Three changes that bring the local harness from "covers what staging
covers minus the SaaS topology" to "exercises every surface we shipped
this session against the prod-shape Dockerfile.tenant image."
1. Drop the /etc/hosts requirement.
Replays previously needed `127.0.0.1 harness-tenant.localhost` in
/etc/hosts to resolve the cf-proxy. That gated the harness behind a
sudo step on every fresh dev box and CI runner. The cf-proxy nginx
already routes by Host header (matches production CF tunnel: URL is
public, Host carries tenant identity), so the no-sudo path is to
target loopback :8080 with `Host: harness-tenant.localhost` set as
a header.
New `tests/harness/_curl.sh` centralises this — curl_anon /
curl_admin / curl_workspace / psql_exec wrappers all set the Host
+ auth headers automatically. seed.sh, peer-discovery-404.sh,
buildinfo-stale-image.sh updated to source it. Legacy /etc/hosts
users still work via env-var override.
2. Fix the seed.sh FK regression that blocked DB-side replays.
POST /workspaces ignores any `id` in the request body and generates
one server-side. seed.sh was minting client-side UUIDs that never
reached the workspaces table, so any replay that INSERTed into
activity_logs (FK-constrained on workspace_id) failed with the
workspace-not-found error. Capture the returned id from the
response instead.
3. Two new replays cover the surfaces shipped this session.
chat-history.sh — exercises the full SaaS-shape wire that PR #2472
(peer_id filter), #2474 (chat_history client tool), and #2476
(before_ts paging) ride on. 8 phases / 16 assertions: peer_id filter,
limit cap, before_ts paging, OR-clause covering both source_id and
target_id, malformed peer_id 400, malformed before_ts 400, URL-encoded
SQLi-shape rejection. Verified PASS against the live harness.
channel-envelope-trust-boundary.sh — exercises PR #2471 + #2481 by
importing from `molecule_runtime.*` (the wheel-rewritten path) so
it catches "wheel build dropped a fix that unit tests still pass."
5 phases / 11 assertions: malicious peer_id scrubbed from envelope,
agent_card_url omitted on validation failure, XML-injection bytes
scrubbed, valid UUID preserved, _agent_card_url_for direct gate.
Verified PASS against published wheel 0.1.79.
run-all-replays.sh auto-discovers — no registration needed. Full
lifecycle (boot → seed → 4 replays → teardown) runs clean.
Roadmap section updated to reflect Phase 1 (this PR) → Phase 2
(multi-tenant + CI gate) → Phase 3 (real CP) → Phase 4 (Miniflare +
LocalStack + traffic replay).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
This monorepo is public. Internal content (positioning, competitive
briefs, sales playbooks, PMM/press drip, draft campaigns) belongs in
Molecule-AI/internal — never here.
## What this PR removes
/research/ (3 competitive briefs)
/marketing/ (45 files: assets, audio, community, copy,
demos, devrel, drip, pmm, press, sales)
/docs/marketing/ (31 draft campaign / blog / brief files)
comment-1172.json + comment-1173.json
test-pmm-temp.txt
tick-reflections-temp.md
83 files removed, 7,141 lines deleted from public history (going forward —
historical commits remain visible in this repo's git log).
## Companion: internal repo absorption
Molecule-AI/internal PR `chore/migrate-monorepo-internal-content-2026-04-23`
absorbs all 79 files into `from-monorepo-2026-04-23/` for curator triage
into the existing internal/marketing/ tree. Bulk-dump avoids file-collision
on overlapping subdirs (audio, devrel, pmm).
## Three-layer enforcement so this can't recur
1. .gitignore — blocks `git add` of /research, /marketing, /docs/marketing,
/comment-*.json, *-temp.{md,txt}, /test-pmm-*, /tick-reflections-*
2. .github/workflows/block-internal-paths.yml — CI hard gate. Fails any PR
that adds a forbidden path. Cannot be silently bypassed.
3. docs/internal-content-policy.md — canonical decision tree for agents
and humans. Linked from the CI failure message.
A separate PR on molecule-ai-org-template-molecule-dev updates SHARED_RULES
to teach every agent role to write internal content directly to
Molecule-AI/internal via gh repo clone + commit + PR (the prevention-at-
source layer; this PR is the mechanical backstop).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Reverts the `.gitignore` checkin-exception for molecule-dev that let it
creep back on every main↔staging sync. Keeping this dir in core meant:
- 800KB of template files shipping with every monorepo clone
- Confusion about which copy is canonical (this one vs the standalone
Molecule-AI/molecule-ai-org-template-dev repo)
- Merge churn — 0506e0c re-added it against #6e6de39's removal intent
just by taking 'theirs' in a conflict resolution
All org-templates now live in their own repos, fetched via
scripts/clone-manifest.sh when needed locally. molecule-dev has no
special status; it's the same shape as every other org template.
The .gitignore rule is now a simple `/org-templates/` with no exceptions,
matching the rule structure already used for `/plugins/` and
`/workspace-configs-templates/`. Future conflict resolutions can't re-add
by accident because git won't track anything under that path.
User flagged this at session start 2026-04-23 ('org-templates should only
exist as standalone template repo'). Fixing for real this time.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
The Canvas template palette was empty on a fresh clone because
`workspace-configs-templates/`, `org-templates/`, and `plugins/` are
gitignored and nothing populated them. The registry already exists —
`manifest.json` at repo root lists every curated
`workspace-template-*`, `org-template-*`, and `plugin-*` repo, and
`scripts/clone-manifest.sh` clones them — but the step was absent
from the README and setup.sh, so new users never ran it.
### What this commit does
**1. `setup.sh` runs `clone-manifest.sh` automatically** (once).
After starting the Docker network but before booting infra, iterate
`manifest.json` and clone any workspace_templates / org_templates /
plugins that aren't already populated. Idempotent — subsequent
runs skip dirs that have content. Requires `jq`; when jq is missing
the step prints a clear install hint and skips (doesn't fail).
**2. `clone-manifest.sh` is idempotent.** Before running `git clone`,
check whether the target directory already exists and is non-empty —
skip if so. Lets `setup.sh` rerun safely without forcing the operator
to delete already-cloned template repos.
**3. `ListTemplates` logs the reason it skips a template.** The
handler previously swallowed `resolveYAMLIncludes` errors with
`continue`, so a broken template showed up as an empty palette with
no log trail. Now the include-expansion and yaml.Unmarshal failure
paths both emit a descriptive `log.Printf` — the exact message that
made the stale `org-templates/molecule-dev/` snapshot debuggable:
ListTemplates: skipping molecule-dev — !include expansion failed:
!include "core-platform.yaml" at line 25: open .../teams/
core-platform.yaml: no such file or directory
**4. Remove the in-tree `org-templates/molecule-dev/` snapshot** (170
files). Matches the explicit intent of prior commit
`bfec9e53` — "remove org-templates/molecule-dev/ — standalone repo
is source of truth". A later "full staging snapshot" re-added a
partial copy that had `!include` references to 7 role files that
never existed in the snapshot (`core-platform.yaml`,
`controlplane.yaml`, `app-docs.yaml`, `infra.yaml`, `sdk.yaml`,
`release-manager/workspace.yaml`, `integration-tester/workspace.yaml`).
`clone-manifest.sh` repopulates it fresh from
`Molecule-AI/molecule-ai-org-template-molecule-dev`.
.gitignore exception for `molecule-dev/` is dropped accordingly
— the whole `/org-templates/*` tree is now gitignored, symmetric
with `/plugins/` and `/workspace-configs-templates/`.
**5. Doc updates** (README, README.zh-CN, CONTRIBUTING) mention `jq`
as a prerequisite and describe what setup.sh now does.
### Verification
On a fresh-nuked DB with the updated branch:
1. `bash infra/scripts/setup.sh` — cleanly clones 33/33 manifest
repos (20 plugins, 8 workspace_templates, 5 org_templates), then
boots infra. Second run skips all 33 (idempotent).
2. `go run ./cmd/server` — "Applied 41 migrations", :8080 healthy.
3. `curl http://localhost:8080/org/templates` returns 4 templates
(was `[]`):
- Free Beats All
- MeDo Smoke Test
- Molecule AI Worker Team (Gemini)
- Reno Stars Agent Team
4. `bash tests/e2e/test_api.sh` — 61/61 pass.
5. `npx vitest run` in canvas — 902/902 pass.
6. `shellcheck infra/scripts/setup.sh` — clean.
### SaaS parity
All changes are local-dev surface. `setup.sh`, `clone-manifest.sh`,
and the local `org-templates/` directory aren't part of the CP
provisioner path — SaaS tenant machines get their templates via
Dockerfile layers or CP-side provisioning, not `clone-manifest.sh`.
The `ListTemplates` log addition is harmless either way (replaces a
silent `continue` with a `log.Printf + continue`).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
These directories are cloned from their standalone repos
(molecule-ai-org-template-*, molecule-ai-plugin-*) and should
never be committed to molecule-core directly.
Removed the !/org-templates/molecule-dev/ exception that allowed
PR #1056 to land template files in the wrong repo.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Comprehensive rewrite of the Molecule AI dev team org template:
- Rename agents to {team}-{role} convention (e.g., core-be, cp-lead, app-qa)
- Add 5 new team leads: Core Platform Lead, Controlplane Lead, App & Docs Lead, Infra Lead, SDK Lead
- Add new roles: Release Manager, Integration Tester, Technical Writer, Infra-SRE, Infra-Runtime-BE, SDK-Dev, Plugin-Dev
- Delete triage-operator and triage-operator-2 (leads own triage now)
- Set default model to MiniMax-M2.7, tier 3, idle_interval_seconds 900
- Update org.yaml category_routing to new agent names
- Add orchestrator-pulse schedules for all leads (*/5 cron)
- Add pick-up-work schedules for engineers (*/15 cron)
- Add qa-review schedules for QA agents (*/15 cron)
- Add security-scan schedules for security agents (*/30 cron)
- Add release-cycle and e2e-test schedules for Release Manager and Integration Tester
- Update marketing agents with web search MCP and media generation capabilities
- All schedule prompts reference Molecule-AI/internal for PLAN.md and known-issues.md
- Un-ignore org-templates/molecule-dev/ in .gitignore for version tracking
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Publish has been failing since the 2026-04-18 open-source restructure
(#964's merge) because workspace-server/Dockerfile still COPYs
./molecule-ai-plugin-github-app-auth/ but the restructure moved that
code out to its own repo. Every main merge since has produced a
"failed to compute cache key: /molecule-ai-plugin-github-app-auth:
not found" error — prod images haven't moved.
Fix: add an actions/checkout step that fetches the plugin repo into
the build context before docker build runs.
Private-repo safe: uses PLUGIN_REPO_PAT secret (fine-grained PAT with
Contents:Read on Molecule-AI/molecule-ai-plugin-github-app-auth).
Falls back to the default GITHUB_TOKEN if the plugin repo is public.
Ops: set repo secret PLUGIN_REPO_PAT before the next main merge, or
publish will fail with a 404 on the checkout step.
Also gitignores the cloned dir so local dev builds don't accidentally
commit it.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Remove entries for org-templates/, plugins/, docs/.vitepress/dist/
that no longer exist. Deduplicate .claude-bridge/ entry.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
CLAUDE.md was a 44KB catch-all mixing architecture docs (useful for
everyone) with agent operating instructions (internal). Split:
- docs/architecture/overview.md — system architecture, component
descriptions, 13 key patterns (import cycles, health detection,
communication rules, WebSocket flow, lifecycle, etc.)
- docs/api-reference.md — full REST API route table + database schema
- CLAUDE.md → gitignored (stays local for agent tooling)
All internal PR/issue references stripped from the new docs.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- Remove compiled workspace-server/server binary from git
- Fix .gitignore, .gitattributes, .githooks/pre-commit for renamed dirs
- Fix CI workflow path filters (workspace-template → workspace)
- Replace real EC2 IP and personal slug in test_saas_tenant.sh
- Scrub molecule-controlplane references in docs
- Fix stale workspace-template/ paths in provisioner, handlers, tests
- Clean tracked Python cache files
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Security:
- Replace hardcoded Cloudflare account/zone/KV IDs in wrangler.toml
with placeholders; add wrangler.toml to .gitignore, ship .example
- Replace real EC2 IPs in docs with <EC2_IP> placeholders
- Redact partial CF API token prefix in retrospective
- Parameterize Langfuse dev credentials in docker-compose.infra.yml
- Replace Neon project ID in runbook with <neon-project-id>
Community:
- Add CONTRIBUTING.md (build, test, branch conventions, CI info)
- Add CODE_OF_CONDUCT.md (Contributor Covenant 2.1)
Cleanup:
- Replace personal runner username/machine name in CI + PLAN.md
- Replace personal tenant URL in MCP setup guide
- Replace personal author field in bundle-system doc
- Replace personal login in webhook test fixture
- Rewrite cryptominer incident reference as generic security remediation
- Remove private repo commit hashes from PLAN.md
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
molecule-medo now lives at Molecule-AI/molecule-ai-plugin-molecule-medo
(same pattern as all other plugins). Removed the gitignore exception
that kept it in the monorepo.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Add org-templates/molecule-dev/system-prompt.md as a canonical org-level
shared-context template for all molecule-dev org agents. The Communication
section explains that /workspace/AGENTS.md is auto-generated at startup from
config.yaml (via agents_md.py / PR #763), describes the AAIF format it
follows, explains the GET /workspace/AGENTS.md peer-discovery contract, and
tells agents to keep their config.yaml name/role/description accurate as the
sole source of truth.
Also restructure the /org-templates/ gitignore rule from a hard directory-ignore
to a content-glob pattern so this specific reference template can be tracked
while all other cloned standalone-repo content remains ignored.
Co-authored-by: Molecule AI Documentation Specialist <documentation-specialist@agents.moleculesai.app>
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
The Baidu MeDo hackathon integration was sitting in builtin_tools/ as dead
code — not imported by any loader but shipped with every workspace image,
misleadingly suggesting it was a core builtin.
Changes:
- Move builtin_tools/medo.py → plugins/molecule-medo/skills/medo-tools/scripts/medo.py
(git detects this as a rename — no code changes, identical tool surface)
- Add plugins/molecule-medo/plugin.yaml (manifest: name, version, runtimes, tags)
- Add plugins/molecule-medo/skills/medo-tools/SKILL.md (frontmatter + setup docs)
- Move workspace-template/tests/test_medo.py → plugins/molecule-medo/tests/test_medo.py
(update _MEDO_PATH to resolve from plugin root; add conftest.py for langchain mock)
- Update .gitignore: change /plugins/ blanket ignore to /plugins/* so this plugin
can be tracked until it gets its own standalone repo
Acceptance criteria met:
- builtin_tools/medo.py removed from core
- plugins/molecule-medo/ created with identical tool surface (9/9 tests pass)
- cd workspace-template && pytest → 1021 passed, 2 xfailed (no regression)
- MEDO_API_KEY was never in default provisioning (.env.example / config.py clean)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds brand-monitor/ — a cron-based X API v2 poller that posts new Molecule AI
brand mentions to Slack #brand-monitoring. Surge mode enables 15-min polling
for launch days / crisis windows; state persisted in .surge_state.json so
restarts within an active window continue in surge mode.
Closes#549
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Integrates github.com/Molecule-AI/molecule-ai-plugin-github-app-auth.
When GITHUB_APP_ID is set, the platform constructs a plugin
Authenticator at boot and registers it as an EnvMutator on the
WorkspaceHandler. Every workspace provision then gets a fresh
GITHUB_TOKEN / GH_TOKEN injected from the App's installation token
(rotates ~hourly, refresh 5 min before expiry).
Verified live this turn:
- Platform boot log: `github-app-auth: registered, 1 mutator(s) in chain`
- `docker exec ws-<id> gh auth status` → `Logged in as molecule-ai[bot] (GH_TOKEN)`
- `gh issue list --repo Molecule-AI/molecule-core` returns real data
(Hermes #498/#499/#500 visible from inside a workspace container)
## Changes
- platform/go.mod + go.sum: new dep on the plugin
- platform/cmd/server/main.go: import + conditional registration
(soft-skip when GITHUB_APP_ID is unset for self-hosted/dev)
- docker-compose.yml: pass GITHUB_APP_* env + bind-mount private key
## Drive-by
.gitignore: exclude /org-templates /plugins /workspace-configs-templates
— these dirs are populated locally by clone-manifest.sh from the
standalone repos, should never be committed to core. Without this rule
my previous git add -A staged 33 embedded git dirs.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Local-only secrets (GitHub App private keys, future per-tenant
credentials) live in .secrets/ on the host. Belt-and-braces with the
existing .env exclusion so a stray copy / rename can't leak.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Skills are opt-in (I have to remember to invoke them). Hooks are
ambient — they fire on every matching event automatically. This PR
moves the careful-mode and learnings discipline from "doc I should
read" to "harness-enforced behavior I cannot bypass".
## 6 new hooks (.claude/hooks/)
- pre-bash-careful — REFUSES git push --force to main, rm -rf at root,
DROP TABLE against prod schema. WARNs on force-with-lease, gh pr/
issue close. Tested: blocks the destructive case, allows safe ones.
- pre-edit-freeze — implements /freeze. When .claude/freeze contains
a path glob, edits outside it are denied. Tested: edits to PLAN.md
blocked when scope locked to platform/internal/handlers/.
- session-start-context — auto-loads last 20 cron-learnings, freeze
status, open-PR/issue counts as additionalContext at session start.
Tested: emits valid SessionStart JSON.
- post-edit-audit — appends every Edit/Write to .claude/audit.jsonl
(gitignored). One-line records {ts, tool, file, ok}. Tested writes.
- user-prompt-tag — injects context warnings when prompt mentions
force-push, drop-table, "delete all", "push to main", etc. Tested:
emits warning for "force push the fix to main".
- subagent-stop-judge — off by default; touch .claude/judge-subagents
to enable. When on, prompts orchestrator to verify subagent's last
message addresses the original task. Cost-free MVP (no LLM call yet).
All hooks are Python (jq isn't on the hook PATH on macOS — Python is).
Shared helpers in _lib.py: read_input, deny_pretooluse, add_context,
warn_to_stderr.
## settings.json — wires all 6 hooks
Adds SessionStart, UserPromptSubmit, SubagentStop event handlers.
Existing PreToolUse:Bash + PostToolUse:Edit chains gain the new hooks
alongside the existing ones (check-inbox.sh, echo reminder).
Adds @modelcontextprotocol/server-sequential-thinking MCP server for
structured chain-of-thought scratchpad — useful when triaging multiple
PRs in parallel without losing context.
## .claude/commands/triage.md — slash command shortcut
Manual /triage runs the same flow as the c5074cd5 hourly cron, on
demand. Saves ~4KB of prompt every invocation by pulling the cron
prompt out of working memory.
## CLAUDE.md additions
New "Agent operating rules (auto-loaded — read first)" section right
after Ecosystem Context. Documents:
- Cron / triage discipline (read learnings, treat docs PRs touching
CLAUDE.md/PLAN.md as noteworthy, write per-tick reflections)
- Table of all 6 hooks active in this repo
- List of skills and how to invoke them
- Standing rules (inviolable) consolidated for the agent
This block auto-loads into every conversation context — free behavior
change without me remembering to opt in.
## .gitignore
audit.jsonl, freeze, judge-subagents, per-tick-reflections.md are all
local operational state, never committed.
## Verification
- echo '{"tool_input":{"command":"git push --force origin main"}}' |
bash pre-bash-careful.sh → emits deny JSON ✓
- Same for git status (safe command) → empty output, exit 0 ✓
- pre-edit-freeze with .claude/freeze=platform/handlers/ blocks
edits to PLAN.md, allows edits inside the locked path ✓
- post-edit-audit appends valid JSONL ✓
- session-start-context emits additionalContext with PR/issue counts ✓
- user-prompt-tag emits warning for "force push to main" prompt ✓
- python3 -c "json.load(open('.claude/settings.json'))" → valid ✓
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- Delete empty platform/plugins/ (dead remnant; plugins/ at repo root is
the real registry; router.go comment updated)
- Gitignore local dev cruft: platform/workspace-configs-templates/,
.agents/ (codex/gemini skill cache), backups/
- Untrack .agents/skills/ (keep local, stop tracking)
- Move examples/remote-agent/ → sdk/python/examples/remote-agent/
(co-locate with the SDK it exercises); update refs in
molecule_agent README + __init__ + PLAN.md + the demo's own README
- Move docs/superpowers/plans/ → plugins/superpowers/plans/
(plans were written by the superpowers plugin's writing-plans
subskill; belong with the plugin, not under docs)
- Add tests/README.md explaining the unit-tests-per-package +
root-E2E split so new contributors don't ask
- Add docs/README.md explaining why site tooling lives under docs/
rather than a separate docs-site/ (VitePress ergonomics)
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
