fix(pipeline): add S_WAIT_READ_RESP state to fix read-noise PRNG timing

- Emit rd_valid_o for exactly one combinational cycle before waiting for
  read response, ensuring the read-noise PRNG advances once per batch issue
- Fix query handshake: wait for query_ready before asserting query_valid
  to avoid valid&&ready handshake drops on clock edges
- Add dynamic timeout estimation in test utilities based on DUT parameters
- Update test-top Makefile to run all noise configurations by default
- Remove uv run prefix from cocotb-config Makefile invocation

.stignore

@@ -15,3 +15,4 @@ outputs
 **/__pycache__
 **/sim_build
 **/__marimo__
+*.fst