docs: ensure_deps SHA pin, Laminar opt-in, Harbor WIDS D2, suite 746

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Summary

Documentation-only sync for post-merge gaps still present on main after #99/#104/#105/#107. Cherry-picks the verified tip from open #110 onto this run's designated branch so one fresher PR can land the same content.

Docs added/updated

• README.md — architecture map for observability/ + tracing.py, Harbor packaging pointer, ensure_deps SHA-pin + dep-cache wipe pitfalls, suite count 746/4, passive named phases / JsonLines
• AGENTS.md — stdlib-by-default + TOOLBENCH_TRACING=1; drop stale logfire from dev; ensure_deps SHA pin + wipe residual; module ownership for named phases, JsonLines, Harbor, Laminar
• SPEC.md / EVALUATION.md / BUILDPLAN.md — S20 tracing contract + T22/T23; Tone/SPEC counts S1–S42
• CLAUDE.md + sequence/{run-state,research/dossier}.md — S1–S42; Harbor + Laminar skill pointers
• docs/superpowers/specs/2026-07-12-complex-debug-probe-design.md — packaged-manifest + SHA-pin notes

Codepaths covered

• complex_runner.ensure_deps / provision_worktree (packaged manifest + git show / git archive SHA pin; existence-based rebuild residual)
• cli.py + observability/setup_tracing.py + tracing.py (optional tracing extra; console-only wrap; TOOLBENCH_TRACING=1)
• benchmarks/harbor/toolbench-complex/ (WIDS D2 build canary only)
• passive.py named phases + transcript.JsonLines + tests/test_shell_safety.py

Knowledge gaps addressed

• Stale “stdlib-only / logfire in dev / suite ~737” claims after Make CLI tracing explicitly opt in #104
• Undocumented Laminar opt-in boundary (key alone does not enable tracing)
• Missing Harbor packaging link and ensure_deps HEAD→SHA pin + wipe workaround (fix(complex): invalidate dep cache when manifest SHA changes #102 not yet merged — do not claim stamp invalidation)
• Navigability for refactor: close the Medium tech-debt findings from 20260803 #107 passive phase split / shared JSONL reader / shell_safety tests

Notes

• Docs-only; no runtime behavior change
• Suite re-verified locally: 746 passed, 4 skipped
• Supersedes open docs drafts docs: ensure_deps SHA pin (#99) and Laminar tracing sync (#97) #100/docs: ensure_deps SHA pin (#99) and Laminar tracing sync (#97) #101/docs: ensure_deps SHA pin (#99), Laminar sync (#97), dep-cache pitfall #103/docs: ensure_deps SHA pin, Laminar opt-in, Harbor WIDS D2, suite 746 #108/docs: ensure_deps SHA pin, Laminar opt-in, Harbor WIDS D2, suite 746 #109/docs: ensure_deps SHA pin, Laminar opt-in, Harbor WIDS D2, suite 746 #110 (same content; this tip is the designated-branch refresh)