2.1.x or later. The flag changed from a bare
+switch to an allowlist that takes tagged entries. See
+[Inbound delivery](#inbound-delivery-universal-poll-optional-push) for
+the right form — short answer:
+
+```bash
+claude --dangerously-load-development-channels server:molecule
+```
+
+### `--dangerously-load-development-channels entries must be tagged: molecule`
+
+The flag value needs the `server:` (or `plugin:`) prefix. Pass
+`server:molecule` (the registered MCP server name), not bare
+`molecule`.
+
+### `Control request timeout: initialize` from the workspace agent
+
+This is the symptom of forwarding the dev-channels flag to a nested
+`claude` CLI through the `claude-agent-sdk` with the wrong shape. If
+you embed the wheel inside an SDK-driven agent (e.g. the claude-code
+workspace template's `claude_sdk_executor.py`), pass the tagged value
+through `extra_args`:
+
+```python
+ClaudeAgentOptions(
+    ...,
+    extra_args={"dangerously-load-development-channels": "server:molecule"},
+)
+```
+
+The SDK forwards `extra_args` keys as `--<key> <value>` to the spawned
+CLI. Passing `None` renders as a bare switch and the post-2.1.x CLI
+rejects it with `argument missing`, which surfaces upstream as
+`Control request timeout: initialize` (the SDK never gets a response
+to its initialize control message).
+
 ## When to use this vs. the manual A2A path
 
 | Scenario | Use |

content/docs/self-hosting.mdx

@@ -17,8 +17,8 @@ description: Run the full Molecule AI stack on your own infrastructure.
 The fastest way to get Molecule AI running locally:
 
 ```bash
-git clone https://github.com/Molecule-AI/molecule-core.git
+git clone https://github.com/Molecule-AI/molecule-monorepo.git
-cd molecule-core
+cd molecule-monorepo
 ./scripts/dev-start.sh
 # Canvas: http://localhost:3000
 # Platform: http://localhost:8080