perf(store): index latest version lookups

[morluto]

Closes #86

Latest-version reads now use SQLite's existing (id, version) index and decode one document. The typed store and namespace router use the same hook; custom stores retain the existing concrete fallback. Exact-version reads and version-conflict retries retain their semantics.

Latest get

Stored versions	Before	After	Speedup
1	7.51 µs	5.36 µs	1.4×
100	148.97 µs	5.53 µs	27.0×
1,000	1,601.40 µs	6.05 µs	264.6×
5,000	8,281.51 µs	6.10 µs	1,357.3×

Put: initial history	Before	After	Speedup
1,000	1,553.35 µs	49.44 µs	31.4×
5,000	7,511.10 µs	59.96 µs	125.3×

Local medians on Python 3.12.13/macOS arm64; full VersionedEntityStore APIs, 128-byte payloads and 1,000 unrelated IDs. Baseline methods come directly from 05b3310; equivalent fixtures and alternating measurement order. Put samples append 84 versions. These are synthetic local results, not cloud or end-to-end task timings.

Profile proof: 100 latest gets over 1,000 versions decode 100,000 → 100 documents. EXPLAIN QUERY PLAN confirms the compound index; returned latest/exact entities and allocated versions match.

Reproduce: PYTHONPATH=src:packages/agentenv-protocol/src .venv/bin/python tst/benchmarks/version_lookup.py

Validation: 6,325 unit/protocol tests passed, 13 existing capability skips; plugin API check passed. Independent correctness and maintainability reviews are clean.

Confidence Score: 5/5

The PR appears safe to merge; the earlier benchmark error is addressed and no new actionable issue was established.

What we checked:

• Benchmark command injection: The command uses a fixed revision and file path. The changed subprocess call does not put a user-supplied value into the command.

Summary

This PR adds an indexed latest-version lookup for SQLite, reducing work on long version histories while keeping exact-version reads unchanged.

• SQLite reads the latest entity version through its existing index.
• Version lookups follow the store that owns each entity ID.

Diagram

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  A[Versioned entity store] --> B[Latest-version hook]
  B --> C[SQLite indexed read]
  B --> D[Other store fallback]
  B --> E[Namespace router]
  E --> C
  E --> D

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_{Reviews (2) · Last reviewed commit: "test(benchmark): cover shallow baseline ..." · Reviewed by Greptile}

[earakely-scale]

Another good PR, thanks @morluto !