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

AGENTS.md

@@ -31,7 +31,6 @@ Use the smallest relevant check while iterating. Before a broad PR, run
 - `packages/client/src` - Vue 3 client, stores, routes, i18n, API helpers.
 - `packages/server/src` - Koa API, Socket.IO, persistence, Hermes integration.
 - `packages/skills` - built-in skills injected into the Hermes skills directory.
-- `packages/ekko-agent` - legacy in-house agent runtime, slated for removal in Phase 003.
 - `tests/client`, `tests/server`, `tests/shared` - Vitest coverage.
 - `tests/e2e` - Playwright browser coverage with mocked backend services.
 - `.github/workflows` - CI, release, and Docker packaging automation.
@@ -56,8 +55,7 @@ Use the smallest relevant check while iterating. Before a broad PR, run
 - `services/hermes/group-chat/`, `lib/context-compressor/`, and
   `services/hermes/context-engine/` are the chat chain: changes require a
   `docs/chat-chain-changes/<date>-<slug>.md` fragment.
-- `packages/desktop`, `packages/website`, and `packages/ekko-agent` are removed or
-  being removed; do not reintroduce them.
+- `packages/desktop` and `packages/website` are removed; do not reintroduce them.
 
 ## When The Agent Gets Stuck