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

tests/server/chat-run-bridge-readiness.test.ts

@@ -2,7 +2,6 @@ import { beforeEach, describe, expect, it, vi } from 'vitest'
 
 const handleBridgeRunMock = vi.hoisted(() => vi.fn(async () => {}))
 const resumeBridgeRunMock = vi.hoisted(() => vi.fn(async () => {}))
-const handleCodingAgentRunMock = vi.hoisted(() => vi.fn(async () => {}))
 const loadSessionStateFromDbMock = vi.hoisted(() => vi.fn())
 const ensureReadyMock = vi.hoisted(() => vi.fn())
 const getRuntimeStateMock = vi.hoisted(() => vi.fn())
@@ -24,10 +23,6 @@ vi.mock('../../packages/server/src/services/hermes/run-chat/load-state', () => (
   resolveRunSource: vi.fn((source?: string) => source || 'cli'),
 }))
 
-vi.mock('../../packages/server/src/services/hermes/run-chat/handle-coding-agent-run', () => ({
-  handleCodingAgentRun: handleCodingAgentRunMock,
-}))
-
 vi.mock('../../packages/server/src/services/hermes/run-chat/session-command', () => ({
   handleSessionCommand: vi.fn(),
   isSessionCommand: vi.fn(() => false),
@@ -109,7 +104,6 @@ describe('ensureBridgeReadyForChatRun', () => {
     bridgeMock.statusIfLoaded.mockReset()
     handleBridgeRunMock.mockReset()
     resumeBridgeRunMock.mockReset()
-    handleCodingAgentRunMock.mockReset()
     loadSessionStateFromDbMock.mockReset()
     getSessionMock.mockReset()
     getSessionMock.mockImplementation((sessionId?: string) => sessionId
@@ -180,7 +174,6 @@ describe('ChatRunSocket bridge readiness gating', () => {
     bridgeMock.statusIfLoaded.mockReset()
     handleBridgeRunMock.mockReset()
     resumeBridgeRunMock.mockReset()
-    handleCodingAgentRunMock.mockReset()
     loadSessionStateFromDbMock.mockReset()
     ensureReadyMock.mockResolvedValue({
       reachable: true,
@@ -263,7 +256,7 @@ describe('ChatRunSocket bridge readiness gating', () => {
     expect(socket.emit).not.toHaveBeenCalledWith('run.failed', expect.anything())
   })
 
-  it('routes global coding-agent runs through the coding-agent path while preserving session source', async () => {
+  it('routes runs with an unknown legacy source through the bridge run path', async () => {
     const { ChatRunSocket } = await import('../../packages/server/src/services/hermes/run-chat')
     const { handlers, io, socket } = makeServerHarness()
     const server = new ChatRunSocket(io as any)
@@ -272,24 +265,18 @@ describe('ChatRunSocket bridge readiness gating', () => {
     await handlers.get('run')?.({
       input: 'hello',
       session_id: 'session-1',
-      source: 'coding_agent',
+      // Sessions stored before Phase 003 can still carry the retired source.
+      source: 'retired_source',
       session_source: 'global_agent',
-      coding_agent_id: 'codex',
     })
 
-    expect(ensureReadyMock).not.toHaveBeenCalled()
-    expect(handleCodingAgentRunMock).toHaveBeenCalledWith(
-      expect.anything(),
-      socket,
-      expect.objectContaining({
-        source: 'coding_agent',
-        session_source: 'global_agent',
-        coding_agent_id: 'codex',
-      }),
-      'default',
-      expect.any(Map),
-    )
-    expect(handleBridgeRunMock).not.toHaveBeenCalled()
+    expect(ensureReadyMock).toHaveBeenCalledTimes(1)
+    expect(handleBridgeRunMock).toHaveBeenCalledTimes(1)
+    expect(handleBridgeRunMock.mock.calls[0][2]).toEqual(expect.objectContaining({
+      source: 'retired_source',
+      session_source: 'global_agent',
+    }))
+    expect(socket.emit).not.toHaveBeenCalledWith('run.failed', expect.anything())
   })
 
   it('continues with remaining queued bridge runs when readiness fails before a dequeued run starts', async () => {
@@ -496,10 +483,17 @@ describe('ChatRunSocket bridge readiness gating', () => {
     expect((server as any).bridgeResumePolls.size).toBe(0)
   })
 
-  it('does not query Hermes bridge status when resuming a coding agent session', async () => {
+  it('reattaches a session stored with a retired source on the bridge', async () => {
     getSessionMock.mockImplementation((sessionId?: string) => sessionId
-      ? { id: sessionId, profile: 'default', source: 'coding_agent', model: 'codex', provider: 'codex' }
+      ? { id: sessionId, profile: 'default', source: 'retired_source', model: 'gpt-test', provider: 'openai' }
       : undefined)
+    bridgeMock.statusIfLoaded.mockResolvedValueOnce({
+      ok: true,
+      exists: true,
+      running: true,
+      current_run_id: 'run-legacy',
+      loaded: true,
+    })
     loadSessionStateFromDbMock.mockResolvedValueOnce({
       messages: [],
       isWorking: false,
@@ -507,7 +501,7 @@ describe('ChatRunSocket bridge readiness gating', () => {
       runId: undefined,
       activeRunMarker: undefined,
       profile: 'default',
-      source: 'coding_agent',
+      source: 'retired_source',
       events: [],
       queue: [],
     })
@@ -518,15 +512,25 @@ describe('ChatRunSocket bridge readiness gating', () => {
     ;(server as any).onConnection(socket)
     await handlers.get('resume')?.({ session_id: 'session-1' })
 
-    expect(ensureReadyMock).not.toHaveBeenCalled()
-    expect(bridgeMock.statusIfLoaded).not.toHaveBeenCalled()
-    expect(resumeBridgeRunMock).not.toHaveBeenCalled()
+    expect(bridgeMock.statusIfLoaded).toHaveBeenCalledWith('session-1', 'default', { timeoutMs: 1000 })
+    expect(resumeBridgeRunMock).toHaveBeenCalledWith(
+      expect.anything(),
+      socket,
+      expect.objectContaining({ sessionId: 'session-1', runId: 'run-legacy' }),
+      expect.any(Map),
+      bridgeMock,
+      expect.any(Function),
+    )
     expect(emitted.some(({ event }) => event === 'run.reattach_failed')).toBe(false)
     expect(socket.emit).toHaveBeenCalledWith('resumed', expect.objectContaining({
       session_id: 'session-1',
-      isWorking: false,
+      isWorking: true,
       events: [],
     }))
+    expect((server as any).sessionMap.get('session-1')).toEqual(expect.objectContaining({
+      isWorking: true,
+      source: 'cli',
+    }))
   })
 
   it('reattaches global-agent bridge runs with the global source preserved', async () => {