Two coupled cleanups for the post-2026-05-06 stack:
#157 — drop molecule-ai-plugin-github-app-auth
============================================
The plugin injected GITHUB_TOKEN/GH_TOKEN via the App's
installation-access flow (~hourly rotation). Per-agent Gitea
identities replaced this approach after the 2026-05-06 suspension —
workspaces now provision with a per-persona Gitea PAT from .env
instead of an App-rotated token. The plugin code itself lived on
github.com/Molecule-AI/molecule-ai-plugin-github-app-auth which is
also unreachable post-suspension; checking it out at CI build time
was already failing.
Removed:
- workspace-server/cmd/server/main.go: githubappauth import + the
`if os.Getenv("GITHUB_APP_ID") != ""` block that called
BuildRegistry. gh-identity remains as the active mutator.
- workspace-server/Dockerfile + Dockerfile.tenant: COPY of the
sibling repo + the `replace github.com/Molecule-AI/molecule-ai-
plugin-github-app-auth => /plugin` directive injection.
- workspace-server/go.mod + go.sum: github-app-auth dep entry
(cleaned up by `go mod tidy`).
- 3 workflows: actions/checkout steps for the sibling plugin repo:
- .github/workflows/codeql.yml (Go matrix path)
- .github/workflows/harness-replays.yml
- .github/workflows/publish-workspace-server-image.yml
Verified `go build ./cmd/server` + `go vet ./...` pass post-removal.
#161 — swap GHCR→ECR for publish-workspace-server-image
=======================================================
Same workflow used to push to ghcr.io/molecule-ai/platform +
platform-tenant. ghcr.io/molecule-ai is gone post-suspension. The
operator's ECR org (153263036946.dkr.ecr.us-east-2.amazonaws.com/
molecule-ai/) already hosts platform-tenant + workspace-template-*
+ runner-base images and is the post-suspension SSOT for container
images. This PR aligns publish-workspace-server-image with that
stack.
- env.IMAGE_NAME + env.TENANT_IMAGE_NAME repointed to ECR URL.
- docker/login-action swapped for aws-actions/configure-aws-
credentials@v4 + aws-actions/amazon-ecr-login@v2 chain (the
standard ECR auth pattern; uses AWS_ACCESS_KEY_ID/SECRET secrets
bound to the molecule-cp IAM user).
The :staging-<sha> + :staging-latest tag policy is unchanged —
staging-CP's TENANT_IMAGE pin still points at :staging-latest, just
with the new registry prefix.
Refs molecule-core#157, #161; parallel to org-wide CI-green sweep.
Consolidates 11 of the 17 open Dependabot PRs (#2215, #2217, #2219-#2225,
#2227, #2229) into one PR. Every entry is a patch / minor / floor bump
where the impact surface is small and CI carries the proof.
Same pattern as the 2026-04-15 batch.
Go (workspace-server/go.mod + go.sum, regenerated via `go mod tidy`):
- golang.org/x/crypto 0.49.0 → 0.50.0 (#2225)
- github.com/golang-jwt/jwt/v5 5.2.2 → 5.3.1 (#2222)
- github.com/gin-contrib/cors 1.7.2 → 1.7.7 (#2220)
- github.com/docker/go-connections 0.6.0 → 0.7.0 (#2223)
- github.com/redis/go-redis/v9 9.7.3 → 9.19.0 (#2217)
Python floor bumps (workspace/requirements.txt; current pip-resolved
versions don't change unless they happen to be below the new floor):
- httpx >=0.27 → >=0.28.1 (#2221)
- uvicorn >=0.30 → >=0.46 (#2229)
- temporalio >=1.7 → >=1.26 (#2227)
- websockets >=12 → >=16 (#2224)
- opentelemetry-sdk >=1.24 → >=1.41.1 (#2219)
GitHub Actions (SHA-pinned per existing convention):
- dorny/paths-filter@d1c1ffe (v3) → @fbd0ab8 (v4.0.1) (#2215)
REMOVED from this batch (lockfile platform mismatch):
- #2231 @types/node ^22 → ^25.6 (npm install on macOS strips
Linux-only @emnapi/* entries from package-lock.json that CI's
`npm ci` then refuses; needs a Linux-side install to land cleanly)
- #2230 jsdom ^25 → ^29.1 (same)
NOT included in this batch (deferred to per-PR human review):
- #2228 github/codeql-action v3 → v4 (CodeQL CLI alignment risk)
- #2218 actions/setup-node v4 → v6 (default Node version drift)
- #2216 actions/upload-artifact v4 → v7 (3 major versions)
- #2214 actions/setup-python v5 → v6 (action major)
NOT merged (CI failing on dependabot's own PR):
- #2233 next 15 → 16
- #2232 tailwindcss 3 → 4
- #2226 typescript 5 → 6
Verified:
- workspace-server: `go mod tidy && go build ./... && go test ./...` — green
- workspace requirements.txt: floor bumps only
Closes the LOW-severity dependabot alert on workspace-server's go-redis
pin. Upstream advisory GHSA-92cp-5422-2mw7: "go-redis allows potential
out-of-order responses when CLIENT SETINFO times out" — fixed in 9.7.3.
Patch bump within the v9.7 line; semver guarantees no API change.
Full workspace-server test suite passes (18/18 packages clean).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Closes the medium-severity dependabot alert #7 on workspace-server's
docker pin: "Moby firewalld reload makes published container ports
accessible from remote hosts" — fixed in v28.3.3, pulling v28.5.2
(latest in the v28 line).
Patch+minor bump within the v28 train; no client-API breaks
(workspace-server only uses docker.Client for container exec /
inspect, all stable since v20+).
Verification: full workspace-server test suite passes (18/18 packages
clean). Build clean.
Out of scope:
- Alerts #10 and #11 (the AuthZ bypass + plugin-priv off-by-one)
require v29.3.1, which is not yet published to the Go module
proxy (latest published is v28.5.2). They'll close in a follow-up
PR once v29 lands as a Go module.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Closes the HIGH-severity dependabot alert on workspace-server's jwt-go
pin. Upstream advisory GHSA-mh63-6h87-95cp / CVE-2025-30204:
"jwt-go allows excessive memory allocation during header parsing" —
fixed in v5.2.2.
Patch bump within the v5.x line; semver guarantees no API change. Full
workspace-server test suite passes (\`go test ./...\` clean across all
18 packages).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Ships the monorepo side of molecule-core#1957 (agent identity collapse).
Companion to molecule-ai-plugin-gh-identity (new repo, merged-and-tagged
separately).
Changes:
- manifest.json: add gh-identity plugin to Tier 1 registry
- workspace-server/go.mod: require github.com/Molecule-AI/molecule-ai-plugin-gh-identity
- cmd/server/main.go: build a shared provisionhook.Registry, register
gh-identity first (always), then github-app-auth (gated on GITHUB_APP_ID)
- workspace_provision.go: propagate workspace.Role into
env["MOLECULE_AGENT_ROLE"] before calling the mutator chain, so the
gh-identity plugin can see which agent is booting
- provisionhook/mutator.go: add Registry.Mutators() accessor so
individual-plugin registries can be merged onto a shared one at boot
Boot log gains a line like:
env-mutator chain: [gh-identity github-app-auth]
Effect per workspace:
- env contains MOLECULE_AGENT_ROLE, MOLECULE_OWNER, MOLECULE_ATTRIBUTION_BADGE,
MOLECULE_GH_WRAPPER_B64, MOLECULE_GH_WRAPPER_SHA
- Each workspace template's install.sh can decode + install the wrapper at
/usr/local/bin/gh, intercepting @me assignment and prepending agent
attribution on PR/issue creates
Does not break existing workspaces — absent workspace.role, the plugin is
a no-op. Absent install.sh updates in each template, the env vars are
simply unused.
Follow-up template PRs (hermes, claude-code, langgraph, etc.) each add
~15 lines to install.sh to decode + install the wrapper.
Ref: #1957
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Ships step 1 of the #1933 fleet-wide GH_TOKEN refresh fix.
The plugin's v0.0.0-20260416194734-2cd28737f845 predates the Mutator.Token()
method added in plugin-repo PR #1 (merged 2026-04-17). Monorepo's
workspace-server/pkg/provisionhook/mutator.go:218 has been emitting
`provisionhook: no Token method on "github-app-auth"` on every boot and
the reflection-fallback at mutator.go:216 is doing extra work every
time a workspace requests a fresh GH token.
This is the one-line pin bump:
v0.0.0-20260416194734-2cd28737f845 → v0.0.0-20260421064811-7d98ae51e31d
Effect: direct-interface path (not the reflection fallback) gets taken,
log noise goes away. Does NOT fix the actual 60-min GH_TOKEN death —
steps 2–5 of #1933 (credential helper install, git config wire-up,
runtime auth context, periodic refresh) are separate, larger PRs.
Verified: workspace-server/go build ./... passes with the new pin.
Ref: #1933
Closes the last CP-provisioned-workspace gap: Terminal tab now works
for workspaces running on separate EC2 instances. Follow-up to
#1531 which added instance_id persistence.
How it works:
- HandleConnect checks workspaces.instance_id
- Empty → existing local Docker path (unchanged)
- Set → spawn `aws ec2-instance-connect ssh --connection-type eice
--instance-id X --os-user ec2-user -- docker exec -it ws-Y
/bin/bash` under creack/pty, bridge pty ↔ canvas WebSocket
Why subprocess AWS CLI instead of native AWS SDK:
- EIC Endpoint tunnel needs a signed WebSocket with specific framing
- aws-cli v2 implements it correctly; reimplementing in Go is ~500
lines of crypto + WS protocol work for zero user-visible benefit
- Tenant image picks up 1MB of aws-cli + openssh-client via apk
Handler design:
- sshCommandFactory is a var so tests can stub it (no real aws calls)
- Context cancellation propagates both ways (WS close → kill ssh;
ssh exit → close WS)
- User-visible error points at docs/infra/workspace-terminal.md when
EIC wiring is incomplete (common bootstrap failure)
Tests:
- TestHandleConnect_RoutesToRemote — instance_id in DB → CP branch
- TestHandleConnect_RoutesToLocal — empty instance_id → local branch
- TestSshCommandFactory_BuildsEICCommand — argv shape regression guard
Dockerfile.tenant: + openssh-client + aws-cli (Alpine main repo)
Refs: #1528, #1531
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
