Instrument recall trace so phase metrics account for total duration (#2361)

[nicoloboschi]

Summary

Fixes #2361. SearchTrace.summary.phase_metrics[] only accounted for ~10-15% of total_duration_seconds; the rest sat in un-instrumented blocks of _search_with_retries. This adds a phase metric for each missing block so the named phases now account for ~100% of the wall clock.

New phase metrics

Phase	Covers	Why it was missing
backend_acquisition	_get_read_backend()	timed inside total, never recorded
combined_scoring	apply_combined_scoring + boosts + final sort + reranked-entry trace serialization	the reranking metric captured step_duration before this block ran
prefer_observations_dedup	Step 4.8 supersession DB query	uninstrumented await
chunk_fetch	obs-source + chunk SQL + tiktoken encoding	no metric
result_serialization	visit recording (O(n²) entry-point check) + dict conversion	no metric
source_fact_fetch	source-fact SQL passes	no metric
entity_build	entity SQL + MemoryFact/EntityState construction	no metric

Diagnostic phases (excluded from the coverage sum)

Flagged details.diagnostic because they overlap or fall outside the timeline:

• retrieval_{semantic,bm25,graph,temporal} — children of the parallel_retrieval umbrella (summing both double-counts retrieval)
• semaphore_wait / connection_wait — surfaced as the issue requested; these waits precede/overlap other phases
• trace_finalize — finalize() snapshots total_duration_seconds at entry, so its own serialization is necessarily after the total; reported for visibility but not part of the sum

On the proposed CI assertion

The issue's assert abs(total - named) < 0.005 can't hold as written: the phase list intentionally keeps an umbrella (parallel_retrieval) plus per-method sub-phases, and trace_finalize runs after the total snapshot. Instead, test_trace_phase_coverage sums only the non-diagnostic partition and asserts it covers total within a small tolerance and never exceeds it — a guard against both un-instrumented regressions and double-counting. Measured 100% coverage locally.

Testing

• tests/test_search_trace.py::test_trace_phase_coverage (new) + existing test_search_with_trace pass
• ./scripts/hooks/lint.sh, ruff, ty all clean