Paper section: PD-sep scaffold + drop --enforce-eager from launch scripts

Adds analysis/pd_sep_paper_section/ as the home for the "PD separation is
net negative under agentic workloads" paper section: plot scripts for C1
(workload chars), C6 (roofline), C7 (routing-vs-PD-sep lever), the C6/C7
PDFs already rendered, and a README mapping candidate claims to required
figures plus open re-run items.

Removes --enforce-eager from bench.sh and all active launch scripts so
cuda graphs are captured -- the prior methodology suppressed one of
PD-sep's structural advantages (D-node fixed-shape decode). Legacy
scripts under scripts/legacy/ are intentionally untouched as historical
records.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

analysis/pd_sep_paper_section/README.md

@@ -0,0 +1,87 @@
+# Paper section: PD separation under agentic workloads
+
+This directory collects everything produced for the "PD-sep is net negative
+on agentic workloads" paper section. It is one section of a larger paper,
+not the whole paper.
+
+## Layout
+
+```
+analysis/pd_sep_paper_section/
+├── README.md                       # this file
+├── scripts/
+│   ├── plot_workload.py            # C1: input/output CDF + KV reuse decomposition
+│   ├── plot_roofline.py            # C6: prefill roofline at varying cache reuse
+│   └── plot_routing_lever.py       # C7: routing vs PD-sep as design levers
+└── figures/
+    ├── fig_c6_roofline.pdf         # rendered locally (analytical, no trace needed)
+    ├── fig_c7_routing_lever.pdf    # rendered locally (from REPORT.md §3.1)
+    └── (fig_c1a_io_cdf.pdf,        # produced on dash0 when trace is available
+          fig_c1b_reuse.pdf)
+```
+
+## Candidate claims -> figures (status)
+
+| Claim | Figure | Status |
+|---|---|---|
+| C1: 98% prefill share + 91% intra-session KV reuse | `figures/fig_c1a_io_cdf.pdf`, `figures/fig_c1b_reuse.pdf` | **needs trace on dash0** |
+| C2: PD-sep vs Combined headline numbers | (not yet) | **needs re-run without --enforce-eager on `traces/w600_r0.0015_st30.jsonl`** |
+| C3: decode KV cache memory wall (time-series) | (not yet) | needs step-level vLLM telemetry during PD-sep run |
+| C4: TTFT stacked breakdown (prefill / KV pull / decode wait) | (not yet) | needs per-request breakdown.json from PD-sep run |
+| C5: cuda-graph ablation (eager vs cudagraph × Combined vs PD-sep) | (not yet) | needs the 2×2 matrix |
+| C6: prefill stays compute-bound at 95% reuse | `figures/fig_c6_roofline.pdf` | **rendered** |
+| C7: cache-aware routing is a larger lever than PD-sep | `figures/fig_c7_routing_lever.pdf` | **rendered** (legacy data, footer caveat) |
+
+## In-place edits made for this task
+
+These edits are in the repo, not in this directory, because they modify
+existing launch scripts. `--enforce-eager` was removed so cuda graphs can be
+captured — PD-sep's D-node is a particularly clean case for cuda-graph
+benefit and the prior methodology suppressed it.
+
+| File | Lines | Change |
+|---|---|---|
+| `scripts/bench.sh` | 150, 161 | drop `--enforce-eager` (elastic + baseline modes) |
+| `scripts/launch_pd_mooncake.sh` | 47, 64 | drop `--enforce-eager` (P and D instances) |
+| `scripts/launch_pd_separated.sh` | 52, 68 | drop `--enforce-eager` (P and D instances) |
+| `scripts/launch_phase1_ps.sh` | 32, 43 | drop `--enforce-eager` (C and PS instances) |
+| `scripts/launch_elastic_p2p.sh` | 57 | drop `--enforce-eager` (kv_both instances) |
+
+`scripts/legacy/*.sh` are intentionally left as-is — they record the
+configuration of past experiments.
+
+`REPORT.md` and `analysis/pd_separation_analysis.md` still describe the
+old `--enforce-eager` setup. Update them once the new runs land.
+
+## Reproducing the figures
+
+From repo root:
+
+```bash
+# C1 (needs sampled trace on dash0)
+.venv/bin/python analysis/pd_sep_paper_section/scripts/plot_workload.py \
+    --trace traces/w600_r0.0015_st30.jsonl
+
+# C6 (analytical, runs anywhere with matplotlib)
+.venv/bin/python analysis/pd_sep_paper_section/scripts/plot_roofline.py
+
+# C7 (hardcoded REPORT.md §3.1 numbers; no inputs)
+.venv/bin/python analysis/pd_sep_paper_section/scripts/plot_routing_lever.py
+```
+
+All three default `--outdir` to `analysis/pd_sep_paper_section/figures`.
+
+## Caveats / open items
+
+- **C7 uses legacy data**. The footer of `fig_c7_routing_lever.pdf` says so:
+  PD-sep numbers come from the random-sampled trace + `--enforce-eager`. Re-run
+  on `traces/w600_r0.0015_st30.jsonl` with cuda-graphs on before paper-grade
+  citation. The plotting code keeps the source numbers in a single `ROWS`
+  table (top of `plot_routing_lever.py`) for a one-line swap.
+- **C2/C3/C4/C5 figures are not produced** because the experiments have not
+  been re-run. The 4h matrix proposed in the prior conversation turn
+  (Combined + RR, Combined + cache-aware, PD-sep 4P+4D, PD-sep 6P+2D, plus
+  eager-vs-cudagraph ablation, ×3 seeds) is the prerequisite.
+- **C6 is analytical**, so it is independent of any re-run. The numbers
+  match `scripts/compute_roofline.py` (constants are duplicated; if one
+  changes, the other must change too).