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>
