fix(mcp): address QA round 1 findings

- Use O_NONBLOCK + clearerr() in Phase 2 fgetc probe to preserve the
  60s idle eviction timeout when both kernel fd and FILE* buffer are
  empty (fgetc on a blocking fd would otherwise block indefinitely,
  bypassing Phase 3 poll timeout and preventing cbm_mcp_server_evict_idle)
- Add #include <fcntl.h> for fcntl()/O_NONBLOCK
- Fix comment: "two-phase" → "three-phase" (implementation has 3 phases)
- Improve Python integration test: verify id:1 (initialize) and id:2
  (tools/list) response IDs are both present, not just "tools" substring

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>