Final Runtime upgrade acceptance and superseded-path cleanup

[ethan-huo]

Objective

Complete the accepted MCP Runtime upgrade with local end-to-end acceptance, superseded-path deletion, and independent review.

Scope

• Run every acceptance criterion in docs/specs/mcp-runtime-upgrade.md.
• Remove obsolete V2 ownership paths, compatibility machinery, temporary token-cache locking, and dead tests after replacement coverage exists.
• Mark superseded BDD documents clearly while retaining useful historical evidence.
• Perform an independent code review focused on lifecycle races, queue fairness, store atomicity, secret exposure, and process cleanup.
• Fix every actionable finding before closure.

TDD acceptance

• Issue bug: parallel cf-api execute processes spin at ~100% CPU after caller exits #16 process-level scenarios pass with at least five concurrent CLI processes and deterministic local fixtures.
• Success, error, cancellation, broken pipe, and final-waiter OAuth cancellation all exit within bounded deadlines.
• No CLI process survives its terminal frame; the idle Runtime does not busy-spin.
• All stdio, Streamable HTTP, notification, migration, auth, and protocol-mismatch suites pass.
• No real OAuth or remote MCP is accessed.

Verification

• Focused acceptance suite.
• Full test suite and typecheck.
• Repository and prototype formatter checks.
• git diff --check.
• Final issue dependency/readiness audit.

[ethan-huo]

Acceptance complete.

Implemented and verified:

• CLI operations route exclusively through the user-local Runtime protocol v3
• caller-owned Call lifecycle, removable FIFO, queued/active cancellation, terminal-before-delivery accounting, and session reuse
• Runtime-owned credential resolution, bearer rotation at queued-to-active transition, explicit OAuth single-flight, transferable/cancellable Caller Input, and stop-time auth cancellation
• serialized three-store transactions with recovery journal, secret-free snapshots including stdio env separation, and reference-aware credential cleanup
• shutdown closes admission across delayed reads, cancels active/queued work, closes pending/late connections, and prevents post-stop connect
• obsolete ProjectService/config/schema-refresh/token-cache and V2 ownership paths removed; historical BDD docs marked superseded

Independent review ran three rounds. All actionable findings were fixed; final review reports no remaining blocker.

Final gates:

• bun run check: 120 passed, 0 failed; typecheck and format pass
• five-process local Streamable HTTP success/error/cancellation/broken-pipe acceptance passes; no surviving CLI PID
• five-process explicit refresh produces one local token request
• Runtime stop vs active refresh passes
• pinned Bun 1.3.14 / SDK 1.29.0 stdio and Streamable HTTP prototype evidence passes
• git diff --check passes

All fixtures were local. No real OAuth, Cloudflare, PostHog, or remote MCP was accessed.

[ethan-huo]

Closed after final independent review confirmed no remaining blocker.