Move MCP session execution behind the Runtime

[ethan-huo]

Objective

Move all MCP connection creation, reuse, execution, notification attribution, and cancellation adaptation behind the MCP Runtime session pool.

Scope

• Resolve server declarations and credentials inside the Runtime; the CLI no longer sends server config or headers.
• Execute one active MCP request per server key through the Call signal.
• Pass RequestOptions.signal alongside timeout and progress options.
• Preserve stdio child and Streamable HTTP session reuse after Call cancellation.
• Treat cancelled-request late responses as diagnostics rather than session corruption.
• Preserve retained-session rejection, 401 eviction, notification buffering, and idle cleanup behavior where compatible with the accepted spec.

Non-goals

• Concurrent upstream requests on one session.
• Authentication initiation.
• Real remote MCP acceptance tests.

TDD acceptance

• Start with failing session-pool tests using deterministic local fixtures.
• Cover cancellation respected, ignored, racing, late, and completion-before-disconnect for stdio and Streamable HTTP.
• A second Call succeeds on the same connection/session before and after a late response.
• Cancellation never evicts a healthy session.
• A 401 follows credential-invalid/session-eviction policy and returns reauth-required; it does not start authentication.
• Existing notification buffering and retained-session cases remain green.

Verification

• Focused session/cancellation integration tests.
• Existing daemon and notification suites.
• Full test suite, typecheck, formatter check, and git diff --check.

[ethan-huo]

Implemented Runtime-owned MCP session execution with TDD and local transport evidence:

• Added a Runtime session pool that resolves declarations and credentials from Runtime stores; callers provide only server/tool names and input.
• Added one cancelable FIFO per stable server key and passes the caller-owned signal with SDK timeout/progress options.
• Added MCPX-owned timeout scheduling, keeping timeout distinct from SDK -32001 and caller disconnect.
• Preserves notification attribution and tools-changed observation.
• Maps 401/unauthorized failures to reauth-required and closes the affected session without starting authentication.
• Added McpRuntime.handle for registry snapshots, Calls, status, and coordinated stop through the caller seam.

Local SDK 1.29.0 evidence covers stdio and Streamable HTTP acknowledge, ignore/late, race, and completion-before-disconnect cases. Every scenario succeeds on the same connection/session both before and after a possible late response; cancellation never evicts the healthy session.

Validation:

• focused Runtime/Call/session suites: 13 pass, 0 fail
• full bun run check: 113 pass, 0 fail; typecheck and formatting pass
• prototype format check and git diff --check: pass

The old CLI adapter remains intentionally unswitched until dependent Issue #22; no remote endpoint was accessed.