docs: sync CLAUDE.md with actual repo structure, archive stale script

[slittycode]

Summary

Six concrete gaps found between CLAUDE.md and the filesystem, all fixed in this PR:

• docs/ repo-layout entry was underspecified — added adr/, SETUP.md, LAYER2_EVALUATION.md, POLYPHONIC_TRANSCRIPTION_SPIKE.md, and SAMPLE_GENERATION.md to the inventory.
• Companion Agent Docs was missing docs/adr/ — added item [codex] Prepare hosted runtime foundation #6 pointing at ADR 0001 (Phase 1 JSON schema v1 stability contract, field-rename policy, CSV column pinning).
• scripts/calibrate_confidence.py entry omitted that its test lives in scripts/tests/test_calibrate_confidence.py.
• src/services/midi/ file list was missing types.ts.
• src/services/sessionMusician/ file list was missing index.ts.
• docs/generate_phase2_truthfulness_doc.js — a stale one-shot docx generator sitting unreferenced at the docs root — moved to docs/history/ where past-tense deliverables belong.

Test plan

• Verify all file paths mentioned in the updated CLAUDE.md entries exist on disk
• Confirm docs/generate_phase2_truthfulness_doc.js is gone from docs/ root and present at docs/history/

https://claude.ai/code/session_01ScX5H3JDVAnSjvk4k7HA7p

---

Generated by Claude Code

[slittycode]

Verdict: APPROVE (self-review restriction — posting as COMMENT)

Summary

Docs-only sync: six CLAUDE.md gaps closed (missing docs/ sub-entries, adr/ pointer, calibrate test location, midi/types.ts, sessionMusician/index.ts) plus a stale one-shot script relocated to docs/history/ where it belongs. All 9 file paths mentioned in the updated entries verified present on disk; the old docs/generate_phase2_truthfulness_doc.js location is correctly gone.

Findings

None.

Test results

No code changed — no test suite run required or meaningful.

Phase boundary check

Clean. No Phase 1/2/3 logic touched.

---

Generated by Claude Code

[slittycode]

Verdict: APPROVE (posted as COMMENT — can't self-approve)

Summary

Docs-only PR that closes six known gaps between CLAUDE.md and the actual filesystem, and moves a stale one-shot script to its graveyard. All six stated file paths were verified against the PR head — every one exists. CI is green across all three jobs (Frontend, Backend, Loudness WASM).

Findings

None.

Test results

Frontend ✓ · Backend ✓ · Loudness WASM ✓ (3/3 pass)

Phase boundary check

Clean. No code touched.

---

Generated by Claude Code