Remove no-op runtime APIs

[snbafana]

Summary

• Remove ignored permission status mode/db options and the no-op onboarding refresh-permissions plumbing
• Collapse adapter auto-sync listing onto the canonical adapter list and remove always-true autoSync metadata
• Remove empty futureFeatures capability output and stale CUED_SIGNAL_CLI_PATH public env docs
• Stop the native onboarding snapshot helper from passing the removed --refresh-permissions flag while preserving native fast refresh behavior

Verification

• rg recheck for removed no-op API names and stale env docs
• pnpm typecheck
• pnpm check:biome
• pnpm test src/runtime/onboarding-permissions.test.ts src/runtime/doctor-status.test.ts src/core/platform-capabilities.test.ts src/platforms/core/runner.test.ts src/runtime/daemon/server.test.ts src/platforms/signal/cli/client.test.ts
• swift build --package-path native/macos/CuedNative -c release
• Commit hook: pnpm check:app-quality
• Push hook: pnpm check:ci-local, including pnpm build, pnpm test, and native Swift release build

Stack

• Base: codex/cued-quality-02-dead-ts-surface (Remove dead TypeScript exports #61)
• Previous: Remove dead TypeScript exports #61
• Next: codex/cued-quality-04-outbound-send-decision