12-agent audit (waves 3+4 Opus+Sonnet) on commit 88de01c found that 2 of
my prior fixes had regressions, plus the prev batch missed 8 stale-text
sites and 2 latent bugs. This batch closes them all.
== Regressions in audit-batch (88de01c) — now fixed ==
1. PRAGMA user_version=9 placement — could silently downgrade schema on
cross-version install (existing v10 DB → re-run reset to 9 →
migrations replay → ALTER TABLE duplicate-column errors)
- install/sql/outcome-only-schema.sql: PRAGMA moved OUTSIDE the
transaction (after COMMIT) for portability across SQLite versions
- install/lib-profile-outcome-only.sh::_outcome_install_ledger:
added downgrade guard — reads existing user_version BEFORE running
ANY init path; if >9, skips entirely (preserves newer schema)
- VERIFIED: simulated v10 DB → re-run prints "skipping init to
preserve newer schema"; user_version stays at 10 (was downgraded
to 9 in the prior batch) [REAL: ran in this session]
2. backup_file mv→cp workaround left orphan backups + bypassed rollback
contract (BACKUP_PAIRS not registered)
- install/lib-profile-outcome-only.sh: now manually appends to
BACKUP_PAIRS so rollback trap restores on later failure;
removes the .bak on success path
- Comment updated to explain the workaround vs backup_file mv
3. CLAUDE.md skip-guard "STATUS-TRUTH MARKER" was too broad —
false-positive on existing kit users (RULE 0.16 doc text matches)
- lib-profile-outcome-only.sh: changed grep to literal HTML comment
marker `<!-- outcome-only profile (KeiSeiKit) -->` (specific marker
written by the installer itself)
== Tier 1 missed in prev batch — now fixed ==
4. _ts_packages/package-lock.json referenced packages/cortex-ui which
does NOT exist on disk → npm ci would fail with ELSPROBLEMS in CI
- Regenerated via fresh `rm package-lock.json && npm install`
- npm ci now exits 0 cleanly [REAL: ran in this session]
- Lockfile shrunk 2403→0 lines on the cortex-ui section (full regen)
5. v3 triggers (branch length cap ≤256) were MISSING from
outcome-only-schema.sql — sqlite3 fallback path skipped a schema
feature that the Rust kei-ledger flow enforces, creating cross-flow
drift
- Added trg_agents_branch_len_ins + trg_agents_branch_len_upd
mirroring migrations_list.rs:30-44
- Header comment in outcome-only-schema.sql rewritten to match
current behavior (was stale)
- VERIFIED: end-to-end install creates 2 triggers [REAL: sqlite3
.schema | grep trg_agents_branch_len returns 2]
6. README.md:232 said "102 crates" while README.md:9 said "105 crates"
— internal contradiction in same doc
- README:232 → "105 workspace crates"
7. ARCHITECTURE.md:165 "53 Rust crates + 13 shell primitives" stale
- Updated to "105 Rust workspace crates (47 declared in MANIFEST.toml
`full` profile) + 14 shell primitives"
8. ARCHITECTURE.md:157 "45 /commands" stale
- Updated to 68
9. plugin.json + marketplace.json description strings still had
pre-fix counts (23 primitives / 39 skills / 9 hooks / 12 agents)
- Both rewritten to match README:9 SSoT (38 agents / 68 skills /
38 hooks / 105 workspace crates / 47 installable + 14 shell)
10. PROFILE-OUTCOME-ONLY.md:28-29 "What does NOT get installed" still
cited 102/67/37/82
- Updated to 105/68/38/85
11. encyclopedia/substrate-overview.md §6/§11/§12 still said
"80-char DNA"; §13 said "495 DNA indices"; §6 said "11 install
profiles (.../Cursor/Continue/etc)"
- All 4 sites fixed to current language (≥33-char variable, 565
DNAs, 12 install profiles)
12. docs/DNA-INDEX.md:1352 said wire format is "(80 chars)"
- Updated to "(≥33 chars; role + caps slugs are variable — see
docs/DNA-FORMAT.md)"
== Tier 2 honesty fixes ==
13. Wagner et al. 2004 citation in SLEEP-LAYER.md:26 lacked [VERIFIED]
marker (W3 doc consistency caught it)
- Added [VERIFIED: doi:10.1038/nature02223] + clarification that
the original study did not isolate a specific sleep stage; SWS
attribution comes from secondary literature (Diekelmann/Born)
14. PHILOSOPHY.md:125 attributed "overnight consolidation of un-finished
intentions" to Wagner 2004 — that paper is about insight gain on
the Number Reduction Task, not Zeigarnik-effect cued memory
- Rewritten to accurately describe Wagner 2004's actual finding +
[VERIFIED: doi:10.1038/nature02223]
Verification:
- `npm ci` in _ts_packages/ exits 0 [REAL: ran in this session]
- `cargo check --workspace` exits 0 in _primitives/_rust [REAL: ran in
this session]
- Outcome-only end-to-end fresh install produces user_version=9 +
2 triggers (correct schema shape)
- Outcome-only re-run against v10 DB preserves user_version=10
(downgrade guard works)
- CLAUDE.md skip-guard now triggers ONLY on literal marker, not on
RULE 0.16 phrase
NOT addressed in this batch (deferred to a future round):
- github KeiSei84/{KeiSeiKit, KeiSeiKit-1.0} 404 (user-side action:
publish repo or update refs)
- keigit user `keisei` does not exist (user-side: create org or
rename scope)
- KEIGIT_TOKEN secret not configured (user-side action)
- Forgejo registration disabled (admin-side)
- safeEqual timing leak in TS server (LOW per W3 reassessment)
- HTTP bind 0.0.0.0 default (MEDIUM)
- Unbounded request body (MEDIUM)
- Outcome-only confirm-screen bypass (RULE 0.1 spirit)
- Ledger fallthrough false summary
- Node 20 deprecation (deadline 2026-06-02, 30 days)
- Hook count triple-discrepancy (38 README / 53 DNA-INDEX / 35 maturity-row)
- 100-row router claim still in README:117 + PROFILE-OUTCOME-ONLY.md
- INSTALL.md numerics without [REAL:] markers
- Stale .bak files accumulation policy (cosmetic)
- README per-claim [REAL: ] markers for 6 of 7 numerics
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
External reviewer raised 7 overclaim/scope concerns. Agents verified each
against source; this commit applies all fixes that landed in docs.
Honesty pass:
- README:25-29 — Cortex daemon track listed as alpha (was beta); MCP server
marked "alpha (unpublished) — install via local dist build"; Phase B
noted "auto-codification not yet wired (manual via /escalate-recurrence)";
keigit framed as author-operated mirror (KeiSei84 / private Forgejo),
not neutral community service
- README:95-97 — Cortex CLI/daemon track downgraded beta→alpha
with rationale (browser-app + VSCode-extension are concept-level)
- docs/ARCHITECTURE.md — added "Model router — current state (2026-05-03)"
subsection: per-call fixed estimate routing, NO 100-row Bayesian threshold
in current source (select.rs:74-124); reviewer suggestion deferred
- docs/SLEEP-LAYER.md — added Phase B scope clarification: morning report
is read-only markdown, no auto-codification path
- docs/PUBLISHING.md — aligned framing with README:43 ("author-operated
mirror" not "community registry"); added vendor-neutrality note that
substrate works against any npm-compatible registry
- mcp-server/package.json — added "private": true and description note
to prevent accidental publish before maturity gate
Portable format specs (reviewer asked for memory-repo agnosticism):
- docs/MEMORY-FORMAT.md (196 LOC) — JSONL schemas for traces / decisions /
agent-events with jq/awk/pandas recipes, grounded in actual writers
- docs/DNA-FORMAT.md (159 LOC) — DNA wire format ("type::caps::sha8")
with shell+python parsers
- docs/LEDGER-SCHEMA.md (199 LOC) — full SQLite DDL (agents +
skill_invocations + indexes + triggers) with sample queries
Auto-regen artifact:
- docs/DNA-INDEX.md — kei-registry regenerated count 564→565
Verification:
- All claims traced to file:line in source by agent a52b29ae
- All new docs ≤200 LOC per Constructor Pattern
- Reality verification verdicts: README/MCP/Phase-B/Cortex VERIFIED;
Bayesian-router PARTIAL (overclaim removed); keigit PARTIAL (framing
fixed in this commit); memory-format VERIFIED-FALSE (spec added)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Parfii-bot