docs(internal): bulk-sed molecule-core .md docs → Gitea (#37 final molecule-core sweep)

Mass-sed across 17 files / 38 active refs in molecule-core .md docs
(README + CONTRIBUTING + docs/architecture/ + docs/blog/ + docs/guides/
+ docs/integrations/ + docs/quickstart.md + scripts/README.md).

Driver: /tmp/sweep_core.py — same pattern set as the
internal-marketing bulk-sed (PR #50). 4 url-substitution patterns +
SKIP_PATTERN preserves /pull/<n> /issues/<n> /commit/<sha>
/releases/... historical refs.

Files NOT touched in this PR:
- docs/workspace-runtime-package.md — owned by molecule-core#15
  (workspace-runtime source-edit per #41). Reverted my bulk-sed of
  that file to avoid merge conflict.
- 2 Go-import-path refs in docs/memory-plugins/testing-your-plugin.md
  (github.com/Molecule-AI/molecule-monorepo/platform/internal/...) —
  Q5 cross-repo Go-module migration territory.
- 1 GitHub Gist link in docs/guides/external-workspace-quickstart.md
  (gist.github.com/molecule-ai/...) — no Gitea equivalent;
  consistent with the same handling in docs#1.

Manual fixes (2):
- docs/blog/2026-04-20-chrome-devtools-mcp-seo/index.md:306 —
  GitHub Discussions (no Gitea equivalent) → issue tracker link
- docs/guides/external-workspace-quickstart.md:218 — tracking-issue
  ?q= query-string url (regex didn't catch) → reformulated text +
  Gitea search-by-query approach

Pattern matches my docs#1 (public docs site) PR + internal#50
(internal/marketing bulk-sed). Standard substitutions:
- https://github.com/Molecule-AI/<repo> → https://git.moleculesai.app/molecule-ai/<repo>
- /blob/<branch>/ + /tree/<branch>/ → /src/branch/<branch>/

Refs: molecule-ai/internal#37, molecule-ai/internal#38

CONTRIBUTING.md

@@ -22,7 +22,7 @@ development workflow, conventions, and how to get your changes merged.
 
 ```bash
 # Clone the repo
-git clone https://github.com/Molecule-AI/molecule-core.git
+git clone https://git.moleculesai.app/molecule-ai/molecule-core.git
 cd molecule-core
 
 # Install git hooks
@@ -57,7 +57,7 @@ See `CLAUDE.md` for a full list of environment variables and their purposes.
 
 This repo is scoped to **code** (canvas, workspace, workspace-server, related
 infra). Public content (blog posts, marketing copy, OG images, SEO briefs,
-DevRel demos) lives in [`Molecule-AI/docs`](https://github.com/Molecule-AI/docs).
+DevRel demos) lives in [`Molecule-AI/docs`](https://git.moleculesai.app/molecule-ai/docs).
 The `Block forbidden paths` CI gate fails any PR that writes to `marketing/`
 or other removed paths — open against `Molecule-AI/docs` instead.
 
@@ -110,7 +110,7 @@ causing a render loop when any node position changed.
 
 1. **Repo-wide:** "Automatically delete head branches" is on. Once a PR merges, the branch is deleted server-side. Any subsequent `git push` to that branch fails with `remote rejected — no such branch`.
 
-2. **CI:** the `pr-guards` workflow (calling [molecule-ci `disable-auto-merge-on-push`](https://github.com/Molecule-AI/molecule-ci/blob/main/.github/workflows/disable-auto-merge-on-push.yml)) fires on every push to an open PR. If auto-merge was already enabled, it's disabled and a comment is posted. You must explicitly re-enable after verifying the new commit.
+2. **CI:** the `pr-guards` workflow (calling [molecule-ci `disable-auto-merge-on-push`](https://git.moleculesai.app/molecule-ai/molecule-ci/src/branch/main/.github/workflows/disable-auto-merge-on-push.yml)) fires on every push to an open PR. If auto-merge was already enabled, it's disabled and a comment is posted. You must explicitly re-enable after verifying the new commit.
 
 **Workflow rules that follow from the guards:**
 - Push **all** commits before running `gh pr merge --auto`.
@@ -180,9 +180,9 @@ and run CI manually.
 Code in this repo lands in molecule-core. Some related runtime artifacts
 live in their own repos:
 
-- [`Molecule-AI/molecule-ai-workspace-runtime`](https://github.com/Molecule-AI/molecule-ai-workspace-runtime) — Python adapter SDK (`molecule_runtime`) that runs inside containerized Molecule workspaces. Bridges Claude Code SDK / hermes / langgraph / etc. → A2A queue.
-- [`Molecule-AI/molecule-sdk-python`](https://github.com/Molecule-AI/molecule-sdk-python) — `A2AServer` + `RemoteAgentClient` for external agents that register over the public `/registry/register` flow.
-- [`Molecule-AI/molecule-mcp-claude-channel`](https://github.com/Molecule-AI/molecule-mcp-claude-channel) — Claude Code channel plugin. Bridges A2A traffic into a running Claude Code session via MCP `notifications/claude/channel`. Polling-based (no tunnel required); install with `claude --channels plugin:molecule@Molecule-AI/molecule-mcp-claude-channel`.
+- [`Molecule-AI/molecule-ai-workspace-runtime`](https://git.moleculesai.app/molecule-ai/molecule-ai-workspace-runtime) — Python adapter SDK (`molecule_runtime`) that runs inside containerized Molecule workspaces. Bridges Claude Code SDK / hermes / langgraph / etc. → A2A queue.
+- [`Molecule-AI/molecule-sdk-python`](https://git.moleculesai.app/molecule-ai/molecule-sdk-python) — `A2AServer` + `RemoteAgentClient` for external agents that register over the public `/registry/register` flow.
+- [`Molecule-AI/molecule-mcp-claude-channel`](https://git.moleculesai.app/molecule-ai/molecule-mcp-claude-channel) — Claude Code channel plugin. Bridges A2A traffic into a running Claude Code session via MCP `notifications/claude/channel`. Polling-based (no tunnel required); install with `claude --channels plugin:molecule@Molecule-AI/molecule-mcp-claude-channel`.
 
 When extending the **A2A surface** in molecule-core (`workspace-server/internal/handlers/a2a_proxy.go` etc.), consider whether the change has a downstream impact on the runtime SDK or the channel plugin — they're versioned independently but share the wire shape.
 

README.md

@@ -39,8 +39,8 @@
   <a href="./docs/agent-runtime/workspace-runtime.md"><strong>Workspace Runtime</strong></a>
 </p>
 
-[![Deploy on Railway](https://railway.app/button.svg)](https://railway.app/new/template?template=https://github.com/Molecule-AI/molecule-monorepo)
-[![Deploy to Render](https://render.com/images/deploy-to-render-button.svg)](https://render.com/deploy?repo=https://github.com/Molecule-AI/molecule-monorepo)
+[![Deploy on Railway](https://railway.app/button.svg)](https://railway.app/new/template?template=https://git.moleculesai.app/molecule-ai/molecule-monorepo)
+[![Deploy to Render](https://render.com/images/deploy-to-render-button.svg)](https://render.com/deploy?repo=https://git.moleculesai.app/molecule-ai/molecule-monorepo)
 
 </div>
 
@@ -249,7 +249,7 @@ Workspace Runtime (Python image with adapters)
 ## Quick Start
 
 ```bash
-git clone https://github.com/Molecule-AI/molecule-monorepo.git
+git clone https://git.moleculesai.app/molecule-ai/molecule-monorepo.git
 cd molecule-monorepo
 
 cp .env.example .env

README.zh-CN.md

@@ -38,8 +38,8 @@
   <a href="./docs/agent-runtime/workspace-runtime.md"><strong>Workspace Runtime</strong></a>
 </p>
 
-[![Deploy on Railway](https://railway.app/button.svg)](https://railway.app/new/template?template=https://github.com/Molecule-AI/molecule-core)
-[![Deploy to Render](https://render.com/images/deploy-to-render-button.svg)](https://render.com/deploy?repo=https://github.com/Molecule-AI/molecule-core)
+[![Deploy on Railway](https://railway.app/button.svg)](https://railway.app/new/template?template=https://git.moleculesai.app/molecule-ai/molecule-core)
+[![Deploy to Render](https://render.com/images/deploy-to-render-button.svg)](https://render.com/deploy?repo=https://git.moleculesai.app/molecule-ai/molecule-core)
 
 </div>
 
@@ -248,7 +248,7 @@ Workspace Runtime (Python image with adapters)
 ## 快速开始
 
 ```bash
-git clone https://github.com/Molecule-AI/molecule-core.git
+git clone https://git.moleculesai.app/molecule-ai/molecule-core.git
 cd molecule-core
 
 cp .env.example .env

docs/architecture/canary-release.md

@@ -4,7 +4,7 @@ How a workspace-server code change reaches the prod tenant fleet — and how to
 
 > **⚠️ State note (2026-04-22):** this doc describes the **intended design**. As of this write, the canary fleet described below is **not actually running** — no canary tenants are provisioned, `CANARY_TENANT_URLS` / `CANARY_ADMIN_TOKENS` / `CANARY_CP_SHARED_SECRET` are empty in repo secrets, and `canary-verify.yml` fails every run.
 >
-> Current merges gate on manual `promote-latest.yml` dispatches, not canary. See [molecule-controlplane/docs/canary-tenants.md](https://github.com/Molecule-AI/molecule-controlplane/blob/main/docs/canary-tenants.md) for the Phase 1 code work that's already shipped + the Phase 2 plan for actually standing up the fleet + a "should we even do this now?" decision framework.
+> Current merges gate on manual `promote-latest.yml` dispatches, not canary. See [molecule-controlplane/docs/canary-tenants.md](https://git.moleculesai.app/molecule-ai/molecule-controlplane/src/branch/main/docs/canary-tenants.md) for the Phase 1 code work that's already shipped + the Phase 2 plan for actually standing up the fleet + a "should we even do this now?" decision framework.
 >
 > **Account-specific identifiers (AWS account ID, IAM role name) referenced below in the original design have been redacted from this public doc.** The actual values — if they exist — are in `Molecule-AI/internal/runbooks/canary-fleet.md`. If you're implementing Phase 2, start there.
 >

docs/architecture/molecule-technical-doc.md

@@ -1,7 +1,7 @@
 # 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-monorepo](https://git.moleculesai.app/molecule-ai/molecule-monorepo) repository.
 
 ---
 
@@ -1149,11 +1149,11 @@ 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
+- **GitHub**: https://git.moleculesai.app/molecule-ai/molecule-monorepo
+- **Architecture Docs**: https://git.moleculesai.app/molecule-ai/molecule-monorepo/src/branch/main/docs/architecture
+- **API Protocol**: https://git.moleculesai.app/molecule-ai/molecule-monorepo/src/branch/main/docs/api-protocol
+- **Agent Runtime**: https://git.moleculesai.app/molecule-ai/molecule-monorepo/src/branch/main/docs/agent-runtime
+- **Product Docs**: https://git.moleculesai.app/molecule-ai/molecule-monorepo/src/branch/main/docs/product
 
 ---
 

docs/architecture/secrets-key-custody.md

@@ -79,7 +79,7 @@ For SOC2 / ISO 27001 / customer security questionnaires:
 
 ## Pointers
 
-- KMS envelope code: [`molecule-controlplane/internal/crypto/kms.go`](https://github.com/Molecule-AI/molecule-controlplane/blob/main/internal/crypto/kms.go)
-- Static-key fallback: [`molecule-controlplane/internal/crypto/aes.go`](https://github.com/Molecule-AI/molecule-controlplane/blob/main/internal/crypto/aes.go)
+- KMS envelope code: [`molecule-controlplane/internal/crypto/kms.go`](https://git.moleculesai.app/molecule-ai/molecule-controlplane/src/branch/main/internal/crypto/kms.go)
+- Static-key fallback: [`molecule-controlplane/internal/crypto/aes.go`](https://git.moleculesai.app/molecule-ai/molecule-controlplane/src/branch/main/internal/crypto/aes.go)
 - Tenant secrets handler: [`workspace-server/internal/crypto/aes.go`](../../workspace-server/internal/crypto/aes.go)
 - Tenant secrets schema: [database-schema.md](./database-schema.md#workspace_secrets)

docs/blog/2026-04-20-chrome-devtools-mcp-seo/index.md

@@ -299,8 +299,8 @@ Or use the Canvas UI: Workspace → Config → MCP Servers → Add browser MCP s
 
 **Try it free** — Molecule AI is open source and self-hostable. Get a workspace running in under 5 minutes.
 
-→ [Get started on GitHub →](https://github.com/Molecule-AI/molecule-core)
+→ [Get started on GitHub →](https://git.moleculesai.app/molecule-ai/molecule-core)
 
 ---
 
-*Have a browser automation use case you want to see covered? Open a discussion on [GitHub Discussions](https://github.com/Molecule-AI/molecule-core/discussions) — or file an issue with the `enhancement` label.*
+*Have a browser automation use case you want to see covered? File an issue with the `enhancement` label on the [molecule-core issue tracker](https://git.moleculesai.app/molecule-ai/molecule-core/issues).*

docs/blog/2026-04-20-remote-workspaces/index.md

@@ -148,7 +148,7 @@ Then follow the [quick-start guide](/docs/guides/remote-workspaces.md).
 Or run the annotated example directly:
 
 ```bash
-git clone https://github.com/Molecule-AI/molecule-sdk-python
+git clone https://git.moleculesai.app/molecule-ai/molecule-sdk-python
 cd molecule-sdk-python/examples/remote-agent
 # Create workspace with runtime:external, grab the ID, then:
 WORKSPACE_ID=<your-id> PLATFORM_URL=https://acme.moleculesai.app python3 run.py
@@ -160,6 +160,6 @@ The agent appears on the canvas within seconds.
 
 → [Remote Workspaces Guide →](/docs/guides/remote-workspaces.md)
 → [External Agent Registration Reference →](/docs/guides/external-agent-registration.md)
-→ [molecule-sdk-python →](https://github.com/Molecule-AI/molecule-sdk-python)
+→ [molecule-sdk-python →](https://git.moleculesai.app/molecule-ai/molecule-sdk-python)
 
 *Phase 30 shipped in PRs #1075–#1083 and #1085–#1100 on `molecule-core`.*

docs/blog/2026-04-22-a2a-v1-agent-platform/index.md

@@ -133,4 +133,4 @@ With protocol-native A2A, you get:
 
 Molecule AI's external agent registration is production-ready. Documentation is live at [External Agent Registration Guide](https://docs.molecule.ai/docs/guides/external-agent-registration). The npm package for the MCP server is available at [`@molecule-ai/mcp-server`](https://www.npmjs.com/package/@molecule-ai/mcp-server).
 
-Read the full [A2A v1.0 protocol spec](https://github.com/Molecule-AI/molecule-core/blob/main/docs/api-protocol/a2a-protocol.md) on GitHub.
+Read the full [A2A v1.0 protocol spec](https://git.moleculesai.app/molecule-ai/molecule-core/src/branch/main/docs/api-protocol/a2a-protocol.md) on GitHub.

docs/blog/2026-04-22-remote-workspaces/index.md

@@ -45,7 +45,7 @@ canonicalUrl: "https://docs.molecule.ai/blog/remote-workspaces"
   " proficiencyLevel": "Expert",
   "genre": ["technical documentation", "product announcement"],
   "sameAs": [
-    "https://github.com/Molecule-AI/molecule-core",
+    "https://git.moleculesai.app/molecule-ai/molecule-core",
     "https://molecule.ai"
   ]
 }
@@ -270,7 +270,7 @@ Configure it in your project's `.mcp.json` and any AI agent (Claude Code, Cursor
 
 → [External Agent Registration Guide](/docs/guides/external-agent-registration) — full step-by-step with Python and Node.js reference implementations
 
-→ [GitHub: molecule-core](https://github.com/Molecule-AI/molecule-core) — source and issues
+→ [GitHub: molecule-core](https://git.moleculesai.app/molecule-ai/molecule-core) — source and issues
 
 → [Phase 30 Launch Thread on X](https://x.com) — follow for updates
 

docs/blog/a2a-v1-production-reference-2026-04-24.md

@@ -170,4 +170,4 @@ The `staging` branch is now on `a2a-sdk` 1.0.0. The `main` branch still carries
 
 If you're running `a2a-sdk` 0.3.x and planning the 1.0.0 migration, this post is the reference. The four breaking changes are well-contained, the migration is a single PR, and the eight smoke scenarios above will tell you whether the upgrade is clean before you merge.
 
-Questions? The [A2A protocol spec](https://github.com/google-a2a/a2a-specification) is the authoritative source. For Molecule AI's production A2A implementation, see [External Agent Registration](https://docs.molecule.ai/docs/guides/external-agent-registration) or open an issue in the [molecule-core](https://github.com/Molecule-AI/molecule-core) repo.
+Questions? The [A2A protocol spec](https://github.com/google-a2a/a2a-specification) is the authoritative source. For Molecule AI's production A2A implementation, see [External Agent Registration](https://docs.molecule.ai/docs/guides/external-agent-registration) or open an issue in the [molecule-core](https://git.moleculesai.app/molecule-ai/molecule-core) repo.

docs/guides/external-workspace-quickstart.md

@@ -215,7 +215,7 @@ 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)).
 
 ---
 

docs/guides/remote-workspaces.md

@@ -143,5 +143,5 @@ 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

docs/guides/skill-catalog.md

@@ -61,7 +61,7 @@ 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`](https://git.moleculesai.app/molecule-ai/skills).
 
 ## Installing via config.yaml
 
@@ -151,7 +151,7 @@ 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`](https://git.moleculesai.app/molecule-ai/skills) with a
 complete skill package. Community skills are reviewed for security and
 correctness before listing.
 

docs/integrations/runtime-native-mcp-status.md

@@ -96,7 +96,7 @@ fork needed in production.
   `resolve_platform_id` for plugin-platform-safe deserialization, and
   `self.adapters[adapter.platform]` keying fix (caught by real-subprocess
   test before merge — see below).
-- **Plugin package**: [Molecule-AI/hermes-platform-molecule-a2a](https://github.com/Molecule-AI/hermes-platform-molecule-a2a)
+- **Plugin package**: [Molecule-AI/hermes-platform-molecule-a2a](https://git.moleculesai.app/molecule-ai/hermes-platform-molecule-a2a)
   v0.1.0 — public, MIT-licensed. 11 unit tests + 8 in-process E2E
   + 4 real-subprocess E2E checkpoints all green.
 - **Workspace template patch**: [Molecule-AI/molecule-ai-workspace-template-hermes#32](https://github.com/Molecule-AI/molecule-ai-workspace-template-hermes/pull/32)
@@ -154,7 +154,7 @@ intermediate shim earns its complexity.
 ## Codex (OpenAI Codex CLI)
 
 **Status:** Template SHIPPED. Repo live at
-[`Molecule-AI/molecule-ai-workspace-template-codex`](https://github.com/Molecule-AI/molecule-ai-workspace-template-codex)
+[`Molecule-AI/molecule-ai-workspace-template-codex`](https://git.moleculesai.app/molecule-ai/molecule-ai-workspace-template-codex)
 (14 files, 1411 LOC, 12/12 tests). molecule-core registration in
 [PR #2512](https://github.com/Molecule-AI/molecule-core/pull/2512).
 E2E with real A2A traffic remains.

docs/quickstart.md

@@ -17,7 +17,7 @@ This path is aligned to the current repository and current UI. It gets you from
 ## The one-command path
 
 ```bash
-git clone https://github.com/Molecule-AI/molecule-monorepo.git
+git clone https://git.moleculesai.app/molecule-ai/molecule-monorepo.git
 cd molecule-monorepo
 ./scripts/dev-start.sh
 ```
@@ -42,7 +42,7 @@ If you'd rather run each component yourself — useful when you're iterating on
 ### Step 1: Clone the repository
 
 ```bash
-git clone https://github.com/Molecule-AI/molecule-monorepo.git
+git clone https://git.moleculesai.app/molecule-ai/molecule-monorepo.git
 cd molecule-monorepo
 ```
 

scripts/README.md

@@ -11,7 +11,7 @@ There are three related scripts; pick the right one:
 |---|---|---|
 | `measure-coordinator-task-bounds.sh` | **Canonical** v1 harness for the RFC #2251 / Issue 4 reproduction. Provisions a PM coordinator + Researcher child via `claude-code-default` + `langgraph` templates, sends a synthesis-heavy A2A kickoff, observes elapsed time + activity trace. | OSS-shape platform — localhost or any `/workspaces`-shaped endpoint. Has tenant/admin-token guards for non-localhost runs. |
 | `measure-coordinator-task-bounds-runner.sh` | Generalised runner for the same measurement contract but with **arbitrary template + secret + model combinations** (Hermes/MiniMax, etc.). Useful for cross-runtime variants without modifying the canonical harness. | Same as above (local or SaaS via `MODE=saas`). |
-| `measure-coordinator-task-bounds.sh` (in [molecule-controlplane](https://github.com/Molecule-AI/molecule-controlplane)) | **Production-shape** variant that bootstraps a real staging tenant via `POST /cp/admin/orgs`, then runs the same measurement against `<slug>.staging.moleculesai.app`. | Staging controlplane only — refuses to run against production. |
+| `measure-coordinator-task-bounds.sh` (in [molecule-controlplane](https://git.moleculesai.app/molecule-ai/molecule-controlplane)) | **Production-shape** variant that bootstraps a real staging tenant via `POST /cp/admin/orgs`, then runs the same measurement against `<slug>.staging.moleculesai.app`. | Staging controlplane only — refuses to run against production. |
 
 See `reference_harness_pair_pattern` (auto-memory) for when to use which
 and the cross-repo design rationale.