fix(effect): preserve context across callback bridges

[kitlangton]

Summary

• capture the active Effect context before crossing callback boundaries in MCP, PTY, plugin, bus, command, and provider bridges
• replace bare Effect.runPromise / Effect.runFork calls at those boundaries with runPromiseWith(ctx) / runForkWith(ctx)
• stop re-providing EffectLogger.layer at those sites now that the runtime logger context is preserved explicitly

Testing

• bun run typecheck
• bun run test test/plugin/trigger.test.ts test/pty/pty-output-isolation.test.ts
• bun run test test/mcp/lifecycle.test.ts