Route CLI Adapter operations exclusively through the Runtime

[ethan-huo]

Objective

Make the CLI Adapter exclusively consume the Runtime protocol for discovery, Calls, registry mutations, refresh, status, and stop.

Scope

• Build the argc router from registrySnapshot rather than direct config reads.
• Route tool Calls and all command-driven registry/schema/credential mutations through Runtime intents.
• Render Runtime events and the single terminal frame without owning MCP transports or OAuth resources.
• Close the Runtime socket and remove CLI signal/output listeners on every terminal path.
• Delete superseded CLI-side reauth retry, direct store mutation, daemon bypass, and dual ownership paths.

Non-goals

• Changing existing tool command names or output rendering semantics unrelated to Runtime frames.
• Backward-compatible V2 code paths.

TDD acceptance

• Start with failing CLI-adapter tests against the in-memory Runtime caller/transport adapters.
• CLI source has no command-driven Registry Store, Credential Store, or Schema Cache write path.
• Ordinary unauthenticated Calls render stable reauth-required without browser activity.
• @add, @remove, and @refresh preserve their accepted user-visible results through Runtime operations.
• Broken pipe, error, cancellation, and normal result paths all exit cleanly.

Verification

• Focused router/adapter tests.
• Local process-level CLI integration suite.
• Full test suite, typecheck, formatter check, and git diff --check.

[ethan-huo]

Implemented the CLI Adapter cutover to Runtime protocol v3:

• Router construction reads only registrySnapshot.
• Tool Calls, @add, @remove, @refresh, status, and stop use Runtime intents over one handshake/one-operation Unix sockets.
• CLI no longer resolves server configuration, headers, credentials, MCP sessions, schema writes, or reauth retry.
• Runtime performs add discovery with interactive auth disabled; only explicit @refresh can authenticate.
• Runtime owns schema-change refresh/write-back and notification spill behavior.
• Terminal/error paths close the socket; a killed active CLI cancels its Call and the same stdio session remains reusable.

Local process evidence:

• add/call/notification/schema-writeback/status/remove dogfood passes
• five ordinary expired-credential Calls all fail without token traffic
• five concurrent explicit refresh CLIs produce one token request, then five Calls succeed
• active CLI termination drives Runtime active count to zero and a subsequent Call succeeds on the same session

Validation:

• full bun run check: 120 pass, 0 fail; typecheck and formatting pass
• prototype format check and git diff --check: pass

Superseded but now-unreachable legacy daemon/client machinery is retained only until dependent final cleanup Issue #23, where its old regression cases will be replaced before deletion. No remote endpoint was accessed.