MoE timing-replay: deterministic emulator timing + route-trace harnesses

[qichao-arlo-wang]

What this PR does

Consolidates the MoE timing-replay stack — previously split across #93, #94, #95, #96 — into a single branch against main, with the review findings from those PRs fixed. It supersedes and replaces all four (which are being closed).

Organized as four thematic commits:

1. emulator: deterministic timing, stage profiling, and overlap model — deterministic event ordering (monotonic timer sequence ids; address-ordered HBM gather / ramulator transfers), cycle-attributed stage profile (schema v2, serde), an opt-in prefetch/compute overlap timing model, and a repeat gate + per-run dump cwd in the Python runner.
2. testbench: MoE route-trace replay harness and validation gates (P1) — dependency-free route-trace schema + validator, sample-trace generator, replay runner, timing validation gates, result export.
3. testbench: Qwen3 MoE route-trace generation and replay (P2) — true Qwen3 router-trace generation from tokenized inputs + local weights, conversion to the validated schema, replay, resumable batch runner, pilot export.
4. testbench: representative MoE timing runner (P3) — stratified largest-remainder subset selection, serial-vs-parallel determinism gate, checkpointed parallel replay.

Fixes applied during consolidation

• Dropped the timing goldens entirely (check_timing_goldens.py, overlap_golden_workloads.json, run_timing_smoke.sh, the timing-smoke recipe): they depended on out-of-repo build artifacts and were not CI-runnable. The overlap-timing engine (timing_overlay.rs, unit-tested) and the standalone timing_validation_gates.py are kept.
• Removed the atomic-global sentinel for overlap report cycles in favor of a documented Mutex<Option<u64>> (a module cell is still needed because Executor::spawn requires Future<Output = ()>), and clarified the muddled overlap log line.
• Output roots no longer escape the repo: window1_p{1,2,3} outputs default to a git-ignored in-repo outputs/ (override the base with PLENA_OUT_ROOT); added /outputs/ to .gitignore.
• Trimmed P3: dropped the superseded run_p3_scale_batch.py and the two personal tmux babysitter scripts (wait_p3_rev_stage_b.py, watch_p3_rev_raw_build.py); removed dead code in run_p3_rev_subset.py.
• Renamed qwen3_trace_replay_test.py → qwen3_trace_replay.py (it is a CLI, not a pytest module) and updated all references.
• Parenthesized a precedence-fragile validator condition; resolved all ruff findings (E402, RUF005).

Validation (local, in nix develop)

• cargo fmt --all --check, cargo build --release, cargo test --workspace --release — all green.
• just test-aten-linear — PASSED, 100% match / 0.0 error.
• Stage-profile schema-v2 emitted end-to-end; total_simulation_cycles == total_profiled_cycles invariant holds.
• ruff check . + ruff format --check . — clean.

Compiler submodule stays pinned at a765612 (row-granular ABI), identical to main.