Phase 003: remove the coding-agent and ekko-agent runtimes

Every chat session now runs through the Hermes bridge, so the three chat
chains become feature-equivalent instead of three partially-maintained
dispatch paths. Keeping the coding-agent and in-house agent runtimes alive
meant every bridge change had to be mirrored into two more runtimes that
had already drifted.

Historical rows are read, not migrated: sessions stored with the retired
source normalize to cli on load, workflow graphs naming the retired agents
keep loading and run on the bridge, and the visible-source check plus
SOURCE_LABELS still recognize the old value so those sessions stay listed.

The public surface follows the code: the OpenAPI generator and the MCP
chat-run tool schema drop the six retired entry fields so external callers
are not told about runtimes that no longer exist.

harness-check gains a RETIRED_RUNTIME scan so the residual check is a
mechanical gate instead of a manual grep, with the two surviving read-side
compat sites recorded with reasons.

Refs: docs/phases/phase_003.md

packages/server/src/services/shutdown.ts

@@ -1,7 +1,6 @@
 import { logger } from './logger'
 import { closeDb } from '../db'
 import { stopPreviewRuntime } from '../controllers/update'
-import { codingAgentRunManager } from './agent-runner/coding-agent-run-manager'
 import { shutdownManagedGateways } from './hermes/gateway-runner'
 import { stopOutboundRelayClient } from './global-agent/outbound-relay-client'
 
@@ -94,9 +93,6 @@ export function createShutdownHandler(server: any, groupChatServer?: any, chatRu
       stopOutboundRelayClient()
       logger.info('Outbound relay clients closed')
 
-      codingAgentRunManager.shutdown()
-      logger.info('Coding agent hidden sessions closed')
-
       // Disconnect Socket.IO before HTTP server to prevent hanging
       if (groupChatServer) {
         groupChatServer.agentClients.disconnectAll()