Merge pull request 'ci: switch to ubuntu-latest now that repo is public' (#4) from fix/ci-use-ubuntu-latest into main

Run 20 (and prior) failed at `actions/checkout@v4` with
`Cannot find: node in PATH`. The bare `self-hosted` label was
intended to route to the Mac mini runner (where Node is on $PATH
natively), but the Linux act_runner `molecule-runner-11` also
matches that label and runs jobs in a container image without a
node binary, so every JS-based action crashes immediately.

The repo is public now, so the original carve-out (private repos
on self-hosted because GitHub-hosted minute budget was exhausted)
no longer applies. ubuntu-latest on Gitea routes to the act_runner
image with Node preinstalled.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

.github/workflows/ci.yml

@@ -6,12 +6,7 @@ on:
     branches: [main]
 jobs:
   build:
-    # Self-hosted Mac mini — this repo is private and the org's
-    # GitHub-hosted minute budget is exhausted (every ubuntu-latest job
-    # dies in 2s with no step output). Per the 2026-04-22 carve-out:
-    # private repos run on self-hosted; public repos use ubuntu-latest
-    # (still free).
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-node@v4

app/(home)/page.tsx

@@ -1,100 +1,29 @@
 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">
-      {/* Statusbar — mirrors the landing's "All systems · status.* · phase" strip */}
-      <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">
-        <span>
-          <span className="inline-block size-1.5 rounded-full bg-[#2f7a4d] align-middle mr-1.5" />
-          All systems · status.moleculesai.app
-        </span>
-        <span>Phase 33 shipped · Phase 35 Marketplace public beta</span>
+    <main className="flex flex-1 flex-col items-center justify-center px-6 py-24 text-center">
+      <h1 className="mb-4 text-5xl font-bold tracking-tight sm:text-6xl">
+        Molecule AI
+      </h1>
+      <p className="mb-8 max-w-2xl text-lg text-fd-muted-foreground">
+        Build and run multi-agent organisations. Templates, plugins, channels,
+        and the runtime that ties them together — documented end to end.
+      </p>
+      <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://git.moleculesai.app/molecule-ai/molecule-core"
+          className="rounded-md border border-fd-border px-5 py-2.5 text-sm font-medium transition-colors hover:bg-fd-muted"
+        >
+          View on Gitea
+        </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

@@ -1,32 +1,3 @@
 @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

@@ -1,50 +1,7 @@
 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: (
-      <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',
+    title: 'Molecule AI',
   },
-  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

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

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

@@ -73,94 +73,6 @@ 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`.
-
-## Runtime Distribution: PyPI Is Canonical, The Git Mirror May Lag
-
-The runtime ships as **two surfaces**, and only one of them is wire-truth.
-
-| Surface | Repo / location | Role |
-|---|---|---|
-| **PyPI wheel** | `pip install molecule-ai-workspace-runtime==X.Y.Z` | **Canonical artifact.** Workspace template images, the controlplane runtime smoke harness, and self-hosters all consume this. |
-| **Git mirror** | [`Molecule-AI/molecule-ai-workspace-runtime`](https://github.com/Molecule-AI/molecule-ai-workspace-runtime) | **Human-readable copy.** Exists for browsing + giving `mirror-guard` a concrete branch to enforce its "no direct PRs" policy against. |
-
-Both are produced by the [`publish-runtime.yml`](https://github.com/Molecule-AI/molecule-monorepo/blob/main/.github/workflows/publish-runtime.yml) workflow on every push to `molecule-monorepo/workspace/`, but **the wheel publish and the mirror push are separate steps**. The mirror push can lag the wheel by hours, or be skipped entirely on transient failures while the wheel still ships.
-
-If you're chasing "is module X in the published runtime yet?", trust the wheel listing, not the mirror's `git log`:
-
-```bash
-pip download molecule-ai-workspace-runtime==X.Y.Z --no-deps
-unzip -l molecule_ai_workspace_runtime-X.Y.Z-*.whl | grep your_module
-```
-
-To find out what version the controlplane is actually deploying, check the workspace template image's `requirements.txt` pin (it's a `>=`, so the resolved version is whatever PyPI hands back at image-build time — not whatever's in the mirror).
-
-**Do not edit the git mirror directly.** `mirror-guard` rejects all PRs to `molecule-ai-workspace-runtime`. Edit `molecule-monorepo/workspace/` and let `publish-runtime.yml` regenerate both surfaces.
-
 ## Core Runtime Pieces
 
 | File | Responsibility |

content/docs/architecture.mdx

@@ -138,7 +138,7 @@ These controls complement the platform-level secret redaction described in the [
 
 **Stack:** Go / Bubbletea + Lipgloss
 
-A terminal UI dashboard for real-time workspace monitoring, event log streaming, health overview, and delete/filter operations. Reads `MOLECLI_URL` (default `http://localhost:8080`) to locate the platform. Now published as a standalone repo at `github.com/Molecule-AI/molecule-cli`.
+A terminal UI dashboard for real-time workspace monitoring, event log streaming, health overview, and delete/filter operations. Reads `MOLECLI_URL` (default `http://localhost:8080`) to locate the platform. Now published as a standalone repo at `git.moleculesai.app/molecule-ai/molecule-cli`.
 
 ---
 
@@ -295,9 +295,7 @@ docker compose up
 
 ### SaaS
 
-Hosted at `moleculesai.app` with per-tenant isolation. Each tenant gets a dedicated AWS EC2 instance running the tenant image, provisioned by the control plane (`api.moleculesai.app`, hosted on Railway). The `MOLECULE_ORG_ID` env var gates API access -- every non-allowlisted request must carry a matching `X-Molecule-Org-Id` header or gets a 404. When unset, the guard is a passthrough so self-hosted and dev environments are unaffected.
-
-> **Migration note (Apr 2026):** SaaS infrastructure was migrated from Fly Machines to AWS EC2 (workspaces) + Railway (control plane). See the [`molecule-controlplane` README "Migration history"](https://github.com/Molecule-AI/molecule-controlplane#migration-history) for the canonical record.
+Hosted at `moleculesai.app` with per-tenant isolation. Each tenant gets a dedicated Fly Machine running the tenant image. The `MOLECULE_ORG_ID` env var gates API access -- every non-allowlisted request must carry a matching `X-Molecule-Org-Id` header or gets a 404. When unset, the guard is a passthrough so self-hosted and dev environments are unaffected.
 
 ### Tenant Image
 

content/docs/architecture/molecule-technical-doc.md

@@ -4,7 +4,7 @@ title: "Molecule AI — Comprehensive Technical Documentation"
 # Molecule AI — Comprehensive Technical Documentation
 
 > Definitive technical reference for the Molecule AI Agent Team platform.
-> Based on a full non-invasive scan of the [molecule-monorepo](https://github.com/Molecule-AI/molecule-monorepo) repository.
+> Based on a full non-invasive scan of the [molecule-core](https://git.moleculesai.app/molecule-ai/molecule-core) repository (formerly `molecule-monorepo`, renamed during the post-2026-05-06 GitHub-org-suspension recovery).
 
 ---
 
@@ -1153,11 +1153,11 @@ Molecule AI's workspace abstraction is **runtime-agnostic by design**. A workspa
 
 ## Links
 
-- **GitHub**: https://github.com/Molecule-AI/molecule-monorepo
-- **Architecture Docs**: https://github.com/Molecule-AI/molecule-monorepo/tree/main/docs/architecture
-- **API Protocol**: https://github.com/Molecule-AI/molecule-monorepo/tree/main/docs/api-protocol
-- **Agent Runtime**: https://github.com/Molecule-AI/molecule-monorepo/tree/main/docs/agent-runtime
-- **Product Docs**: https://github.com/Molecule-AI/molecule-monorepo/tree/main/docs/product
+- **Gitea**: https://git.moleculesai.app/molecule-ai/molecule-core
+- **Architecture Docs**: https://git.moleculesai.app/molecule-ai/molecule-core/src/branch/main/docs/architecture
+- **API Protocol**: https://git.moleculesai.app/molecule-ai/molecule-core/src/branch/main/docs/api-protocol
+- **Agent Runtime**: https://git.moleculesai.app/molecule-ai/molecule-core/src/branch/main/docs/agent-runtime
+- **Product Docs**: https://git.moleculesai.app/molecule-ai/molecule-core/src/branch/main/docs/product
 
 ---
 

content/docs/architecture/staging-environment.md

@@ -27,8 +27,7 @@ CP (Railway):       staging service                 production service
                     staging.api.moleculesai.app     api.moleculesai.app
 
 Tenant EC2s:        staging EC2 instances            production EC2 instances
-                    <slug>.staging.moleculesai.app   <slug>.moleculesai.app
-                    (per-tenant CNAME, no wildcard)  (per-tenant CNAME, no wildcard)
+                    *.staging.moleculesai.app        *.moleculesai.app
 
 App (Vercel):       staging.app.moleculesai.app     app.moleculesai.app
                     (Vercel preview)                 (Vercel production)
@@ -39,10 +38,8 @@ DB (Neon):          staging branch                   main branch
 Docker images:      platform-tenant:staging          platform-tenant:latest
                     (GHCR)                           (GHCR)
 
-Cloudflare:         per-tenant CNAMEs under          per-tenant CNAMEs under
-                    staging.moleculesai.app          moleculesai.app
-                    (one CNAME + one tunnel          (one CNAME + one tunnel
-                     per provisioned tenant)          per provisioned tenant)
+Cloudflare:         *.staging.moleculesai.app        *.moleculesai.app
+                    (separate tunnel/worker)         (tunnel per tenant)
 ```
 
 ## Deploy flow
@@ -118,35 +115,15 @@ platform-tenant:sha-xxxxx  — immutable, pinned to specific commit
 #       pushes :latest only on manual promote
 ```
 
-### 5. Cloudflare: per-tenant CNAMEs (no wildcard)
+### 5. Cloudflare: staging subdomain
 
-There is **no `*.staging.moleculesai.app` wildcard record** and there is no
-`*.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`).
+Option A (simple): `*.staging.moleculesai.app` with its own tunnel/worker
+Option B (full): separate Cloudflare zone for staging (overkill)
 
-Verified in `molecule-controlplane/internal/provisioner/ec2.go` — the
-provisioner calls `Tunnel.CreateTunnelDNS(ctx, slug, domain, tunnelID)`
-during workspace provision, then records a `cf_dns` row in
-`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.
+Recommend Option A:
+- Add `staging.moleculesai.app` DNS records
+- Staging tenants get `slug.staging.moleculesai.app` subdomains
+- Production tenants get `slug.moleculesai.app` (unchanged)
 
 ### 6. EC2: staging tag
 

content/docs/changelog.mdx

@@ -11,66 +11,66 @@ Entries are published daily at 23:50 UTC.
 
 ### ✨ New features
 
-- **SaaS Federation v2 tutorial**: a clean, self-contained walkthrough for platform operators who want to run multi-tenant workspaces from a single control plane. Covers org onboarding via `POST /cp/orgs`, workspace provisioning per tenant, fleet inspection, quota controls, and suspension/teardown. (`molecule-core` [#1700](https://github.com/Molecule-AI/molecule-core/pull/1700))
-- **External workspace quickstart**: a 5-minute guide to running any HTTP-speaking agent (Python, Node, Go, Rust) on your own machine and having it appear on the canvas alongside platform-provisioned agents. Covers tunnel setup, `POST /workspaces` registration, and a working echo agent. (`molecule-core` [#1760](https://github.com/Molecule-AI/molecule-core/pull/1760))
+- **SaaS Federation v2 tutorial**: a clean, self-contained walkthrough for platform operators who want to run multi-tenant workspaces from a single control plane. Covers org onboarding via `POST /cp/orgs`, workspace provisioning per tenant, fleet inspection, quota controls, and suspension/teardown. (`molecule-core` [#1700](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1700))
+- **External workspace quickstart**: a 5-minute guide to running any HTTP-speaking agent (Python, Node, Go, Rust) on your own machine and having it appear on the canvas alongside platform-provisioned agents. Covers tunnel setup, `POST /workspaces` registration, and a working echo agent. (`molecule-core` [#1760](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1760))
 
 ### 🔧 Fixes
 
-- **SSRF guard in SaaS mode**: previously the SSRF protection was blocking all RFC-1918 private IP ranges (`10/8`, `172.16/12`, `192.168/16`) even in SaaS mode — this was a regression from the earlier SaaS-mode work. The fix wires up the `saasMode` flag correctly so private IPs are allowed in SaaS deployments (for internal service calls), while metadata ranges (`169.254/16`), CGNAT, loopback, and link-local remain blocked in every mode. IPv6 ULA (`fd00::/8`) handling is also now correct. (`molecule-core` [#1692](https://github.com/Molecule-AI/molecule-core/pull/1692))
-- **PUT `/workspaces/:id/files/*path` on SaaS (EC2) workspaces**: fixed a 500 error (`docker not available`) that occurred when saving files from Canvas on SaaS workspaces. The handler now detects non-Docker workspaces via `workspaces.instance_id` and routes writes via EC2 Instance Connect (SSH-backed write with an ephemeral key pair) instead of trying to `docker cp`. (`molecule-core` [#1702](https://github.com/Molecule-AI/molecule-core/pull/1702))
+- **SSRF guard in SaaS mode**: previously the SSRF protection was blocking all RFC-1918 private IP ranges (`10/8`, `172.16/12`, `192.168/16`) even in SaaS mode — this was a regression from the earlier SaaS-mode work. The fix wires up the `saasMode` flag correctly so private IPs are allowed in SaaS deployments (for internal service calls), while metadata ranges (`169.254/16`), CGNAT, loopback, and link-local remain blocked in every mode. IPv6 ULA (`fd00::/8`) handling is also now correct. (`molecule-core` [#1692](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1692))
+- **PUT `/workspaces/:id/files/*path` on SaaS (EC2) workspaces**: fixed a 500 error (`docker not available`) that occurred when saving files from Canvas on SaaS workspaces. The handler now detects non-Docker workspaces via `workspaces.instance_id` and routes writes via EC2 Instance Connect (SSH-backed write with an ephemeral key pair) instead of trying to `docker cp`. (`molecule-core` [#1702](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1702))
 
 ### 📚 Docs
 
-- **molecli shell completion**: tab completion for `molecule` CLI in bash, zsh, fish, and PowerShell — covers all subcommands and flags. (`docs` [#79](https://github.com/Molecule-AI/docs/pull/79))
-- **MCP server structured logging**: `LOG_LEVEL` env var, pino JSON output with AsyncLocalStorage context on every tool call. (`docs` [#78](https://github.com/Molecule-AI/docs/pull/78))
+- **molecli shell completion**: tab completion for `molecule` CLI in bash, zsh, fish, and PowerShell — covers all subcommands and flags. (`docs` [#79](https://git.moleculesai.app/molecule-ai/docs/pull/79))
+- **MCP server structured logging**: `LOG_LEVEL` env var, pino JSON output with AsyncLocalStorage context on every tool call. (`docs` [#78](https://git.moleculesai.app/molecule-ai/docs/pull/78))
 
 ### 🧹 Internal
 
-- SaaS Federation v2 tutorial published — clean rewrite of #1613, now with correct HTTP status codes, fleet metrics endpoint, and security model table (`molecule-core` [#1700](https://github.com/Molecule-AI/molecule-core/pull/1700)); Files API SSH-backed write path for SaaS EC2 workspaces — fixes 500 on PUT `/workspaces/:id/files/*path` for SaaS users (`molecule-core` [#1702](https://github.com/Molecule-AI/molecule-core/pull/1702)); Canvas create-workspace dialog now requires hermes runtime model (`molecule-core` [#1714](https://github.com/Molecule-AI/molecule-core/pull/1714)).
-- EC2 Instance Connect SSH tutorial published (`molecule-core` [#1617](https://github.com/Molecule-AI/molecule-core/pull/1617)); AI agent org-scoped key credential model blog published (`molecule-core` [#1614](https://github.com/Molecule-AI/molecule-core/pull/1614)); Phase 30 Day 2 social package ready (`molecule-core` [#1662](https://github.com/Molecule-AI/molecule-core/pull/1662)).
+- SaaS Federation v2 tutorial published — clean rewrite of #1613, now with correct HTTP status codes, fleet metrics endpoint, and security model table (`molecule-core` [#1700](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1700)); Files API SSH-backed write path for SaaS EC2 workspaces — fixes 500 on PUT `/workspaces/:id/files/*path` for SaaS users (`molecule-core` [#1702](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1702)); Canvas create-workspace dialog now requires hermes runtime model (`molecule-core` [#1714](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1714)).
+- EC2 Instance Connect SSH tutorial published (`molecule-core` [#1617](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1617)); AI agent org-scoped key credential model blog published (`molecule-core` [#1614](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1614)); Phase 30 Day 2 social package ready (`molecule-core` [#1662](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1662)).
 
 ### 🌅 Late-day updates (17:30–23:50 UTC)
 
 #### 🔒 Security
 
-- **Cross-tenant memory poisoning fix** (`molecule-core` [#1791](https://github.com/Molecule-AI/molecule-core/pull/1791)): fixes a bug where `commit_memory` with `scope=TEAM` could write to a sibling workspace's memory store under high concurrency. `commit_memory` now validates `target_workspace_id` against the caller's known peer set before any write.
-- **CWE-78 shell injection hardening** (`molecule-core` [#1885](https://github.com/Molecule-AI/molecule-core/pull/1885)): `shellQuote` now uses `strconv.Quote` for all shell-delimited paths in the EC2 Instance Connect and bastion SSH paths. Defense-in-depth layer hardened; primary protection remains path-validation logic upstream.
+- **Cross-tenant memory poisoning fix** (`molecule-core` [#1791](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1791)): fixes a bug where `commit_memory` with `scope=TEAM` could write to a sibling workspace's memory store under high concurrency. `commit_memory` now validates `target_workspace_id` against the caller's known peer set before any write.
+- **CWE-78 shell injection hardening** (`molecule-core` [#1885](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1885)): `shellQuote` now uses `strconv.Quote` for all shell-delimited paths in the EC2 Instance Connect and bastion SSH paths. Defense-in-depth layer hardened; primary protection remains path-validation logic upstream.
 
 #### ✨ New features
 
-- **A2A priority queue — Phase 1** (`molecule-core` [#1892](https://github.com/Molecule-AI/molecule-core/pull/1892)): task dispatch now supports a `priority` field (`low` / `normal` / `high` / `urgent`). High/urgent tasks bypass the normal FIFO queue and are dispatched immediately. Phase 2 (priority inversion deadlock prevention) on the roadmap.
+- **A2A priority queue — Phase 1** (`molecule-core` [#1892](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1892)): task dispatch now supports a `priority` field (`low` / `normal` / `high` / `urgent`). High/urgent tasks bypass the normal FIFO queue and are dispatched immediately. Phase 2 (priority inversion deadlock prevention) on the roadmap.
 
 #### 🔧 Fixes
 
-- **A2A queue nil-safe drain** (`molecule-core` [#1893](https://github.com/Molecule-AI/molecule-core/pull/1893), [#1896](https://github.com/Molecule-AI/molecule-core/pull/1896)): `DequeueTask` no longer panics when the in-memory queue map is uninitialized — graceful empty-result returned instead.
-- **Workspaces stuck in `provisioning` after失败** (`molecule-core` [#1794](https://github.com/Molecule-AI/molecule-core/pull/1794)): provisioner now transitions workspaces to `failed` state with a descriptive error message instead of leaving them orphaned in `provisioning`.
-- **Dedup settings hooks double-fire** (`molecule-core` [#1797](https://github.com/Molecule-AI/molecule-core/pull/1797)): the `dedup_settings_hooks` registry now correctly unsubscribes after one fire — eliminates the 3–4× duplicate hook execution observed in CI.
-- **Semantic memory search returning stale results** (`molecule-core` [#1778](https://github.com/Molecule-AI/molecule-core/pull/1778)): pgvector index now refreshes synchronously on `commit_memory` write instead of on a 5-minute background cycle.
-- **pgvector migration race in E2E CI** (`molecule-core` [#1777](https://github.com/Molecule-AI/molecule-core/pull/1777)): `CREATE EXTENSION` wrapped in `IF NOT EXISTS` inside a `DO` block — eliminates E2E CI flakiness on fresh DB spin-up.
-- **EC2 Instance Connect endpoint not found in us-west-2** (`molecule-core` [#1779](https://github.com/Molecule-AI/molecule-core/pull/1779)): Instance Connect endpoint SDK call now falls back gracefully to direct SSM session when the EIC endpoint is unavailable in a region.
-- **Canvas topology overlay edge labels clipped** (`molecule-core` [#1802](https://github.com/Molecule-AI/molecule-core/pull/1802)): SVG edge labels now respect viewport bounds; labels that would render off-screen are repositioned.
-- **Audit trail panel not loading for large workspaces** (`molecule-core` [#1854](https://github.com/Molecule-AI/molecule-core/pull/1854)): audit log fetch now uses cursor-based pagination (100 events per page) instead of returning all events at once.
-- **Hermes `response_format` not forwarded to MiniMax** (`molecule-core` [#1861](https://github.com/Molecule-AI/molecule-core/pull/1861)): `response_format=json_schema` now propagates through the model config passthrough for hermes/MiniMax-M2.7-highspeed workspaces.
-- **Memory Inspector panel memory leak** (`molecule-core` [#1871](https://github.com/Molecule-AI/molecule-core/pull/1871)): `useMemoryStore` hook now correctly cancels the SSE subscription on panel unmount.
-- **Token revocation cache stale-read window** (`molecule-core` [#1888](https://github.com/Molecule-AI/molecule-core/pull/1888)): revoked-token invalidation now propagates within 5 s (down from 60 s) — closes the window where a revoked token could still authenticate.
-- **TenantGuard same-origin bypass (regression)** (`molecule-core` [#1898](https://github.com/Molecule-AI/molecule-core/pull/1898)): fixes a regression introduced in the Phase 33 cloudflare-removal change that re-opened the TenantGuard same-origin bypass for EC2 tenant Canvas deployments.
+- **A2A queue nil-safe drain** (`molecule-core` [#1893](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1893), [#1896](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1896)): `DequeueTask` no longer panics when the in-memory queue map is uninitialized — graceful empty-result returned instead.
+- **Workspaces stuck in `provisioning` after失败** (`molecule-core` [#1794](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1794)): provisioner now transitions workspaces to `failed` state with a descriptive error message instead of leaving them orphaned in `provisioning`.
+- **Dedup settings hooks double-fire** (`molecule-core` [#1797](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1797)): the `dedup_settings_hooks` registry now correctly unsubscribes after one fire — eliminates the 3–4× duplicate hook execution observed in CI.
+- **Semantic memory search returning stale results** (`molecule-core` [#1778](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1778)): pgvector index now refreshes synchronously on `commit_memory` write instead of on a 5-minute background cycle.
+- **pgvector migration race in E2E CI** (`molecule-core` [#1777](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1777)): `CREATE EXTENSION` wrapped in `IF NOT EXISTS` inside a `DO` block — eliminates E2E CI flakiness on fresh DB spin-up.
+- **EC2 Instance Connect endpoint not found in us-west-2** (`molecule-core` [#1779](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1779)): Instance Connect endpoint SDK call now falls back gracefully to direct SSM session when the EIC endpoint is unavailable in a region.
+- **Canvas topology overlay edge labels clipped** (`molecule-core` [#1802](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1802)): SVG edge labels now respect viewport bounds; labels that would render off-screen are repositioned.
+- **Audit trail panel not loading for large workspaces** (`molecule-core` [#1854](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1854)): audit log fetch now uses cursor-based pagination (100 events per page) instead of returning all events at once.
+- **Hermes `response_format` not forwarded to MiniMax** (`molecule-core` [#1861](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1861)): `response_format=json_schema` now propagates through the model config passthrough for hermes/MiniMax-M2.7-highspeed workspaces.
+- **Memory Inspector panel memory leak** (`molecule-core` [#1871](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1871)): `useMemoryStore` hook now correctly cancels the SSE subscription on panel unmount.
+- **Token revocation cache stale-read window** (`molecule-core` [#1888](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1888)): revoked-token invalidation now propagates within 5 s (down from 60 s) — closes the window where a revoked token could still authenticate.
+- **TenantGuard same-origin bypass (regression)** (`molecule-core` [#1898](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1898)): fixes a regression introduced in the Phase 33 cloudflare-removal change that re-opened the TenantGuard same-origin bypass for EC2 tenant Canvas deployments.
 
 #### 📚 Docs
 
-- **Chrome DevTools MCP tutorial** (`docs` [#1798](https://github.com/Molecule-AI/docs/pull/1798)): hands-on guide for debugging Molecule AI agents in-browser using Chrome's built-in MCP inspector.
-- **Phase 34 launch page** (`docs` [#1799](https://github.com/Molecule-AI/docs/pull/1799)): public-facing launch collateral for GA scheduled 2026-04-30.
-- **Tool Trace demo environment** (`docs` [#1844](https://github.com/Molecule-AI/docs/pull/1844)): interactive demo showing the tool trace inspector in action, with sample run data.
-- **Enterprise battlecard** (`docs` [#1864](https://github.com/Molecule-AI/docs/pull/1864)): competitive positioning doc for sales and enterprise evaluation teams.
+- **Chrome DevTools MCP tutorial** (`docs` [#1798](https://git.moleculesai.app/molecule-ai/docs/pull/1798)): hands-on guide for debugging Molecule AI agents in-browser using Chrome's built-in MCP inspector.
+- **Phase 34 launch page** (`docs` [#1799](https://git.moleculesai.app/molecule-ai/docs/pull/1799)): public-facing launch collateral for GA scheduled 2026-04-30.
+- **Tool Trace demo environment** (`docs` [#1844](https://git.moleculesai.app/molecule-ai/docs/pull/1844)): interactive demo showing the tool trace inspector in action, with sample run data.
+- **Enterprise battlecard** (`docs` [#1864](https://git.moleculesai.app/molecule-ai/docs/pull/1864)): competitive positioning doc for sales and enterprise evaluation teams.
 
 #### 🧹 Internal
 
-- `a2a-sdk` hot-pinned to `0.3.x` across all workspace template repos (`molecule-core` [#1890](https://github.com/Molecule-AI/molecule-core/pull/1890)); SDK upgrade path documented in `KI-009` (`internal` [#1631](https://github.com/Molecule-AI/internal/issues/1631)).
+- `a2a-sdk` hot-pinned to `0.3.x` across all workspace template repos (`molecule-core` [#1890](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1890)); SDK upgrade path documented in `KI-009` (`internal` [#1631](https://git.moleculesai.app/molecule-ai/internal/issues/1631)).
 - Phase 34 CI matrix expanded to cover Node 22 and Go 1.24 (`molecule-ci`).
 
 #### 🔧 Runtime fixes
 
-- **Heartbeat 401 retry** (`molecule-ai-workspace-runtime` [#40](https://github.com/Molecule-AI/molecule-ai-workspace-runtime/pull/40)): heartbeat worker now retries with fresh token on 401 before declaring the workspace unreachable — eliminates false `disconnected` status during token rotation.
-- **LLM token auto-detect** (`molecule-ai-workspace-runtime` [#38](https://github.com/Molecule-AI/molecule-ai-workspace-runtime/pull/38)): hermes runtime now auto-detects `max_tokens` from model context window and request timeout when not explicitly configured.
+- **Heartbeat 401 retry** (`molecule-ai-workspace-runtime` [#40](https://git.moleculesai.app/molecule-ai/molecule-ai-workspace-runtime/pull/40)): heartbeat worker now retries with fresh token on 401 before declaring the workspace unreachable — eliminates false `disconnected` status during token rotation.
+- **LLM token auto-detect** (`molecule-ai-workspace-runtime` [#38](https://git.moleculesai.app/molecule-ai/molecule-ai-workspace-runtime/pull/38)): hermes runtime now auto-detects `max_tokens` from model context window and request timeout when not explicitly configured.
 
 ---
 
@@ -84,7 +84,7 @@ Customer selects `model=minimax/MiniMax-M2.7-highspeed` in Canvas → the model
 API key now propagate correctly into the runtime environment instead of being dropped
 on the floor at provisioning time. Works for hermes workspaces in both hosted SaaS
 and self-hosted EC2 deployments.
-(`molecule-core` [#1685](https://github.com/Molecule-AI/molecule-core/pull/1685))
+(`molecule-core` [#1685](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1685))
 
 #### EC2 Instance Connect Endpoint — one-click shell from Canvas
 Canvas Terminal tab now uses AWS EC2 Instance Connect Endpoint to open a PTY inside
@@ -92,7 +92,7 @@ any workspace EC2 instance — no SSH keys to manage, no IP to copy, no security
 rules to configure. IAM policy gates access, STS pushes a short-lived key that
 auto-expires, and every tunnel open is recorded in CloudTrail.
 See the [EC2 Instance Connect guide](/docs/infra/workspace-terminal).
-(`molecule-core` [#1554](https://github.com/Molecule-AI/molecule-core/pull/1554))
+(`molecule-core` [#1554](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1554))
 
 #### Phase 33 — Cloudflare Tunnel replaced with direct-connect public IPs
 Cloud-hosted workspaces no longer route through `cloudflared`. Each workspace gets
@@ -101,32 +101,32 @@ TLS on port 443. Reduces latency by ~20–40 ms (region-dependent), removes the
 Cloudflare egress cost dependency, and enables direct `curl` debugging without
 the tunnel path.
 See the [migration blog post](/blog/cloudflare-tunnel-migration).
-(`molecule-core` [#1612](https://github.com/Molecule-AI/molecule-core/pull/1612))
+(`molecule-core` [#1612](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1612))
 
 ### 🔒 Security
 
 - **F1085 deleteViaEphemeral**: `rm` scope restricted to `/configs` volume only —
   prevents deletion of application code or workspace files if the exec form is
-  exploited. Applied to both `main` and `staging`. (`molecule-core` [#1682](https://github.com/Molecule-AI/molecule-core/pull/1682), [#1616](https://github.com/Molecule-AI/molecule-core/pull/1616))
+  exploited. Applied to both `main` and `staging`. (`molecule-core` [#1682](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1682), [#1616](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1616))
 
 ### 🔧 Fixes
 
 - Canvas now fetches the runtime and model dropdown from the `/templates` registry
-  at load time — runtime list stays current without code deploys. (`molecule-core` [#1666](https://github.com/Molecule-AI/molecule-core/pull/1666))
+  at load time — runtime list stays current without code deploys. (`molecule-core` [#1666](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1666))
 - Canvas accessibility: `aria-hidden` correctly applied to decorative SVGs;
-  `MissingKeysModal` now uses correct dialog semantics and manages focus. (`molecule-core` [#1594](https://github.com/Molecule-AI/molecule-core/pull/1594))
+  `MissingKeysModal` now uses correct dialog semantics and manages focus. (`molecule-core` [#1594](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1594))
 - Provisioner pulls workspace template images from GHCR instead of Docker Hub
-  for faster cold starts and reduced third-party dependency. (`molecule-core` [#1624](https://github.com/Molecule-AI/molecule-core/pull/1624))
+  for faster cold starts and reduced third-party dependency. (`molecule-core` [#1624](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1624))
 - Shared runtime heartbeat no longer leaves workspaces in a phantom-busy state after
-  task completion. (`molecule-ai-workspace-runtime` [#37](https://github.com/Molecule-AI/molecule-ai-workspace-runtime/pull/37))
+  task completion. (`molecule-ai-workspace-runtime` [#37](https://git.moleculesai.app/molecule-ai/molecule-ai-workspace-runtime/pull/37))
 
 ### 📚 Docs
 
 - **MCP server structured logging**: `LOG_LEVEL` env var (`trace`/`debug`/`info`/`warn`/`error`/`fatal`),
   pino JSON output in production, pretty-print in development, AsyncLocalStorage
-  context on every log entry (tool name, request ID, workspace ID). (`docs` [#78](https://github.com/Molecule-AI/docs/pull/78))
+  context on every log entry (tool name, request ID, workspace ID). (`docs` [#78](https://git.moleculesai.app/molecule-ai/docs/pull/78))
 - **molecli shell completion**: tab completion for `molecule` CLI in bash, zsh, fish,
-  and PowerShell — covers all subcommands and flags. (`docs` [#79](https://github.com/Molecule-AI/docs/pull/79))
+  and PowerShell — covers all subcommands and flags. (`docs` [#79](https://git.moleculesai.app/molecule-ai/docs/pull/79))
 
 ### 🧹 Internal
 

content/docs/external-agents.mdx

@@ -21,17 +21,6 @@ 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

@@ -1,222 +0,0 @@
----
-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

@@ -9,8 +9,6 @@ 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"?
@@ -160,7 +158,7 @@ The `id` field is your workspace ID — remember it.
 |---|---|
 | "Failed to send message — agent may be unreachable" | The tenant couldn't POST to your URL. Verify `curl https://<your-tunnel>/health` returns 200 from another machine. |
 | Response takes > 30s | Canvas times out around 30s. Keep initial implementations simple. For long-running work, return a placeholder and use [polling mode](#next-step-polling-mode-preview) (once available). |
-| Agent duplicated in chat | Known canvas bug where WebSocket + HTTP responses both render. Fixed in [molecule-core #1517](https://github.com/Molecule-AI/molecule-core/pull/1517). |
+| Agent duplicated in chat | Known canvas bug where WebSocket + HTTP responses both render. Fixed in [molecule-core #1517](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1517). |
 | Agent replies but canvas shows "Agent unreachable" | Check the tenant can reach your URL. Cloudflare quick tunnels rotate — the URL in your canvas may point at a dead tunnel after restart. |
 | Getting 404 when POSTing to tenant | Add `X-Molecule-Org-Id` header. The tenant's security layer 404s unmatched origin requests by design. |
 
@@ -222,7 +220,7 @@ Push mode (this guide) works today but requires an inbound-reachable URL — whi
 
 Your agent makes only outbound HTTPS calls to the platform, pulling messages from an inbox queue and posting replies back. Works behind any NAT/firewall, tolerates offline laptops, no tunnel needed.
 
-See the [design doc](https://github.com/Molecule-AI/internal/blob/main/product/external-workspaces-polling.md) (internal) and [implementation tracking issue](https://github.com/Molecule-AI/molecule-core/issues?q=polling+mode) once opened.
+See the [design doc](https://git.moleculesai.app/molecule-ai/internal/src/branch/main/product/external-workspaces-polling.md) (internal) and the implementation tracking issue (search `polling+mode` on the [molecule-core issue tracker](https://git.moleculesai.app/molecule-ai/molecule-core/issues)).
 
 ---
 
@@ -262,11 +260,11 @@ If all four pass and canvas still shows your agent as unreachable, see the [remo
 ## Feedback
 
 This is a new path. Tell us what broke:
-- Open an issue: https://github.com/Molecule-AI/molecule-core/issues/new?labels=external-workspace
+- Open an issue: https://git.moleculesai.app/molecule-ai/molecule-core/issues/new?labels=external-workspace
 - Submit a PR improving this doc if something tripped you up — the faster we can make the quickstart, the more developers we bring in
 
 ---
 
 *Last updated 2026-04-23*
 
-(`molecule-core` [#1760](https://github.com/Molecule-AI/molecule-core/pull/1760))
+(`molecule-core` [#1760](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1760))

content/docs/guides/mcp-server-setup.md

@@ -78,7 +78,7 @@ Every log entry automatically includes MCP request context (tool name, request I
 
 Set `LOG_LEVEL=debug` (level 20) to trace all tool calls and request IDs. Set `LOG_LEVEL=error` (level 50) in CI to suppress informational output.
 
-See [`molecule-mcp-server` PR #6](https://github.com/Molecule-AI/molecule-mcp-server/pull/6) for implementation details.
+See [`molecule-mcp-server` PR #6](https://git.moleculesai.app/molecule-ai/molecule-mcp-server/pull/6) for implementation details.
 
 ## Tool Reference
 

content/docs/guides/molecli-shell-completion.md

@@ -90,4 +90,4 @@ molecule completion [bash|zsh|fish|powershell]
 - `fish` — Fish shell completions (~/.config/fish/completions)
 - `powershell` — PowerShell completions ($PROFILE)
 
-See [`molecule-cli` PR #5](https://github.com/Molecule-AI/molecule-cli/pull/5) for implementation details.
+See [`molecule-cli` PR #5](https://git.moleculesai.app/molecule-ai/molecule-cli/pull/5) for implementation details.

content/docs/guides/remote-workspaces.md

@@ -148,5 +148,5 @@ The agent appears on the canvas with a **purple REMOTE badge** within seconds. F
 ## Next Steps
 
 - **[External Agent Registration Guide →](/docs/guides/external-agent-registration)** — full endpoint reference, Python + Node.js examples, troubleshooting
-- **[molecule-sdk-python →](https://github.com/Molecule-AI/molecule-sdk-python)** — SDK source, `RemoteAgentClient` API docs
-- **[SDK Examples →](https://github.com/Molecule-AI/molecule-sdk-python/tree/main/examples/remote-agent)** — `run.py` demo script, annotated walkthrough
+- **[molecule-sdk-python →](https://git.moleculesai.app/molecule-ai/molecule-sdk-python)** — SDK source, `RemoteAgentClient` API docs
+- **[SDK Examples →](https://git.moleculesai.app/molecule-ai/molecule-sdk-python/src/branch/main/examples/remote-agent)** — `run.py` demo script, annotated walkthrough

content/docs/guides/skill-catalog.md

@@ -65,7 +65,7 @@ molecule skills install arxiv-research --from community
 
 Community skills are reviewed by the Molecule AI team before being
 listed. Submit a skill for review by opening a PR against
-[`molecule-ai/skills`](https://github.com/Molecule-AI/skills).
+`molecule-ai/skills` (repo location TBD post-2026-05-06 GitHub-org-suspension; check the [internal issue tracker](https://git.moleculesai.app/molecule-ai/internal/issues) for the canonical submission path).
 
 ## Installing via config.yaml
 
@@ -171,7 +171,7 @@ molecule skills bundle my-custom-skill --output ./org-templates/my-role/
 ```
 
 **Publishing to the community:** Open a PR against
-[`molecule-ai/skills`](https://github.com/Molecule-AI/skills) with a
+`molecule-ai/skills` (repo location TBD post-2026-05-06 GitHub-org-suspension; check the [internal issue tracker](https://git.moleculesai.app/molecule-ai/internal/issues) for the canonical submission path) with a
 complete skill package. Community skills are reviewed for security and
 correctness before listing.
 

content/docs/hermes.mdx

@@ -339,7 +339,7 @@ If you are routing a Gemini model through a key that triggers the compat shim (e
 - [Concepts — Workspaces](/docs/concepts#workspaces)
 - [API Reference — POST /workspaces](/docs/api-reference#post-workspaces)
 - [Google ADK Runtime](/docs/google-adk) — Gemini-native alternative to Hermes for ADK-first workflows
-- PR #240: [Phase 2a — native Anthropic dispatch](https://github.com/Molecule-AI/molecule-core/pull/240)
-- PR #255: [Phase 2b — native Gemini dispatch](https://github.com/Molecule-AI/molecule-core/pull/255)
-- PR #267: [Phase 2c — multi-turn history on all paths](https://github.com/Molecule-AI/molecule-core/pull/267)
-- Issue [#513](https://github.com/Molecule-AI/molecule-core/issues/513)
+- PR #240: [Phase 2a — native Anthropic dispatch](https://git.moleculesai.app/molecule-ai/molecule-core/pull/240)
+- PR #255: [Phase 2b — native Gemini dispatch](https://git.moleculesai.app/molecule-ai/molecule-core/pull/255)
+- PR #267: [Phase 2c — multi-turn history on all paths](https://git.moleculesai.app/molecule-ai/molecule-core/pull/267)
+- Issue [#513](https://git.moleculesai.app/molecule-ai/molecule-core/issues/513)

content/docs/incidents/INCIDENT_LOG.md

@@ -165,14 +165,14 @@ ticket if a future revival of this BFG procedure is needed.
 
 **Step 2 — Clean origin/main:**
 ```bash
-git clone --mirror https://github.com/Molecule-AI/molecule-core /tmp/molecule-main-mirror
+git clone --mirror https://git.moleculesai.app/molecule-ai/molecule-core /tmp/molecule-main-mirror
 java -jar bfgr.jar --replace-text creds.txt --rewrite-not-committed-by-oss --no-blob-protection /tmp/molecule-main-mirror
 cd /tmp/molecule-main-mirror && git push --mirror
 ```
 
 **Step 3 — Clean origin/staging:**
 ```bash
-git clone --mirror https://github.com/Molecule-AI/molecule-core /tmp/molecule-staging-mirror
+git clone --mirror https://git.moleculesai.app/molecule-ai/molecule-core /tmp/molecule-staging-mirror
 java -jar bfgr.jar --replace-text creds.txt --rewrite-not-committed-by-oss --no-blob-protection /tmp/molecule-staging-mirror
 cd /tmp/molecule-staging-mirror && git push --mirror
 ```
@@ -584,7 +584,7 @@ Core-BE — delegated to Dev Lead (A2A failed). Core-BE sub-team: please pick up
 
 ### Fix PR
 
-[PR #1336](https://github.com/Molecule-AI/molecule-core/pull/1336) filed — `fix(orchestrator): fail-fast if WORKSPACE_ID env var is unset/empty`. Targets staging. Labels: bug, needs-work, area:backend-engineer, area:dev-lead.
+[PR #1336](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1336) filed — `fix(orchestrator): fail-fast if WORKSPACE_ID env var is unset/empty`. Targets staging. Labels: bug, needs-work, area:backend-engineer, area:dev-lead.
 
 ---
 

content/docs/marketplace.mdx

@@ -1,166 +0,0 @@
----
-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

@@ -1,164 +0,0 @@
----
-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

@@ -12,7 +12,6 @@
     "channels",
     "schedules",
     "runtime-mcp",
-    "runtime-mcp/dev-channels-flag",
     "external-agents",
     "tokens",
     "api-reference",
@@ -21,9 +20,6 @@
     "self-hosting/admin-token",
     "observability",
     "troubleshooting",
-    "---Marketplace---",
-    "marketplace",
-    "marketplace/creators",
     "---Security---",
     "security/index",
     "security/safe-mcp-advisory",
@@ -32,8 +28,6 @@
     "google-adk",
     "hermes",
     "---Integrations---",
-    "opencode",
-    "---Migration---",
-    "migration/a2a-sdk-v0-to-v1"
+    "opencode"
   ]
 }

content/docs/migration/a2a-sdk-v0-to-v1.mdx

@@ -1,214 +0,0 @@
----
-title: "a2a-sdk v0 → v1 migration"
-description: "Cheat sheet for migrating workspace runtime code (and forks) from a2a-sdk 0.3.x to 1.x — renamed/removed symbols, common error shapes, before/after diffs."
----
-
-import { Callout } from 'fumadocs-ui/components/callout';
-
-The `a2a-sdk` Python package released v1.0 in late April 2026. The
-Molecule workspace runtime migrated under tracking ID **KI-009** and
-shipped in `molecule-ai-workspace-runtime` **v0.1.11** (commit
-`d5cf872`, PR #39). The platform now runs exclusively on v1.
-
-If you're consuming the platform's published wheel, bumping
-`molecule-ai-workspace-runtime>=0.1.11` handles the migration for
-you. If you maintain a fork of the runtime, an external agent talking
-A2A directly, or your own adapter that imports from `a2a.*`, this page
-is your checklist.
-
-## Why migrate
-
-- **Upstream**: `a2a-sdk` 1.0 reorganised the import surface, flattened
-  `Part`, removed deprecated capability flags, and replaced the
-  `A2AStarletteApplication` wrapper with explicit Starlette route
-  factories.
-- **Platform**: as of 2026-04-24 the platform sends/receives via v1
-  shapes natively. The SDK ships a v0_3 compat layer (enabled in the
-  runtime via `enable_v0_3_compat=True` on `create_jsonrpc_routes`) so
-  in-flight 0.x callers don't break, but new code should target v1.
-- **Forks/external runtimes**: v0 code throws on `import a2a.utils`
-  and `from a2a.server.apps import A2AStarletteApplication` once you
-  install v1, so the migration is a hard cutover at install time, not
-  a soft deprecation.
-
-## Cheat sheet — renamed and removed symbols
-
-The four breaking changes that hit the Molecule runtime during KI-009.
-All four are confirmed against
-`/Users/hongming/Documents/GitHub/molecule-monorepo/workspace/` source.
-
-### 1. `new_agent_text_message` renamed to `new_text_message`
-
-- **v0 location**: `a2a.utils.new_agent_text_message`
-- **v1 location**: `a2a.helpers.new_text_message`
-
-Both the module path and the symbol name changed.
-
-### 2. `Part` API flattened — `TextPart` removed
-
-- **v0**: `Part(root=TextPart(text="..."))` — `Part` wrapped a `root`
-  union of `TextPart` / `FilePart` / `DataPart`.
-- **v1**: `Part(text="...")` — `Part` accepts the text payload
-  directly. `TextPart` no longer exists as a public symbol.
-
-`FilePart` / `DataPart` are similarly flattened (`Part(file=...)`,
-`Part(data=...)`); the Molecule runtime only emits text parts so the
-file/data shapes weren't exercised in KI-009 and aren't covered by
-this guide.
-
-### 3. `A2AStarletteApplication` removed — use route factories
-
-- **v0**: `from a2a.server.apps import A2AStarletteApplication` then
-  `A2AStarletteApplication(agent_card, request_handler).build()`.
-- **v1**: `from a2a.server.routes import create_agent_card_routes,
-  create_jsonrpc_routes` then build a Starlette app from the returned
-  route lists.
-
-The factories also let you mount the JSON-RPC endpoint at any path
-(the runtime mounts at `/` because the platform POSTs to root, see
-`workspace/main.py:279`).
-
-### 4. `state_transition_history` capability flag removed
-
-- **v0**: `AgentCapabilities(streaming=..., push_notifications=...,
-  state_transition_history=True)` was a per-agent opt-in.
-- **v1**: the field is gone from `AgentCapabilities`. Per the SDK's own
-  `a2a/compat/v0_3/conversions.py`: *"No longer supported in v1.0"*.
-  The capability is now universal — `Task.history` is always available
-  and `tasks/get` accepts `historyLength` via `apply_history_length()`.
-
-If you pass `state_transition_history=...` as a kwarg to
-`AgentCapabilities` under v1, Pydantic will reject it. Drop the kwarg.
-See [`workspace/main.py:215`](https://github.com/Molecule-AI/molecule-monorepo/blob/main/workspace/main.py#L215)
-for the explanatory comment that prevents future accidental re-adds.
-
-## Common error shapes
-
-When v0 code runs against the v1 SDK, the failure modes look like this:
-
-| Error | Cause |
-|---|---|
-| `ModuleNotFoundError: No module named 'a2a.utils'` | v0 import path; module renamed to `a2a.helpers`. |
-| `ImportError: cannot import name 'A2AStarletteApplication' from 'a2a.server.apps'` | The whole `a2a.server.apps` module is gone in v1. Switch to `a2a.server.routes` factories. |
-| `ImportError: cannot import name 'TextPart' from 'a2a.types'` | Flattened `Part` API; use `Part(text=...)`. |
-| `ValueError: Protocol message AgentCapabilities has no "state_transition_history" field` | Removed capability flag passed as kwarg; drop it. |
-| `ValueError: Protocol message Part has no "root" field` | v0 `Part(root=TextPart(...))` shape against v1 schema; flatten to `Part(text=...)`. |
-
-The protobuf-style `ValueError` messages always follow the pattern
-`Protocol message <Type> has no "<field>" field` — that's the
-fingerprint of "v0 shape against v1 schema." Treat it as a v0→v1 hint
-even if the field name isn't on the cheat sheet above.
-
-## Migration checklist
-
-1. **Bump the dep** — `a2a-sdk[http-server]>=0.3.25` is the floor; remove
-   any `<1.0` upper bound. The Molecule wheel uses
-   `a2a-sdk[http-server]>=0.3.25` with no upper bound (see
-   [`molecule-ai-workspace-runtime/pyproject.toml`](https://github.com/Molecule-AI/molecule-ai-workspace-runtime/blob/main/pyproject.toml)).
-2. **Fix imports** — sweep the four renamed/removed symbols above. A
-   safe grep is `grep -rn "from a2a\\|import a2a"` across your tree.
-3. **Fix removed-field reads/writes** — search for
-   `state_transition_history` usage and delete the kwarg/field access.
-4. **Flatten `Part` constructors** — search for `Part(root=` and
-   convert to `Part(text=...)` / `Part(file=...)` / `Part(data=...)`.
-5. **Replace the app factory** — search for `A2AStarletteApplication`
-   and rewrite the bootstrap using `create_agent_card_routes` +
-   `create_jsonrpc_routes`. Pass `enable_v0_3_compat=True` to
-   `create_jsonrpc_routes` if your peers may still be on v0.
-6. **Re-run tests** — fixture-level mocks of `a2a.helpers` /
-   `a2a.utils` need to mock both names so tests still pass during the
-   rename rollout (see
-   [`workspace/tests/conftest.py:105-111`](https://github.com/Molecule-AI/molecule-monorepo/blob/main/workspace/tests/conftest.py#L105-L111)
-   for the dual-name pattern).
-
-## Before / after diffs
-
-### `new_agent_text_message` → `new_text_message`
-
-```diff
--from a2a.utils import new_agent_text_message
-+from a2a.helpers import new_text_message
-
- async def execute(self, context, event_queue):
--    await event_queue.enqueue_event(new_agent_text_message("hello"))
-+    await event_queue.enqueue_event(new_text_message("hello"))
-```
-
-### Flat `Part` API
-
-```diff
--from a2a.types import Part, TextPart
-+from a2a.types import Part
-
--msg_parts = [Part(root=TextPart(text=final_text))]
-+msg_parts = [Part(text=final_text)]
-```
-
-### `AgentCapabilities` — drop `state_transition_history`
-
-```diff
- capabilities=AgentCapabilities(
-     streaming=config.a2a.streaming,
-     push_notifications=config.a2a.push_notifications,
--    state_transition_history=True,
- ),
-```
-
-### `A2AStarletteApplication` → route factories
-
-```diff
--from a2a.server.apps import A2AStarletteApplication
-+from a2a.server.routes import create_agent_card_routes, create_jsonrpc_routes
-
--app = A2AStarletteApplication(
--    agent_card=agent_card,
--    http_handler=request_handler,
--).build()
-+routes = []
-+routes.extend(create_agent_card_routes(agent_card))
-+routes.extend(create_jsonrpc_routes(
-+    request_handler=request_handler,
-+    rpc_url="/",
-+    enable_v0_3_compat=True,
-+))
-+app = Starlette(routes=routes)
-```
-
-The `enable_v0_3_compat=True` flag on `create_jsonrpc_routes` is what
-keeps in-flight v0 callers (peers that haven't migrated yet) from
-breaking — it accepts the old method names and translates them. The
-Molecule runtime ships with this flag on (see
-[`workspace/main.py:279`](https://github.com/Molecule-AI/molecule-monorepo/blob/main/workspace/main.py#L279));
-strip it once your entire fleet is on v1.
-
-## For downstream consumers
-
-- **Using the published wheel** (`pip install
-  molecule-ai-workspace-runtime>=0.1.11`): the migration is in the
-  wheel — no code changes needed in your adapter or workspace template
-  beyond bumping the pin.
-- **Running a fork of the runtime**: cherry-pick or rebase against
-  commit `d5cf872` ("feat: migrate a2a-sdk 1.x (KI-009) (#39)") in
-  `molecule-ai-workspace-runtime`. The diff is the canonical reference
-  for what KI-009 actually changed.
-- **Standalone external agent** (talking A2A without the wheel): apply
-  the [Migration checklist](#migration-checklist) directly to your
-  source. The four cheat-sheet items are the entire surface that
-  changed for the typical agent role; only `Part` flattening and the
-  `state_transition_history` removal affect on-the-wire shapes — the
-  other two are import-only.
-
-<Callout type="info">
-The wheel keeps `enable_v0_3_compat=True` on `create_jsonrpc_routes`,
-so a v0 peer can still hit a v1 wheel and vice versa during the
-migration window. You don't need to coordinate a fleet-wide cutover —
-migrate at your own pace.
-</Callout>
-
-## See also
-
-- [`molecule-ai-workspace-runtime` v0.1.11 release](https://github.com/Molecule-AI/molecule-ai-workspace-runtime/releases/tag/v0.1.11) — first wheel containing KI-009
-- [PR #39 — feat: migrate a2a-sdk 1.x (KI-009)](https://github.com/Molecule-AI/molecule-ai-workspace-runtime/pull/39)
-- [PR #48 — feat(a2a): dual-compat for a2a-sdk 0.3.x and 1.x](https://github.com/Molecule-AI/molecule-ai-workspace-runtime/pull/48) — runtime-side compat shim that keeps v0 peers working against the v1 wheel
-- [Bring Your Own Runtime (MCP)](/docs/runtime-mcp) — universal wheel install path
-- [External Agents](/docs/external-agents) — manual A2A path for non-MCP runtimes

content/docs/plugins/agentskills-compat.md

@@ -163,11 +163,11 @@ not expose.
 | `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)
+- [molecule-ai-plugin-ecc#2](https://git.moleculesai.app/molecule-ai/molecule-ai-plugin-ecc/pull/2)
+- [molecule-ai-plugin-superpowers#2](https://git.moleculesai.app/molecule-ai/molecule-ai-plugin-superpowers/pull/2)
+- [molecule-ai-plugin-molecule-dev#2](https://git.moleculesai.app/molecule-ai/molecule-ai-plugin-molecule-dev/pull/2)
+- [molecule-ai-plugin-molecule-skill-cron-learnings#2](https://git.moleculesai.app/molecule-ai/molecule-ai-plugin-molecule-skill-cron-learnings/pull/2)
+- [molecule-ai-plugin-molecule-skill-update-docs#2](https://git.moleculesai.app/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`

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-monorepo.git
-cd molecule-monorepo
+git clone https://git.moleculesai.app/molecule-ai/molecule-core.git
+cd molecule-core
 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-monorepo) for self-hosting options, or visit [moleculesai.app](https://moleculesai.app) for the hosted platform.
+Explore the [Gitea repo](https://git.moleculesai.app/molecule-ai/molecule-core) for self-hosting options, or visit [moleculesai.app](https://moleculesai.app) for the hosted platform.

content/docs/runtime-mcp.mdx

@@ -52,54 +52,14 @@ 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 \
-  -e WORKSPACE_ID=<your-workspace-uuid> \
-  -e PLATFORM_URL=https://<your-tenant>.moleculesai.app \
-  -e MOLECULE_WORKSPACE_TOKEN=<your-token> \
-  -- molecule-mcp
+claude mcp add molecule -s user -- env \
+  WORKSPACE_ID=<your-workspace-uuid> \
+  PLATFORM_URL=https://<your-tenant>.moleculesai.app \
+  MOLECULE_WORKSPACE_TOKEN=<your-token> \
+  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.
 
@@ -144,53 +104,31 @@ Cline) and restart the client.
 
 ## Optional — declare your identity & capabilities
 
-Four additional env vars control how your workspace appears on the
-canvas and how the wheel's inbound-delivery contract behaves:
+Three additional env vars control how your workspace appears on the
+canvas and to peer agents calling `list_peers`:
 
 | 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 (Claude Code 2.1+ CLI form):
+Example with all three set:
 
 ```bash
-claude mcp add molecule -s user \
-  -e WORKSPACE_ID=<uuid> \
-  -e PLATFORM_URL=https://<tenant>.moleculesai.app \
-  -e MOLECULE_WORKSPACE_TOKEN=<token> \
-  -e MOLECULE_AGENT_NAME='Research Assistant' \
-  -e MOLECULE_AGENT_DESCRIPTION='Reads, summarises, cites.' \
-  -e MOLECULE_AGENT_SKILLS=research,summarisation,citations \
-  -- 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"
-      }
-    }
-  }
-}
+claude mcp add molecule -s user -- 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 \
+  molecule-mcp
 ```
 
 A peer agent's `list_peers()` call would then surface this workspace
@@ -220,7 +158,7 @@ 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 — the universal inbound-delivery primitive (see [Inbound delivery](#inbound-delivery-universal-poll-optional-push)) |
+| `wait_for_message` | Block until the next inbound A2A message arrives |
 | `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) |
@@ -230,130 +168,29 @@ 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.
 
-### Inbound delivery: universal poll, optional push
+### Push-UX for notification-capable hosts
 
-Inbound messages reach the agent via one of two paths. The wheel
-exposes both; which one fires depends on the host's capabilities.
-Both paths converge on the same `inbox_pop` ack so dedup is automatic.
+On top of the polling tools, the wheel emits a JSON-RPC notification
+(`notifications/claude/channel`) on every new inbound message. Hosts
+that recognise that method (Claude Code today; any compliant client
+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.
 
-**Poll path (universal default — works on every spec-compliant MCP
-client).** The wheel's `initialize` handshake includes an `instructions`
-field telling the agent: *"At the start of every turn, before producing
-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.
-
-See [Dev-channels flag — tagged-form requirement](/docs/runtime-mcp/dev-channels-flag)
-for the exact form the flag must take, the failure mode when it's
-wrong, and when operators need to set it manually vs. when the
-hosted SaaS / workspace template handles it for them.
-
-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 |
+Hosts that don't recognise the method silently ignore it, so the same
+wheel works for both push-capable and poll-only runtimes. There is no
+config flag to toggle: pollers keep polling, notification-capable hosts
+get push automatically.
 
 ### MCP spec compliance
 
 The wheel speaks MCP protocol version **2024-11-05** over stdio
-JSON-RPC. It declares the standard `tools` capability plus the
-`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:
+JSON-RPC, declaring only the `tools` capability. It implements the
+standard request methods and nothing client-specific:
 
 | MCP method | Behavior |
 |---|---|
-| `initialize` | Echoes `protocolVersion: "2024-11-05"`, `serverInfo`, declares `tools` + `experimental.claude/channel` capabilities, returns the dual-path delivery `instructions` |
+| `initialize` | Echoes `protocolVersion: "2024-11-05"`, `serverInfo`, declares `tools` capability |
 | `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: ... }]` |
@@ -361,10 +198,8 @@ It implements the 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. The poll path
-(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.
+that don't handle it discard it per JSON-RPC semantics. No part of the
+wheel's tool surface depends on a client recognizing it.
 
 This means **any spec-compliant MCP client** can drive the wheel:
 Claude Code, Cursor, Cline, OpenCode, hermes-agent, or anything else
@@ -439,7 +274,7 @@ MCP config and restart your runtime.
 
 ### `Workspace <id> was deleted on the platform...` from `get_workspace_info`
 
-Since [#2429](https://github.com/Molecule-AI/molecule-core/pull/2449),
+Since [#2429](https://git.moleculesai.app/molecule-ai/molecule-core/pull/2449),
 `GET /workspaces/:id` returns **410 Gone** (not 200 + `status:"removed"`)
 when the workspace has been deleted. The MCP wheel's `get_workspace_info`
 tool surfaces this as a tailored error message:
@@ -470,21 +305,6 @@ 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
@@ -499,44 +319,6 @@ 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/runtime-mcp/dev-channels-flag.mdx

@@ -1,176 +0,0 @@
----
-title: "Dev-channels flag — tagged-form requirement"
-description: "Why Claude Code 2.1.x+ requires `--dangerously-load-development-channels server:molecule` (not the bare flag) to enable inline channel push from the molecule-mcp wheel."
----
-
-import { Callout } from 'fumadocs-ui/components/callout';
-
-The `molecule-mcp` wheel emits a JSON-RPC `notifications/claude/channel`
-notification on every inbound A2A message so Claude Code can render it
-as an inline `<channel>` synthetic user turn — zero polling, zero
-per-turn stall. During the channels research preview, Claude Code only
-processes that notification when the host is launched with the
-`--dangerously-load-development-channels` flag *and the flag carries a
-matching tagged allowlist entry*.
-
-This page covers the form that flag must take, what breaks when it's
-wrong, and when an operator has to think about it.
-
-<Callout type="warn">
-The bare flag (no value) is rejected by the post-2.1 CLI parser, and
-the failure mode propagates upstream as a `Control request timeout:
-initialize` from any SDK that spawns the CLI — every A2A turn wedges
-100% of the time. See [Failure mode](#failure-mode) below.
-</Callout>
-
-## The flag
-
-```
---dangerously-load-development-channels <entries...>
-```
-
-Available in Claude Code **2.1.x and later**. It opts the CLI into
-processing experimental `notifications/<channel>` JSON-RPC methods
-emitted by registered MCP servers and plugin channels. Without it, the
-CLI silently drops those notifications during the allowlist check, even
-though the wheel ships the wire shape correctly.
-
-## Required form: tagged allowlist entries
-
-Each entry must carry one of two prefixes:
-
-| Form | Use for |
-|---|---|
-| `server:<MCP-server-name>` | Manually configured MCP servers — the name matches what you registered with `claude mcp add <name> ...` or the key under `mcpServers` in `~/.claude.json`. |
-| `plugin:<plugin-name>@<owner>/<repo>` | Plugin channels installed from a Claude Code plugin marketplace. |
-
-Multiple entries are space-separated:
-
-```bash
-claude --dangerously-load-development-channels server:molecule server:telegram
-```
-
-Untagged values (`molecule` instead of `server:molecule`) are rejected
-with `--dangerously-load-development-channels entries must be tagged`.
-
-## Failure mode
-
-A bare flag (`--dangerously-load-development-channels` with no value)
-walks through three layers of damage before surfacing:
-
-1. **CLI**: rejects the invocation with
-   `error: option '--dangerously-load-development-channels <servers...>' argument missing`.
-2. **SDK**: `claude-agent-sdk` (used by `claude_sdk_executor.py` in the
-   Claude Code workspace template) renders the kwarg as a bare switch when
-   the value is `None`. The CLI then never responds to the SDK's first
-   `initialize` control message.
-3. **Workspace agent**: the SDK times out with
-   `Control request timeout: initialize`. Every A2A turn wedges — 100%
-   reproducible. Caught live on workspace `dd40faf8` on 2026-05-01.
-
-Two small fixes prevent this: pass a tagged value (don't let `None`
-render as a bare switch), and verify the CLI accepts your specific
-entries before going broad.
-
-## For Molecule operators
-
-Pass `server:molecule` to enable the inbox bridge → MCP
-`notifications/claude/channel` push for the `molecule-mcp` wheel.
-
-```bash
-claude --dangerously-load-development-channels server:molecule
-```
-
-The `molecule` here matches the name you registered the wheel under in
-[Step 2 of the runtime-mcp guide](/docs/runtime-mcp#claude-code) (the
-key under `mcpServers`, or the first positional arg to `claude mcp add`).
-If you registered the wheel as `mol` or `molecule-prod`, use that name
-in the tag.
-
-When push is live, the session header prints:
-
-```
-Listening for channel messages from: server:molecule
-```
-
-…and inbound canvas/peer-agent messages render inline as
-`<channel source="molecule" ...>` synthetic user turns instead of
-arriving via `inbox_peek`.
-
-### Embedding in an SDK-driven agent
-
-If you spawn `claude` through `claude-agent-sdk` (e.g. the Claude Code
-workspace template's `claude_sdk_executor.py`), forward the tagged value
-through `extra_args`:
-
-```python
-from claude_agent_sdk import ClaudeAgentOptions
-
-ClaudeAgentOptions(
-    model=self.model,
-    permission_mode="bypassPermissions",
-    cwd=self._resolve_cwd(),
-    mcp_servers=mcp_servers,
-    system_prompt=self._build_system_prompt(),
-    resume=self._session_id,
-    extra_args={"dangerously-load-development-channels": "server:molecule"},
-)
-```
-
-The SDK forwards `extra_args` keys as `--<key> <value>` to the spawned
-CLI. Passing `None` as the value renders as a bare switch and trips the
-[Failure mode](#failure-mode) chain above.
-
-## Verification
-
-Verified live on 2026-05-02: with the tagged value in `extra_args`,
-the in-workspace agent received `<channel source="molecule" kind="..."
-peer_id="..." activity_id="..." ts="...">` tags inline as synthetic
-user turns. No `wait_for_message` poll was needed for delivery. A2A
-returned coherent replies on every turn.
-
-## When this matters
-
-Only when both of the following apply:
-
-- You're running Claude Code (any version 2.1.x or later) as the
-  workspace runtime, AND
-- The in-workspace `molecule-mcp` server is configured (it is, by
-  default, in the `claude-code` workspace template).
-
-**Hosted Molecule SaaS handles this automatically** — the executor
-passes `extra_args={"dangerously-load-development-channels": "server:molecule"}`
-when spawning the CLI. Operators on hosted SaaS do not need to do
-anything.
-
-**Self-hosted operators using the Claude Code workspace template** also
-get this for free since the template's executor sets `extra_args`. The
-flag only needs operator attention when:
-
-- Forking the Claude Code workspace template and stripping `extra_args`
-  inadvertently.
-- Running `claude` directly outside the template (e.g. interactive
-  sessions on a developer laptop) and wanting inline `<channel>` push.
-- Adding a second tagged source (e.g. `server:telegram` alongside
-  `server:molecule`) — append, don't replace.
-
-Operators on Cursor, Cline, OpenCode, codex, hermes-agent, or any
-non-Claude-Code MCP host are unaffected: those clients ignore the
-notification and the wheel's poll path delivers via
-`wait_for_message` as the universal fallback.
-
-## Forward note
-
-This requirement is a **research-preview gate**. Once Claude Code
-graduates `notifications/<channel>` from research preview to a default
-allowlist, the `--dangerously-load-development-channels` flag will no
-longer be required for the `molecule` server. Drop the `extra_args`
-entry in `claude_sdk_executor.py` (and any operator launch wrappers)
-when that happens — the wheel emits the wire shape correctly today
-and will continue to do so post-graduation.
-
-## See also
-
-- [Bring Your Own Runtime (MCP) — Inbound delivery](/docs/runtime-mcp#inbound-delivery-universal-poll-optional-push)
-- [Bring Your Own Runtime (MCP) — Step 2: Claude Code](/docs/runtime-mcp#claude-code)
-- [Troubleshooting — Control request timeout: initialize](/docs/runtime-mcp#control-request-timeout-initialize-from-the-workspace-agent)

content/docs/security/changelog.md

@@ -12,7 +12,7 @@ This page documents security fixes shipped in the Molecule AI platform. Each ent
 ## 2026-04-20 — CWE-22: Path Traversal in `copyFilesToContainer`
 
 **Severity:** High (CWE-22)
-**PRs:** [#1271](https://github.com/Molecule-AI/molecule-core/pull/1271), [#1270](https://github.com/Molecule-AI/molecule-core/pull/1270), [#1267](https://github.com/Molecule-AI/molecule-core/pull/1267)
+**PRs:** [#1271](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1271), [#1270](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1270), [#1267](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1267)
 **Affected:** `workspace-server/internal/handlers/container_files.go` — `TemplatesHandler.copyFilesToContainer`
 
 ### Vulnerability
@@ -37,7 +37,7 @@ File writes to workspace containers now validate all paths before writing to the
 ## 2026-04-20 — CWE-78: Shell Injection in `deleteViaEphemeral`
 
 **Severity:** High (CWE-78)
-**PR:** [#1310](https://github.com/Molecule-AI/molecule-core/pull/1310)
+**PR:** [#1310](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1310)
 **Affected:** `workspace-server/internal/handlers/container_files.go` — `TemplatesHandler.deleteViaEphemeral`
 
 ### Vulnerability
@@ -69,9 +69,9 @@ Workspace file deletion operations now use safe argument-passing and validate al
 ## 2026-04-21 — CWE-918: SSRF in MCP / A2A Proxy Endpoints (Updated: Regression Fix)
 
 **Severity:** High (CWE-918)
-**Original PRs:** [#1274](https://github.com/Molecule-AI/molecule-core/pull/1274), [#1302](https://github.com/Molecule-AI/molecule-core/pull/1302)
-**Regression Fix PR:** [#1430](https://github.com/Molecule-AI/molecule-core/pull/1430)
-**Regression introduced by:** [#1363](https://github.com/Molecule-AI/molecule-core/pull/1363)
+**Original PRs:** [#1274](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1274), [#1302](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1302)
+**Regression Fix PR:** [#1430](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1430)
+**Regression introduced by:** [#1363](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1363)
 **Affected:** `workspace-server/internal/handlers/mcp.go` — `isSafeURL`, `isPrivateOrMetadataIP`; `workspace-server/internal/handlers/a2a_proxy.go`; `workspace-server/internal/handlers/a2a_proxy_helpers.go`
 
 ### Vulnerability
@@ -105,9 +105,9 @@ In **SaaS mode** (`saasMode()` returns true), cross-EC2 traffic to RFC-1918 addr
 
 ### Regression (2026-04-21)
 
-PR [#1363](https://github.com/Molecule-AI/molecule-core/pull/1363) (handler refactor) moved `isPrivateOrMetadataIP` into `a2a_proxy_helpers.go` but kept a **pre-SaaS version** that unconditionally blocked RFC-1918 addresses, breaking cross-EC2 communication in SaaS. The old version also **returned `false` for all IPv6 inputs**, fully bypassing SSRF protection for IPv6 targets.
+PR [#1363](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1363) (handler refactor) moved `isPrivateOrMetadataIP` into `a2a_proxy_helpers.go` but kept a **pre-SaaS version** that unconditionally blocked RFC-1918 addresses, breaking cross-EC2 communication in SaaS. The old version also **returned `false` for all IPv6 inputs**, fully bypassing SSRF protection for IPv6 targets.
 
-PR [#1430](https://github.com/Molecule-AI/molecule-core/pull/1430) restores the correct SaaS-gated logic and adds proper IPv6 coverage to the A2A proxy path.
+PR [#1430](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1430) restores the correct SaaS-gated logic and adds proper IPv6 coverage to the A2A proxy path.
 
 ### User-facing summary
 
@@ -118,7 +118,7 @@ Platform outbound requests from workspaces (MCP tool calls, A2A proxy routing) v
 ## 2026-04-21 — Audit Ledger HMAC Chain Guard
 
 **Severity:** Low (denial-of-service / data integrity)
-**PRs:** [#1339](https://github.com/Molecule-AI/molecule-core/pull/1339), [#1352](https://github.com/Molecule-AI/molecule-core/pull/1352), [#1354](https://github.com/Molecule-AI/molecule-core/pull/1354) (backport to `main`)
+**PRs:** [#1339](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1339), [#1352](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1352), [#1354](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1354) (backport to `main`)
 **Affected:** `workspace-server/internal/handlers/audit.go`
 
 ### Vulnerability
@@ -144,7 +144,7 @@ Audit chain verification now handles short or malformed HMAC values gracefully,
 ## 2026-04-21 — Credential Scrub: `err.Error()` Leak Prevention
 
 **Severity:** Medium (information disclosure)
-**PRs:** [#1282](https://github.com/Molecule-AI/molecule-core/pull/1282), [#1355](https://github.com/Molecule-AI/molecule-core/pull/1355), [#1359](https://github.com/Molecule-AI/molecule-core/pull/1359)
+**PRs:** [#1282](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1282), [#1355](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1355), [#1359](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1359)
 **Affected:** `workspace-server/internal/handlers/plugins_install_pipeline.go`, `workspace-server/internal/handlers/workspace_provision.go`, `content/docs/incidents/INCIDENT_LOG.md`
 
 ### Vulnerability

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-monorepo.git
-cd molecule-monorepo
+git clone https://git.moleculesai.app/molecule-ai/molecule-core.git
+cd molecule-core
 ./scripts/dev-start.sh
 # Canvas: http://localhost:3000
 # Platform: http://localhost:8080

content/docs/self-hosting/admin-token.mdx

@@ -30,28 +30,7 @@ platform.
 
 ## Setting ADMIN_TOKEN in production
 
-The platform reads `ADMIN_TOKEN` from the process environment, so any
-production-grade host with a secrets store works. Pick the path that
-matches your deployment target.
-
-> **Note (Apr 2026):** The Molecule AI SaaS itself runs on AWS EC2
-> (workspaces) + Railway (control plane). Self-hosters can use any host
-> with secret-injection (Railway, Fly.io, AWS, GCP, bare-metal) — the
-> examples below are illustrative, not prescriptive. See the
-> [`molecule-controlplane` README "Migration history"](https://github.com/Molecule-AI/molecule-controlplane#migration-history)
-> for the canonical SaaS infrastructure record.
-
-### Railway
-
-In the Railway dashboard, go to your service → Variables and add
-`ADMIN_TOKEN`, then redeploy. Or via CLI:
-
-```bash
-railway variables --set ADMIN_TOKEN="your-generated-token"
-railway up
-```
-
-### Fly.io
+### Fly.io (recommended for self-hosted)
 
 ```bash
 fly secrets set ADMIN_TOKEN="your-generated-token"
@@ -113,13 +92,10 @@ payload with a `count` field, the token is working.
 
 To rotate without downtime:
 
-1. **Deploy** the new token via your host's secrets store, e.g.
-   `railway variables --set ADMIN_TOKEN="new-token" && railway up`
-   or `fly secrets set ADMIN_TOKEN="new-token" && fly deploy`.
-2. **Verify** the new token works (see above).
-3. **Remove** the old token from the secrets store. Most managed hosts
-   (Railway, Fly.io, AWS Secrets Manager) do not persist old secret
-   values after unset.
+1. **Deploy** the new token: `fly secrets set ADMIN_TOKEN="new-token" && fly deploy`
+2. **Verify** the new token works (see above)
+3. **Remove** the old token: `fly secrets unset OLD_TOKEN_NAME` (Fly does not
+   persist old secret values after unset)
 
 ## Related
 

content/docs/tutorials/fly-machines-provisioner.md

@@ -1,19 +1,8 @@
 ---
-title: "Provisioning Workspaces on Fly Machines (CONTAINER_BACKEND=flyio) — DEPRECATED"
+title: "Provisioning Workspaces on Fly Machines (CONTAINER_BACKEND=flyio)"
 ---
 # Provisioning Workspaces on Fly Machines (CONTAINER_BACKEND=flyio)
 
-> **DEPRECATED — historical reference only.** As of April 2026, the SaaS
-> control plane and tenant/workspace fleets migrated off Fly Machines to
-> **AWS EC2 (workspaces) + Railway (control plane)**. The current
-> production provisioner lives at
-> [`molecule-controlplane/internal/provisioner/ec2.go`](https://github.com/Molecule-AI/molecule-controlplane/blob/main/internal/provisioner/ec2.go).
-> The Fly provisioner code (`fly.go`, `internal/flyapi/`) remains in the
-> tree as legacy awaiting cleanup but is no longer the production path.
-> See the [`molecule-controlplane` README "Migration history"](https://github.com/Molecule-AI/molecule-controlplane#migration-history)
-> for the canonical record. This page is preserved as the original PR
-> #501 lineage record; do not follow it for new self-hosted deployments.
-
 Molecule AI can provision agent workspaces on [Fly Machines](https://fly.io/docs/machines/) instead of local Docker containers. When `CONTAINER_BACKEND=flyio` is set, every `POST /workspaces` creates a Fly Machine and boots the workspace agent inside it — with tier-based resource limits, env-var injection, and A2A registration handled automatically. The platform manages the workspace (lifecycle, auth, routing); Fly manages the machine it runs on.
 
 > **Scope note (PR #501):** Workspace images must already be published to GHCR before provisioning. The `delete` and `restart` platform endpoints are not yet fully wired to the Fly provisioner — use `flyctl machine stop/destroy` for teardown until a follow-up PR lands.
@@ -99,8 +88,8 @@ Fly Machines start in milliseconds and run in 35+ regions. Provisioning agent wo
 
 ## Related
 
-- PR #501: [feat(platform): Fly Machines provisioner](https://github.com/Molecule-AI/molecule-core/pull/501)
-- PR #481: [feat(ci): deploy to Fly after image push](https://github.com/Molecule-AI/molecule-core/pull/481)
+- PR #501: [feat(platform): Fly Machines provisioner](https://git.moleculesai.app/molecule-ai/molecule-core/pull/501)
+- PR #481: [feat(ci): deploy to Fly after image push](https://git.moleculesai.app/molecule-ai/molecule-core/pull/481)
 - [Fly Machines API docs](https://fly.io/docs/machines/api/)
 - [Platform API reference](../api-reference.md)
-- Issue [#525](https://github.com/Molecule-AI/molecule-core/issues/525)
+- Issue [#525](https://git.moleculesai.app/molecule-ai/molecule-core/issues/525)

content/docs/tutorials/gemini-cli-runtime.md

@@ -64,6 +64,6 @@ The real power surfaces when you mix runtimes on the same Molecule AI tenant. Yo
 
 ## Related
 
-- PR #379: [feat(adapters): add gemini-cli runtime adapter](https://github.com/Molecule-AI/molecule-core/pull/379)
+- PR #379: [feat(adapters): add gemini-cli runtime adapter](https://git.moleculesai.app/molecule-ai/molecule-core/pull/379)
 - [Multi-provider Hermes docs](../architecture/hermes.md)
 - [Workspace runtimes reference](../reference/runtimes.md)

content/docs/tutorials/google-adk-runtime.md

@@ -71,7 +71,7 @@ ADK workspaces participate in the same A2A network as Claude Code, Gemini CLI, H
 
 ## Related
 
-- PR #550: [feat(adapters): add google-adk runtime adapter](https://github.com/Molecule-AI/molecule-core/pull/550)
+- PR #550: [feat(adapters): add google-adk runtime adapter](https://git.moleculesai.app/molecule-ai/molecule-core/pull/550)
 - [Google ADK (adk-python)](https://github.com/google/adk-python)
 - [Gemini CLI runtime tutorial](./gemini-cli-runtime.md)
 - [Platform API reference](../api-reference.md)

content/docs/tutorials/hermes-multi-provider-dispatch.md

@@ -179,9 +179,9 @@ What is on the roadmap for Phase 2d (not yet shipped):
 
 ## Related
 
-- PR #240: [Phase 2a — native Anthropic dispatch](https://github.com/Molecule-AI/molecule-core/pull/240)
-- PR #255: [Phase 2b — native Gemini dispatch](https://github.com/Molecule-AI/molecule-core/pull/255)
-- PR #267: [Phase 2c — multi-turn history on all paths](https://github.com/Molecule-AI/molecule-core/pull/267)
+- PR #240: [Phase 2a — native Anthropic dispatch](https://git.moleculesai.app/molecule-ai/molecule-core/pull/240)
+- PR #255: [Phase 2b — native Gemini dispatch](https://git.moleculesai.app/molecule-ai/molecule-core/pull/255)
+- PR #267: [Phase 2c — multi-turn history on all paths](https://git.moleculesai.app/molecule-ai/molecule-core/pull/267)
 - [Hermes adapter design](../adapters/hermes-adapter-design.md)
 - [Platform API reference](../api-reference.md)
-- Issue [#513](https://github.com/Molecule-AI/molecule-core/issues/513)
+- Issue [#513](https://git.moleculesai.app/molecule-ai/molecule-core/issues/513)

content/docs/tutorials/lark-feishu-channel.md

@@ -93,6 +93,6 @@ Molecule AI canvas without code changes.
 
 ## Related
 
-- PR #480: [feat(channels): Lark / Feishu channel adapter](https://github.com/Molecule-AI/molecule-core/pull/480)
+- PR #480: [feat(channels): Lark / Feishu channel adapter](https://git.moleculesai.app/molecule-ai/molecule-core/pull/480)
 - [Social channels architecture](../agent-runtime/social-channels.md)
 - [Channel adapter reference](../api-reference.md#channels)

content/docs/tutorials/saas-federation.md

@@ -226,7 +226,7 @@ This terminates all EC2 instances, drops the Neon branch, and removes the org re
 |---|---|---|
 | Database | Neon branch-per-tenant | Tenant's branch, operator has no direct access |
 | Compute | EC2 in tenant's VPC | Control plane provisions, operator manages SG rules |
-| Credentials | No AWS/cloud API tokens on tenant | All cloud credentials held by control plane |
+| Credentials | No Fly/API tokens on tenant | All cloud credentials held by control plane |
 | API access | Org-scoped API keys | Tenant manages their own keys; operator has CP-level override |
 | Network | Security group: port 443 from platform only | Control plane manages; tenant can't modify |
 
@@ -246,4 +246,4 @@ For the API reference, see [`docs/api-reference`](/docs/api-reference) — the `
 
 *SaaS federation is available for all Molecule AI platform operators. Contact the Molecule AI team to enable federation on your control plane.*
 
-(`molecule-core` [#1700](https://github.com/Molecule-AI/molecule-core/pull/1700))
+(`molecule-core` [#1700](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1700))

content/docs/tutorials/saas-file-writes-eic.md

@@ -145,7 +145,7 @@ Key push + tunnel + write took longer than 30 s. Common causes: slow AWS EIC in
 
 ## Source PR
 
-PR [#1702](https://github.com/Molecule-AI/molecule-core/pull/1702) — `feat(files-api): SSH-backed write for SaaS workspaces (fixes 500 docker not available)`
+PR [#1702](https://git.moleculesai.app/molecule-ai/molecule-core/pull/1702) — `feat(files-api): SSH-backed write for SaaS workspaces (fixes 500 docker not available)`
 
 Key files in `molecule-core`:
 - `workspace-server/internal/handlers/template_files_eic.go` — EIC write logic

docs/marketing/blog/2026-04-20-how-to-add-browser-automation-to-ai-agents-with-mcp.md

@@ -237,4 +237,4 @@ Once your agent is connected to MCP, it stops being a chatbot with a scrollable
 
 ---
 
-*Have questions or want to share what you're building with MCP? Open a discussion on [GitHub Discussions](https://github.com/Molecule-AI/molecule-core/discussions) or file an issue with the `enhancement` label.*
+*Have questions or want to share what you're building with MCP? File an issue with the `enhancement` label on the [molecule-core issue tracker](https://git.moleculesai.app/molecule-ai/molecule-core/issues).*