feat: combine 17 open PRs (cluster, supply-chain, workflows, plugins, messaging, mcp, exploration + more) onto current main (#740)

## Summary

Combines **all 17 open PRs by @arielshad** (everything in the open list
**except #731**, as requested) into a single branch, rebased onto
**current `main` (v1.210.0)** with conflicts resolved.

These PRs forked from an **old main (Mar–Apr)**; the repo history was
later rewritten and `main` advanced ~3 months. Each PR's real commits
were replayed onto current `main` via 3‑way rebase (reconstructed exact
fork points), conflicts resolved, then assembled here. Where `main` had
already implemented a PR's feature differently, **main's version was
kept** and only genuinely net‑new functionality was integrated (per
agreed strategy).

**Local verification:** `pnpm typecheck` ✓ (0 errors) · `pnpm lint`
(changed files) ✓ · `pnpm build` ✓ · adopt‑branch unit+integration tests
✓. Full unit/int suite run is in progress as follow‑up.

## PRs integrated

| PR | Feature | Verdict |
|----|---------|---------|
| #566 | Cluster entity + agent + CLI + web UI (k8s) | NET‑NEW |
| #527 | Policy‑driven supply‑chain security | NET‑NEW (renamed
`SecurityPolicy`→`SupplyChainSecurityPolicy` to avoid ASPM clash) |
| #441 | Scheduled workflows engine | NET‑NEW (renamed to `Scheduled*` /
`scheduled-workflows/` to avoid main's workflow‑steps clash) |
| #555 | Pluggable AI tool system (MCP lifecycle) | NET‑NEW |
| #512 | Messaging remote control | NET‑NEW |
| #513 | Prototype exploration mode | PARTIAL — mapped onto main's
existing `BuildMode` (added `Exploration`); dropped the obsolete
`fast`→enum migration |
| #469 | MCP server for AI agent integration | NET‑NEW |
| #367 | Per‑repo webhook enable/disable | NET‑NEW (token renamed
`IWebhookService`→`IGitHubWebhookService` to avoid clash) |
| #538 | Feature reparenting + auto‑rebase | NET‑NEW (adapted onto
main's evolved graph‑state) |
| #430 + #434 | `--remote` flag + auto‑fork | PARTIAL — main already had
fork fields/import use case; kept main's, added the net‑new bits |
| #417 | AgentRun + spec init on adopted branches | NET‑NEW (refactored
to inject `ISettingsProvider` for clean‑arch) |
| #384 | Agent‑based dev‑environment analysis | PARTIAL — kept main's
deploy use cases; added agent ports/services (see note) |
| #470 | Evidence image lightbox | NET‑NEW |
| #443 | File‑tree merge‑review diff | NET‑NEW |
| #409 | `repo init-remote` command | SUPERSEDED — main already has it;
kept specs, dropped a stale test |
| #399 | Restore deploy state across drawer cycles | SUPERSEDED — main's
store‑based deploy architecture already solves it; specs only |

## Integration notes

- **Migrations** renumbered to a unique, sequential `120–134` range
(above main's `119`); loader globs by filename so no index changes
needed.
- **TypeSpec** `generated/output.ts` regenerated authoritatively from
the merged `tsp/` sources (`pnpm tsp:compile`).
- **New deps:** `@modelcontextprotocol/sdk`, `@types/which`, `ws`,
`cloudflared`.
- **Feature flags** added: `clusters`, `supplyChainSecurity`,
`scheduledWorkflows` (wired through
tsp/mapper/repo/defaults/feature‑flags/sidebar/settings + all 9
locales).

## Follow‑ups (called out honestly)

- **#384**: `AgentDeploymentService`/`DevEnvironmentAgentService` are
registered but not yet wired to a consumer — main's deploy flows use
their own use cases. Main's `DeploymentService.start()` doesn't accept a
command override, so the agent‑analyzed command is currently logged
rather than passed; wiring an explicit override is a follow‑up.
- Full unit/integration/e2e suite still to be run end‑to‑end;
web/Storybook build not yet exercised.

🐑 Combined and reconciled with Shep.

https://claude.ai/code/session_01TzQM4PuyfCbUi5dSNezXPE

---
_Generated by [Claude
Code](https://claude.ai/code/session_01TzQM4PuyfCbUi5dSNezXPE)_

---------

Co-authored-by: Claude <noreply@anthropic.com>
Co-authored-by: Shep Bot <shep-agent@users.noreply.github.com>

Author: 3 people

.github/workflows/ci.yml

@@ -7,9 +7,9 @@
 #   ┌──────┬───────────┬─────────────────┬─────────────────┬─────────┬─────────┬───────────┬─────────────────────┐
 #   │ Lint │ Typecheck │ Unit (lin+win)  │ E2E CLI (l+w)   │ E2E TUI │ E2E Web │ Storybook │ Electron (m+w+l)    │
 #   └──────┴───────────┴─────────────────┴─────────────────┴─────────┴─────────┴───────────┴─────────────────────┘
-#   ┌──────────┬─────────┐
-#   │ Gitleaks │ Semgrep │
-#   └──────────┴─────────┘
+#   ┌──────────┬─────────┬──────────────────┐
+#   │ Gitleaks │ Semgrep │ Security Enforce │
+#   └──────────┴─────────┴──────────────────┘
 #                  (all parallel)
 #
 #   On push to main only:
@@ -308,6 +308,34 @@ jobs:
             p/javascript
             p/security-audit
 
+  # ===========================================================================
+  # Supply Chain Security Enforcement
+  # Runs shep security enforce to validate dependency risk, release integrity,
+  # and governance posture. Gates release and dev-release jobs.
+  #
+  # Master kill switch: set the repository variable or workflow env
+  # SHEP_SUPPLY_CHAIN_SECURITY=false to make this job a no-op.
+  # The CLI honors the env var and exits 0 with a "flag disabled" note.
+  # ===========================================================================
+  security-enforce:
+    name: Security Enforce
+    runs-on: ubuntu-latest
+    env:
+      # Default: inherit from repo vars, fall back to true. Flip to 'false' (repo var
+      # or workflow-level env) to disable the entire feature in CI.
+      SHEP_SUPPLY_CHAIN_SECURITY: ${{ vars.SHEP_SUPPLY_CHAIN_SECURITY || 'true' }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pnpm/action-setup@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: ${{ env.NODE_VERSION }}
+          cache: 'pnpm'
+      - run: pnpm install --frozen-lockfile
+      - run: pnpm run tsp:compile
+      - name: Run security enforcement
+        run: pnpm dev:cli security enforce --output json
+
   # ===========================================================================
   # Security Summary Comment (PRs only)
   # Posts aggregated security scan results as a PR comment
@@ -364,6 +392,7 @@ jobs:
       - build-electron-apps-only
       - security-gitleaks
       - security-semgrep
+      - security-enforce
     if: github.event_name == 'push' && github.ref == 'refs/heads/main' && !contains(github.event.head_commit.message, '[skip ci]')
 
     permissions:
@@ -455,6 +484,7 @@ jobs:
       - build-electron
       - security-gitleaks
       - security-semgrep
+      - security-enforce
     if: github.event_name == 'pull_request'
 
     permissions:

.gitignore

@@ -104,4 +104,5 @@ node_modules/.cache/prettier/
 *.bak
 storybook-static/
 .worktrees/
-.plan/
+.plan/
+.superpowers/

.gitleaksignore

@@ -1,6 +1,8 @@
 dc0ca49a66f0ffe3ce9b37bd283513bb714ecada:src/presentation/web/components/common/feature-drawer/feature-drawer.stories.tsx:generic-api-key:124
 42204c37eaad7947bf332782e4609f6480593abb:tests/unit/infrastructure/services/agents/executors/cursor-executor.test.ts:generic-api-key:599
+1c6b4761ae042411095cb1af81524853ef48bad7:tests/unit/infrastructure/services/messaging/content-sanitizer.test.ts:generic-api-key:24
 3173676049f52fb4ff16805d1c50c27e652b7b75:tests/unit/infrastructure/services/messaging/content-sanitizer.test.ts:generic-api-key:24
+1c6b4761ae042411095cb1af81524853ef48bad7:tests/unit/infrastructure/services/messaging/content-sanitizer.test.ts:generic-api-key:24
 cbe61f9d8b22bc0176339855f08b06ceee68fb49:src/presentation/web/components/features/settings/agent-settings-section.stories.tsx:generic-api-key:68
 cbe61f9d8b22bc0176339855f08b06ceee68fb49:src/presentation/web/components/features/settings/agent-settings-section.stories.tsx:generic-api-key:78
 d05e96264388c5293b05819845dd77053b97e477:src/presentation/web/components/features/settings/agent-settings-section.stories.tsx:generic-api-key:68
@@ -14,5 +16,3 @@ f2099f97e4e447aac7f141b14a2eb38a39df56f7:src/presentation/web/components/feature
 # These are UI fixtures rendered in Storybook to preview the token-auth form — no real
 # credentials are involved. PR #554 (one-click cloud deploy) does not touch this file;
 # the allowlist is added here only because gitleaks scans full git history.
-d05e96264388c5293b05819845dd77053b97e477:src/presentation/web/components/features/settings/agent-settings-section.stories.tsx:generic-api-key:68
-d05e96264388c5293b05819845dd77053b97e477:src/presentation/web/components/features/settings/agent-settings-section.stories.tsx:generic-api-key:78

.storybook/mocks/app/actions/get-workflow-history.ts

@@ -0,0 +1,5 @@
+export async function getWorkflowHistory() {
+  return {
+    executions: [],
+  };
+}

.storybook/mocks/app/actions/import-github-repository.ts

@@ -1,5 +1,13 @@
 export async function importGitHubRepository(input: { url: string; dest?: string }): Promise<{
-  repository?: { id: string; name: string; path: string; remoteUrl?: string };
+  repository?: {
+    id: string;
+    name: string;
+    path: string;
+    remoteUrl?: string;
+    isFork?: boolean;
+    upstreamUrl?: string;
+  };
+  forked?: boolean;
   error?: string;
 }> {
   const name = input.url.split('/').pop() ?? 'unknown';
@@ -10,5 +18,6 @@ export async function importGitHubRepository(input: { url: string; dest?: string
       path: `/repos/${name}`,
       remoteUrl: input.url.startsWith('http') ? input.url : `https://github.com/${input.url}`,
     },
+    forked: false,
   };
 }

.storybook/mocks/app/actions/list-workflows.ts

@@ -0,0 +1,5 @@
+export async function listWorkflows() {
+  return {
+    workflows: [],
+  };
+}

.storybook/mocks/app/actions/messaging.ts

@@ -0,0 +1,41 @@
+import type { MessagingPlatform } from '@shepai/core/domain/generated/output';
+
+export async function beginMessagingPairingAction(input: {
+  platform: MessagingPlatform;
+  gatewayUrl: string;
+}): Promise<{
+  success: boolean;
+  error?: string;
+  session?: {
+    platform: MessagingPlatform;
+    code: string;
+    expiresAt: string;
+    gatewayUrl: string;
+    publicUrl: string;
+    routeId: string;
+  };
+}> {
+  return {
+    success: true,
+    session: {
+      platform: input.platform,
+      code: '482913',
+      expiresAt: new Date(Date.now() + 10 * 60 * 1000).toISOString(),
+      gatewayUrl: input.gatewayUrl,
+      publicUrl: `${input.gatewayUrl.replace(/\/$/, '')}/integrations/route-demo/token-demo`,
+      routeId: 'route-demo',
+    },
+  };
+}
+
+export async function confirmMessagingPairingAction(
+  _input: unknown
+): Promise<{ success: boolean; error?: string }> {
+  return { success: true };
+}
+
+export async function disconnectMessagingAction(
+  _input: unknown
+): Promise<{ success: boolean; error?: string }> {
+  return { success: true };
+}

.storybook/mocks/app/actions/reparent-feature.ts

@@ -0,0 +1,6 @@
+export async function reparentFeature(
+  _featureId: string,
+  _parentId: string | null
+): Promise<{ success: boolean; error?: string }> {
+  return { success: true };
+}

.storybook/mocks/app/actions/security.ts

@@ -0,0 +1,17 @@
+export async function getSecurityStateAction(
+  _repositoryPath: string
+): Promise<{ state?: unknown; error?: string }> {
+  return { state: undefined };
+}
+
+export async function enforceSecurityAction(
+  _repositoryPath: string
+): Promise<{ result?: unknown; error?: string }> {
+  return { result: undefined };
+}
+
+export async function updateSecurityModeAction(
+  _mode: string
+): Promise<{ success: boolean; error?: string }> {
+  return { success: true };
+}

.storybook/mocks/app/actions/toggle-workflow.ts

@@ -0,0 +1,5 @@
+export async function toggleWorkflow() {
+  return {
+    success: true,
+  };
+}