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

ARCHITECTURE.md

@@ -11,7 +11,6 @@ Agent Bridge (see "Hermes Integration" below).
 | Client | `packages/client/src` | Vue UI, routing, Pinia stores, API wrappers, i18n, browser-visible state. |
 | Server | `packages/server/src` | HTTP API, auth, Socket.IO, SQLite stores, file access, Hermes runtime integration. |
 | Skills | `packages/skills` | Built-in skills injected into the Hermes skills directory. |
-| Legacy agent | `packages/ekko-agent` | In-house agent runtime. Slated for removal in Phase 003; do not extend it. |
 | Tests | `tests` | Vitest unit/integration tests and Playwright browser tests. |
 | CI | `.github/workflows` | Build, e2e, lockfile, Docker, and release automation. |