Speed up inspect and refresh Windows benchmarks

[lzehrung]

Summary

• make inspect duplicate analysis opt-in with --duplicates and report duplicates.enabled
• auto-enable the existing native-worker policy for inspect scans with at least 250 files
• make npm run bench:docs regenerate the checked JSON and README table directly
• replace the stale WSL benchmark artifact with current Windows results and clarify that the direct-read baseline is not equivalent work

Why

inspect always paid for duplicate extraction and candidate scoring even when callers only needed architecture summaries. It also missed the automatic native-worker policy already used by agent sessions.

The checked documentation benchmark required a manual promotion step and still described an older WSL checkout, which made regeneration and interpretation unclear.

Impact

On this checkout, the warm-disk inspect median improved from 11,515 ms to 7,505 ms when duplicate analysis became opt-in, then to 6,065 ms with automatic workers: about 47% overall.

Duplicate summaries remain available through inspect --duplicates and the dedicated duplicates command. Default inspect JSON now reports { "duplicates": { "enabled": false } }.

The regenerated Windows documentation benchmark reports cold one-shot explore medians of 461-523 ms with complete evidence anchors.

Validation

• npm run test:integration: 130 tests passed
• targeted CLI and AgentSession suites: 170 tests passed
• public benchmark harness: 23 tests passed
• npm run bench:docs:check
• git diff --check
• npm run check: lint, format, and build passed; the full test stage remains red on 24 Windows path/permission expectations outside this diff

[kilo-code-bot]

Code Review Summary

Status: No Issues Found | Recommendation: Merge

Files Reviewed (11 files)

• src/cli/inspect.ts — opt-in duplicates, auto-native-worker threshold
• src/cli/options.ts — --duplicates flag schema and CLI value option handling
• src/agent/session.ts — exported NATIVE_WORKER_AUTO_FILE_THRESHOLD
• src/cli/help.ts — help text updates
• tests/cli-command-modules.test.ts — native worker threshold test
• tests/cli-regressions.test.ts — updated inspect assertions for new duplicates shape
• docs/cli.md — updated inspect command docs
• codegraph-skill/codegraph/SKILL.md — added --duplicates note
• docs/benchmarks/README.md — regenerated benchmark docs
• docs/benchmarks/results.example.json — regenerated benchmark results
• package.json — updated bench:docs script

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_{Reviewed by kimi-k2.6-20260420 · Input: 77.7K · Output: 12.1K · Cached: 210.9K}