Add trace-aware stage summaries + plotting helper for profiling

[jioffe502]

Description

• Plumbed enable_traces/trace_output_dir through the test config and e2e case so trace payloads are captured automatically during scripted runs.
• Added trace_summary generation in scripts/tests/cases/e2e.py, writing per-stage aggregates plus per-document totals; run.py now records trace flags in results.json.
• Documented how to enable tracing, run baseline vs RC comparisons, and consume the new artifacts (README updates + profiling workflow notes).
• Introduced scripts/tests/tools/plot_stage_totals.py, a helper that reads any results.json and emits a PNG + textual summary showing cumulative resident seconds per stage (with options to sort, collapse nested entries, filter network noise, etc.).
• Document-level wall time: _summarize_traces now records each doc’s elapsed span (first stage entry → last exit) so the trace artifacts report realistic wall clocks in addition to resident totals.
• Dual visualization flow: plot_stage_totals.py grew an optional wall-time chart (results.wall_time.png) that contrasts per-doc wall vs resident seconds, highlights effective parallelism (resident/wall ratio), and prints summaries alongside the existing stage-resident PNG.

Testing:

• Generated bo20 and bo767 runs with ENABLE_TRACES=true; verified results.json contains the new trace_summary, trace files land under artifacts/.../traces/, and the plotting tool produces the expected charts (*.stage_time.png) using both collapsed and nested views.

Checklist

• I am familiar with the Contributing Guidelines.
• New or existing tests cover these changes.
• The documentation is up to date with these changes.
• If adjusting docker-compose.yaml environment variables have you ensured those are mimicked in the Helm values.yaml file.