Reproducing the README's quickstart on a clean clone surfaced seven
independent bugs between `git clone` and seeing the Canvas in a browser.
Each fix is minimal and local-dev-only — the SaaS/EC2 provisioner path
(issue #1822) is untouched.
Bugs fixed:
1. `infra/scripts/setup.sh` applied migrations via raw psql, bypassing
the platform's `schema_migrations` tracker. The platform then re-ran
every migration on first boot and crashed on non-idempotent ALTER
TABLE statements (e.g. `036_org_api_tokens_org_id.up.sql`). Dropped
the migration block — `workspace-server/internal/db/postgres.go:53`
already tracks and skips applied files.
2. `.env.example` shipped `DATABASE_URL=postgres://USER:PASS@postgres:...`
with literal `USER:PASS` placeholders and the Docker-internal hostname
`postgres`. A `cp .env.example .env` followed by `go run ./cmd/server`
on the host failed with `dial tcp: lookup postgres: no such host`.
Replaced with working `dev:dev@localhost:5432` defaults that match
`docker-compose.infra.yml`.
3. `docker-compose.infra.yml` and `docker-compose.yml` set
`CLICKHOUSE_URL: clickhouse://...:9000/...`. Langfuse v2 rejects
anything other than `http://` or `https://`, so the container
crash-looped and returned HTTP 500. Switched to
`http://...:8123` (HTTP interface) and added `CLICKHOUSE_MIGRATION_URL`
for the migration-time native-protocol connection. Also removed
`LANGFUSE_AUTO_CLICKHOUSE_MIGRATION_DISABLED` so migrations actually
run.
4. `canvas/package.json` dev script crashed with `EADDRINUSE :::8080`
when `.env` was sourced before `npm run dev` — Next.js reads `PORT`
from env and the platform owns 8080. Pinned `dev` to
`-p 3000` so sourced env can't hijack it. `start` left as-is because
production `node server.js` (Dockerfile CMD) must respect `PORT`
from the orchestrator.
5. README/CONTRIBUTING told users to clone `Molecule-AI/molecule-monorepo`
— that repo 404s; the actual name is `molecule-core`. The Railway
and Render deploy buttons had the same broken URL. Replaced in both
English and Chinese READMEs and in CONTRIBUTING. Internal identifiers
(Go module path, Docker network `molecule-monorepo-net`, Python helper
`molecule-monorepo-status`) deliberately left alone — renaming those
is an invasive refactor orthogonal to this fix.
6. README quickstart was missing `cp .env.example .env`. Users who went
straight from `git clone` to `./infra/scripts/setup.sh` got a script
that warned about an unset `ADMIN_TOKEN` (harmless) but then couldn't
run the platform without figuring out the env setup on their own.
Added the step in both READMEs and CONTRIBUTING. Deliberately NOT
generating `ADMIN_TOKEN`/`SECRETS_ENCRYPTION_KEY` here — the e2e-api
suite (`tests/e2e/test_api.sh`) assumes AdminAuth fallback mode
(no server-side `ADMIN_TOKEN`), which is how CI runs it.
7. CI shellcheck only covered `tests/e2e/*.sh` — `infra/scripts/setup.sh`
is in the critical path of every new-user onboarding but was never
linted. Extended the `shellcheck` job and the `changes` filter to
cover `infra/scripts/`. `scripts/` deliberately excluded until its
pre-existing SC3040/SC3043 warnings are cleaned up separately.
Verification (fresh nuke-and-rebuild following the updated README):
- `docker compose -f docker-compose.infra.yml down -v` + `rm .env`
- `cp .env.example .env` → defaults work as-is
- `bash infra/scripts/setup.sh` — clean, no migration errors, all 6
infra containers healthy
- `cd workspace-server && go run ./cmd/server` — "Applied 41 migrations
(0 already applied)", platform on :8080/health 200
- `cd canvas && npm install && npm run dev` — Canvas on :3000/ 200
even with `.env` sourced (PORT=8080 in env)
- `bash tests/e2e/test_api.sh` — **61 passed, 0 failed**
- `cd canvas && npx vitest run` — **900 tests passed**
- `cd canvas && npm run build` — production build clean
- `shellcheck --severity=warning infra/scripts/*.sh` — clean
- Langfuse `/api/public/health` 200 (was 500)
Scope notes:
- SaaS/EC2 parity (issue #1822): all files touched here are local-dev
surface. Canvas container uses `node server.js` with `ENV PORT=3000`
in `canvas/Dockerfile` — the `-p 3000` pin in `package.json` dev
script only affects `npm run dev`, not the production CMD.
- Test coverage (issue #1821): project policy is tiered coverage floors,
not a blanket 100% target. Files touched here are shell scripts,
YAML, Markdown, and one package.json script — not classes covered
by the coverage matrix.
- No overlap with open PRs — searched `setup.sh`, `quickstart`,
`langfuse`, `clickhouse`, `migration`, `README`; nothing conflicts.
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-authored-by: molecule-ai[bot] <276602405+molecule-ai[bot]@users.noreply.github.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>
Replace the anthropic:claude-sonnet-4-6 default across config, handlers,
env example, and litellm proxy config. All tests updated to match the new
default; sonnet-4-6 alias kept in litellm_config.yml for pinned workspaces.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Backend Engineer's PR #729 introduces ADMIN_TOKEN — when set, only that value
is accepted on /admin/* and /approvals/* routes, replacing the vulnerable
workspace-bearer fallback. Without the env var wired into deployments the fix
is code-only and the vulnerability stays open in every running instance.
Changes:
- `docker-compose.yml`: adds ADMIN_TOKEN env var to the platform service
(blank default = backward-compat fallback, i.e. still vulnerable until set).
NOTE: docker-compose.infra.yml has no platform service — the platform lives
only in the full-stack docker-compose.yml, so that is the correct file.
- `.env.example`: documents ADMIN_TOKEN with generation instructions and a
clear warning that it must be set to close#684.
- `infra/scripts/setup.sh`: prints a visible warning when ADMIN_TOKEN is unset
so operators know the vulnerability is still open in that deployment.
- `CLAUDE.md`: adds ADMIN_TOKEN to the env vars reference section.
No Go code changed — go build ./... passes clean.
Part of fix for #684 / PR #729
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
