[technical-writer-agent]

fix(tutorials): update GitHub.com → Gitea URLs in EC2 provisioner tutorial

Post-suspension URL migration — all molecule-controlplane references
now point to git.moleculesai.app/molecule-ai/molecule-controlplane.

Co-Authored-By: Claude Opus 4.7 <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

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/guides/external-workspace-quickstart.md

@@ -158,7 +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. |
 
@@ -260,11 +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/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/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/runtime-mcp.mdx

@@ -274,7 +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:

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/tutorials/aws-ec2-provisioner.md

@@ -0,0 +1,284 @@
+---
+title: "Provisioning Workspaces on AWS EC2 (production SaaS provisioner)"
+description: "How the molecule-controlplane EC2 provisioner turns POST /cp/orgs and POST /workspaces calls into running tenant + workspace EC2 instances — env vars, lifecycle, tier sizing, and the migration off Fly Machines."
+---
+
+# Provisioning Workspaces on AWS EC2 (production SaaS provisioner)
+
+As of April 2026, Molecule AI's SaaS control plane provisions both **tenants**
+(per-org platform VMs) and **workspaces** (per-agent inference VMs) on
+AWS EC2 instances. The provisioner lives at
+[`molecule-controlplane/internal/provisioner/ec2.go`](https://git.moleculesai.app/molecule-ai/molecule-controlplane/blob/main/internal/provisioner/ec2.go)
+and is auto-wired by [`cmd/server/main.go`](https://git.moleculesai.app/molecule-ai/molecule-controlplane/blob/main/cmd/server/main.go)
+whenever AWS credentials are present in the control-plane environment. The
+platform manages workspace lifecycle, auth, and routing; AWS manages the
+underlying EC2, security groups, and network plumbing.
+
+This tutorial documents what env vars the provisioner reads, what AWS
+actions it performs on a `POST /workspaces`, and how to operate it. It is
+the replacement for the deprecated [Fly Machines provisioner](./fly-machines-provisioner.md)
+tutorial.
+
+> **Audience:** operators running a self-hosted Molecule AI control plane
+> against their own AWS account, and contributors debugging the
+> production CP. End-users of `*.moleculesai.app` do not need any of
+> this — provisioning happens transparently when you create an org or
+> workspace in the canvas.
+
+## When EC2 is the active provisioner
+
+`cmd/server/main.go` switches on whether `AWS_ACCESS_KEY_ID` is set in the
+process environment. If yes, it constructs an `*provisioner.EC2` from the
+config below and registers it as the tenant provisioner. There is **no**
+`CONTAINER_BACKEND=ec2` switch — the dispatcher key is presence of AWS
+credentials. (The legacy `flyio` backend still has dead code in the tree
+but is no longer wired in `main.go`.)
+
+A typical Railway-hosted control plane log line on boot:
+
+```
+provisioner: EC2 (region=us-east-2, ami=ami-0ea3c35c5c3284d82)
+tenant provisioner: EC2 ✓
+```
+
+If `AWS_ACCESS_KEY_ID` is unset, you'll see `provisioner: disabled`
+instead — useful for local dev where you want orgs CRUD to work without
+AWS access.
+
+## Environment variables
+
+The full list of env vars `cmd/server/main.go` passes into
+`provisioner.EC2Config`. Anything not listed here is unused by the
+provisioner.
+
+### Required for any EC2 provisioning
+
+| Var | Default | Purpose |
+|-----|---------|---------|
+| `AWS_ACCESS_KEY_ID` | — | Toggle: presence enables EC2 wiring at all |
+| `AWS_SECRET_ACCESS_KEY` | — | Standard AWS SDK credential pair |
+| `AWS_REGION` | `us-east-1` | Region for tenant + workspace launches |
+| `EC2_AMI` | `ami-0ea3c35c5c3284d82` (Ubuntu 22.04 us-east-2) | Default AMI when no `thin_ami_pins` row matches |
+| `EC2_VPC_ID` | — | VPC for per-tenant SG creation; falls back to `EC2_SECURITY_GROUP` if unset |
+| `EC2_SUBNET_ID` | — | Subnet for `RunInstances` |
+| `SECRETS_ENCRYPTION_KEY` | — | KMS-envelope DEK for tenant secret-at-rest; provisioner stays disabled until set |
+
+### Required for production (#44 secure bootstrap)
+
+| Var | Purpose |
+|-----|---------|
+| `EC2_TENANT_IAM_PROFILE` | Instance profile attached to every tenant EC2 so it can fetch its bootstrap bundle from Secrets Manager at boot. Without this set, `Provision` returns the error `"Secrets Manager + IAM instance profile are required (#113 — plaintext user-data path removed)"`. |
+| `PROVISION_SHARED_SECRET` | Shared HMAC-secret stored alongside the tenant bootstrap bundle so workspace-server can authenticate inbound `/cp/...` callbacks |
+| `CP_ADMIN_API_TOKEN` | Token the tenant uses to call admin endpoints back on the control plane |
+| `CP_BASE_URL` | URL the tenant boot script uses to reach the control plane (typically `https://api.moleculesai.app`) |
+
+### Required for the canvas Terminal tab
+
+| Var | Purpose |
+|-----|---------|
+| `EIC_ENDPOINT_SG_ID` | Security-group ID of the region's [EC2 Instance Connect endpoint](https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/ec2-instance-connect-endpoint.html). The provisioner adds a `tcp/22` ingress rule to every per-tenant + per-workspace SG sourced from this SG, so the canvas Terminal can EIC-tunnel into the box for diagnostic ssh. Empty leaves the canvas Terminal broken with `failed to open EIC tunnel`. Discover with `aws ec2 describe-instance-connect-endpoints --region <region>`. |
+
+### Cloudflare integration (per-tenant subdomains)
+
+| Var | Purpose |
+|-----|---------|
+| `CLOUDFLARE_API_TOKEN` | Enables CF DNS client; provisioner creates the per-tenant `<slug>.<APP_DOMAIN>` CNAME |
+| `CLOUDFLARE_ACCOUNT_ID` | Enables CF Tunnel client (preferred over Worker + wildcard DNS) |
+| `CLOUDFLARE_ZONE_ID` | DNS zone the tenant CNAMEs are written under |
+| `APP_DOMAIN` | Default `moleculesai.app`; tenant FQDN becomes `<slug>.<APP_DOMAIN>` |
+
+### Optional — runtime images, tier image, backups, canary, multi-env
+
+| Var | Purpose |
+|-----|---------|
+| `MOLECULE_ENV` | `dev` / `staging` / `prod`; stamped on every EC2 tag and scopes the orphan-report's AWS lister so envs don't false-positive each other |
+| `EC2_INSTANCE_TYPE` | Default `t3.small` for tenant VMs (workspaces use the per-tier table below) |
+| `EC2_SECURITY_GROUP` | Fallback shared SG when `EC2_VPC_ID` is unset; production should leave this empty |
+| `EC2_KEY_NAME` | Optional EC2 KeyPair name for emergency console SSH |
+| `TENANT_IMAGE` | OCI ref for the tenant platform image (e.g. `ghcr.io/molecule-ai/platform-tenant:staging-<sha>`) |
+| `CANARY_TENANT_IMAGE` | Override `TENANT_IMAGE` for orgs flagged `is_canary=true` |
+| `CANARY_ROLE_ARN`, `CANARY_REGION`, `CANARY_VPC_ID`, `CANARY_SUBNET_ID` | Second-AWS-account target for canary tenant launches; all four required together |
+| `TENANT_BACKUP_S3_PREFIX` | Empty disables nightly `pg_dump`; set `s3://bucket/path` to enable |
+| `TENANT_BACKUP_REPORT_URL` | Defaults to `${CP_BASE_URL}/cp/tenants/backup-report` |
+| `GHCR_PULL_TOKEN` | GHCR pull token written into the tenant bootstrap bundle (private images only) |
+
+For the always-current set, grep
+[`cmd/server/main.go` lines 86–158](https://git.moleculesai.app/molecule-ai/molecule-controlplane/blob/main/cmd/server/main.go#L86-L158)
+for `os.Getenv` calls inside the `provisioner.NewEC2` block.
+
+## What happens on `POST /cp/orgs` (tenant provision)
+
+`OrgsHandler.Create` calls into `(*EC2).Provision(ctx, cfg)`. Roughly:
+
+1. **Cloudflare cleanup** — `cleanupStaleSlugArtifacts` scrubs any
+   leftover tunnel/DNS rows from a previously-purged org with the same
+   slug, so the slug is reusable.
+2. **Cloudflare Tunnel + DNS** — `CreateTunnel` → `CreateTunnelDNS`
+   (writes `<slug>.<APP_DOMAIN>` → `<tunnel-id>.cfargotunnel.com`) →
+   `ConfigureTunnelIngress` (registers the hostname on the tunnel's
+   remote config so CF's edge knows to forward). DNS or ingress
+   failures roll back the tunnel and abort the provision — fail-fast
+   behavior added 2026-04-26 after a six-hour outage in which
+   unreachable tenants timed out at 600–900s instead of surfacing the
+   real CF API problem.
+3. **Bootstrap secrets to AWS Secrets Manager** — the provisioner
+   generates a per-tenant DB password + admin token, packages them with
+   the GHCR pull token, tunnel token, encryption key, and shared
+   secret, and `PutSecret`s them at `awsapi.TenantSecretName(orgID)`.
+   The tenant fetches this bundle at boot via its instance profile —
+   no plaintext secrets in user-data (see #113).
+4. **Per-tenant SG creation** — `createPerTenantSG` calls
+   `CreateSecurityGroup` with the resolved VPC, the per-org name, and
+   the ingress rules from `tenantIngressRules(vpcCidr, EICEndpointSGID)`.
+   The SG ingress always includes the canvas-terminal EIC `tcp/22`
+   rule sourced from the EIC endpoint's own SG (UserIdGroupPairs, not
+   `0.0.0.0/0` — only AWS EIC's endpoint can use it).
+5. **`RunInstances`** — `awsClient.RunInstance(ctx, awsapi.LaunchConfig{...})`
+   launches with `InstanceType = TenantInstanceType` (default
+   `t3.small`), the resolved AMI, IAM instance profile, base64-encoded
+   user-data, and tags `OrgID` / `OrgSlug` / `Role=tenant` / `TunnelID`
+   / `SGID`. Volume size is 30 GB.
+6. **Audit row** — every CF, SG, Secrets Manager, and EC2 lifecycle
+   event is recorded in the `tenant_resources` audit table (#2343)
+   so the orphan reconciler can diff claims vs live state.
+
+`Provision` returns a `*Result` whose fields (`FlyMachineID`, `FlyRegion`,
+`AdminToken`) are still named after Fly. The EC2 provisioner fake-fills
+them with EC2 equivalents (`InstanceID`, `AWSRegion`); a column-rename
+migration is on the controlplane backlog.
+
+## What happens on `POST /workspaces` (workspace provision)
+
+`workspace-server`'s `POST /workspaces` reaches the control plane via
+`/cp/workspaces/provision`, which calls
+`(*EC2).ProvisionWorkspace(ctx, workspaceID, runtime, orgID, tier, platformURL, env)`:
+
+1. **Resolve tier resources** — `workspaceTierResources(tier)` returns
+   `(instanceType, volumeSize)` per the table below. Hermes runtime
+   floors `volumeSize` to 50 GB regardless of tier (uv + Python venv +
+   Node.js gateway pegs disk at 18–25 GB during install).
+2. **Resolve AMI** — `resolveWorkspaceAMI` looks up `thin_ami_pins`
+   for the runtime + region. A pin row means the AMI is pre-baked
+   (per `packer/scripts/install-base.sh`) and user-data can skip
+   apt-update + the Python/Node installs (60–140 s saved per
+   provision, RFC #388). Fallback to the static `WorkspaceAMI`.
+3. **Resolve runtime image** — `resolveRuntimeImage` looks up
+   `runtime_image_pins` and emits the containerized user-data path
+   (docker pull + run) when present. Independent of the AMI gate
+   above; the new path also installs Docker if missing on a thin/stock
+   AMI.
+4. **Per-workspace SG creation** — same `createPerTenantSG` call with
+   `namePrefix="workspace"`. Workspace SGs get
+   `workspaceIngressRules(EICEndpointSGID)` — currently the EIC
+   `tcp/22` rule and nothing else (workspaces sit behind the
+   Cloudflare Tunnel for HTTP).
+5. **`RunInstance`** — launches with `wsShort = workspaceID[:12]`
+   prefixed name, the resolved instance type + volume + AMI +
+   user-data, and tags `WorkspaceID` / `Runtime` / `Role=workspace`
+   / `SGID` / `OrgID`. The `OrgID` tag is what lets
+   `DeprovisionInstance` cascade-terminate workspace EC2s when their
+   tenant is deleted (incident 2026-04-23: ~27 orphaned workspace
+   EC2s pinned staging at the 64 vCPU limit before the tag was
+   added).
+6. **Audit row** — `tenant_resources` `KindEC2Instance` `StateCreated`
+   with role / runtime / tier / workspace metadata.
+
+The boot script registers the workspace agent with the platform via
+`/workspaces/:id/register`, the platform issues an A2A auth token, and
+the agent comes up ready for `message/send` calls.
+
+## Tier-based resource sizing
+
+`workspaceTierResources` is the single source of truth. As of writing,
+all tiers below T4 are clamped up to T4 (the SaaS floor) and tiers
+above T4 are also clamped down to T4 (today's max):
+
+| Tier | Instance type | Volume | Effective use |
+|------|---------------|--------|---------------|
+| T1 / T2 | clamped to T4 | clamped to T4 | not in production |
+| T3 | `t3.medium` | 40 GB | reserved (clamped today) |
+| T4 | `t3.large` | 80 GB | all production workspaces |
+
+If you set a tier outside `[3, 4]` the clamp lifts it to T4 — a cheap
+mis-provision rather than a fall-through to the unset `t3.small`
+default. The clamp was added in PR #434 follow-up after `tier=5`
+silently yielded `t3.small`.
+
+Hermes overrides volume to 50 GB minimum regardless of tier.
+
+## Lifecycle — stop, restart, redeploy, teardown
+
+| Operation | Mechanism |
+|-----------|-----------|
+| **Stop / start a tenant** | `POST /cp/admin/tenants/:slug/{stop,start}` → `(*EC2).Stop` / `Start` via the EC2 API (no termination) |
+| **Redeploy a tenant** (in-place new image) | `POST /cp/admin/tenants/:slug/redeploy` → SSM Run Command pulls the latest `TENANT_IMAGE` and recreates the platform container; never reboots EC2 |
+| **Refresh workspace template images** | `POST /cp/admin/tenants/:slug/workspaces/redeploy` (single-tenant) or `POST /cp/admin/tenants/workspaces/redeploy-fleet` (canary-batched fleet); HTTP-only, no SSM |
+| **Delete a workspace** | platform `DELETE /workspaces/:id` → CP `DeprovisionInstance(workspaceInstanceID, ...)` terminates the EC2 + cleans DNS + SG |
+| **Delete a tenant (Art. 17 cascade)** | `DELETE /cp/orgs/:slug` → cascade-terminates all workspace EC2s tagged with this `OrgID`, then terminates the tenant EC2, then deletes the SG, Secrets Manager bundle, CF tunnel + CNAME |
+| **Orphan recovery** | `tenant_resources` audit table + 30-min reconciler that diffs claims vs live AWS state and exposes orphan counts via `/cp/admin/stats` |
+
+`DeprovisionInstance` polls termination under its own deadline so a
+stuck shutdown surfaces as a deprovision failure (and the caller's
+retry replays the cascade) instead of becoming a silent leak (#263).
+
+## Why EC2 (vs Fly Machines)
+
+The control plane has migrated infrastructure twice in April 2026 — both
+documented in the
+[molecule-controlplane README "Migration history"](https://git.moleculesai.app/molecule-ai/molecule-controlplane#migration-history):
+
+- **Apr 2026 — CP host:** Fly (`molecule-cp.fly.dev`) → Railway
+  (`api.moleculesai.app`).
+- **Apr 2026 — tenant + workspace compute:** Fly Machines → AWS EC2
+  with SSM Run Command for redeploy.
+
+The drivers were production needs Fly couldn't easily meet:
+
+- **Region + data-residency control.** EU customers required
+  EU-resident tenant data; AWS regional pinning per tenant is
+  straightforward, Fly's region routing is per-app and harder to
+  guarantee per-tenant.
+- **AWS-native auth chain for the canvas Terminal.** EC2 Instance
+  Connect lets the platform open SSH tunnels to a tenant box via
+  short-lived (60 s) IAM-signed public keys — no shared SSH keys,
+  no inbound `0.0.0.0/0` rules. The same path powers the Files API
+  EIC writes (see [SaaS file writes via EC2 Instance Connect](./saas-file-writes-eic.md)).
+- **Secrets Manager + IAM instance profiles** for tenant bootstrap
+  secrets (#113 removed the plaintext user-data path).
+- **Cloudflare Tunnels** instead of public IPs — no inbound exposure
+  on tenant EC2s; CF edge is the only ingress.
+- **`tenant_resources` audit table + reconciler** for cascade-cleanup
+  guarantees that Fly's flat machine list couldn't enforce.
+
+Old `internal/flyapi/` and `internal/provisioner/fly.go` files remain
+in the controlplane tree as legacy code awaiting cleanup; they are not
+wired in `cmd/server/main.go`.
+
+## Operating notes
+
+- **Schema names still say "fly".** The `org_instances` columns
+  `fly_app` / `fly_machine_id` / `fly_region` are fake-filled with EC2
+  equivalents; a rename migration is on the controlplane backlog
+  (`PLAN.md`).
+- **`SECRETS_ENCRYPTION_KEY` gates the whole provisioner.** The crypto
+  envelope is required even when only AWS creds are present; without
+  it, `tenant provisioner: DISABLED` is logged and `POST /cp/orgs`
+  accepts the row but never spins a tenant.
+- **Per-tenant SG creation needs `EC2_VPC_ID`.** If you only set
+  `EC2_SECURITY_GROUP` (the legacy shared-SG fallback), every tenant
+  shares one SG — caught the bug in PR #434 review. Production must
+  set `EC2_VPC_ID`.
+- **`EIC_ENDPOINT_SG_ID` is silently load-bearing.** If unset, the
+  canvas Terminal hangs with `failed to open EIC tunnel` and the
+  Files API EIC write path returns 500 — the EC2 boots fine, the
+  symptom only shows when an operator opens the canvas Terminal tab.
+
+## References
+
+- [`molecule-controlplane/internal/provisioner/ec2.go`](https://git.moleculesai.app/molecule-ai/molecule-controlplane/blob/main/internal/provisioner/ec2.go) — provisioner source
+- [`molecule-controlplane/cmd/server/main.go`](https://git.moleculesai.app/molecule-ai/molecule-controlplane/blob/main/cmd/server/main.go) — env-var wiring
+- [`molecule-controlplane` README "Migration history"](https://git.moleculesai.app/molecule-ai/molecule-controlplane#migration-history) — canonical record
+- [AWS EC2 Instance Connect endpoints](https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/ec2-instance-connect-endpoint.html)
+- [AWS Secrets Manager](https://docs.aws.amazon.com/secretsmanager/latest/userguide/intro.html)
+- [SaaS file writes via EC2 Instance Connect](./saas-file-writes-eic.md) — EIC is also the Files API write channel
+- [Fly Machines provisioner (DEPRECATED)](./fly-machines-provisioner.md) — previous backend, retained for migration history

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

@@ -88,8 +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

@@ -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