@lh8ppl/claude-memory-kit 0.3.0 → 0.3.1

package/README.md

@@ -11,8 +11,9 @@
 - **Explicit capture when you want it** — say "remember this" / "from now on" / "we decided" / "forget X" (the `memory-write` skill), or run `cmk remember "<fact>"`. Both dedup, screen for secrets, abstract machine paths to `~`, and write silently. For backtick/quote-heavy rich facts, capture them shell-safe as JSON: `cmk remember --from-file fact.json` (or `--json` from stdin) — content never touches the shell.
 - **Search + MCP — Claude runs every memory op for you, in conversation** — `cmk search "<term>"` (keyword over facts + scratchpads; with the optional local embedder, **semantic + hybrid recall**: ask in your own words and get the fact even with zero keyword overlap — measured R@5 0.941 / paraphrase 1.000 on the kit's benchmark, no API calls). `cmk install` registers the kit's **MCP server**, so Claude can do the whole memory surface as tools without you ever typing `cmk`: capture (`mk_remember`, rich Why/How too), recall (`mk_search` / `mk_get` / `mk_timeline` / `mk_cite`), adjust trust (`mk_trust`), promote a fact across projects (`mk_lessons_promote`), forget (`mk_forget` — previews first, then deletes on confirm), and clear the review/conflict queues (`mk_queue_list` / `mk_queue_resolve`). The tools are allow-listed on install, so they run prompt-free.
 - **Bounded by compression** — session → daily → weekly Haiku rollups (cron or lazy-on-read) keep the snapshot small as history grows. The session-buffer rollup self-heals at session start too, so memory stays bounded even if you never cleanly close the window.
+- **Don't start empty — import the rules you already own** — `cmk import-claude-md` parses an existing `CLAUDE.md` / `.cursorrules` / `AGENTS.md` into typed, searchable facts through the same safe write path (secret screening, sanitization, dedup), with provenance back to source file + line. `--dry-run` previews first.
 - **Per-project, in-repo** — `context/` lives inside your project and travels with `git clone`. Each project keeps its own memory.
-- **7 health checks** — `cmk doctor` validates hook wiring, distill freshness, transcript firing, INDEX consistency, cron registration, native-memory coexistence, and stale locks — each failure with a repair command.
+- **8 health checks** — `cmk doctor` validates hook wiring, distill freshness, transcript firing, INDEX consistency, cron registration, native-memory coexistence, stale locks, and native-binding health (npm 12 readiness) — each failure with a repair command.
 
 ## Install — pick ONE route
 
@@ -26,10 +27,11 @@ cd ~/my-project
 cmk install        # scaffolds context/ + the memory-write + memory-search skills AND wires the lifecycle hooks into .claude/settings.json
 cmk install --with-semantic   # (optional) local semantic recall — one-time ~260 MB, search defaults to hybrid
 cmk register-crons            # (optional) scheduled background compression — otherwise self-heals lazily
+cmk import-claude-md --yes    # (optional) seed memory from an existing CLAUDE.md / .cursorrules (--dry-run previews)
 cmk doctor         # verify, then restart Claude Code
 ```
 
-`cmk install` is a complete entry point: it scaffolds `context/`, drops the `memory-write` + `memory-search` skills into `.claude/skills/` (committed — travels with `git clone`), and writes the 5 lifecycle hooks (PATH-resolved, cross-OS) into the project's `.claude/settings.json`. It also **registers the kit's MCP server** in `.mcp.json` and allow-lists its tools (`mcp__cmk__*`) in `.claude/settings.json`, so Claude can drive memory as tools with no per-call prompt. No separate `/plugin` step needed. Use `cmk install --no-hooks` to skip the hooks + MCP wiring (scaffold-only).
+`cmk install` is a complete entry point: it scaffolds `context/`, drops the `memory-write` + `memory-search` skills into `.claude/skills/` (committed — travels with `git clone`), and writes the 5 lifecycle hooks (PATH-resolved, cross-OS) into the project's `.claude/settings.json`. It also **registers the kit's MCP server** in `.mcp.json` and allow-lists its tools (`mcp__cmk__*`) in `.claude/settings.json`, so Claude can drive memory as tools with no per-call prompt, and writes a `.gitattributes` block pinning committed memory to LF (so a Windows clone can't mangle line endings — your memory stays readable cross-platform). No separate `/plugin` step needed. Use `cmk install --no-hooks` to skip the hooks + MCP wiring (scaffold-only).
 
 > Installing the package globally adds the `cmk` CLI **and** the installer. It's the `cmk install` *subcommand* that wires the hooks — not the bare `npm install`.
 
@@ -51,7 +53,7 @@ Most-used commands (full list via `cmk --help`):
 | Command | Purpose |
 | --- | --- |
 | `cmk install` | Scaffold `context/` + the `memory-write`/`memory-search` skills + `.gitignore` + CLAUDE.md block + wire hooks (`--no-hooks` for scaffold-only) |
-| `cmk doctor` | Run HC-1..HC-7 health checks, surface repair commands |
+| `cmk doctor` | Run HC-1..HC-8 health checks, surface repair commands |
 | `cmk repair --hooks` / `--locks` / `--index` / `--all` | Idempotent self-repair |
 | `cmk search "<query>" [--mode keyword\|semantic\|hybrid] [--scope facts\|transcripts]` | Search memory — by meaning with the embedder (hybrid default after `--with-semantic`); `--scope transcripts` = the raw session record |
 | `cmk get <id…>` / `cmk timeline <id>` / `cmk cite <id>` / `cmk recent-activity` | Read the index back — full fact bodies + provenance, sequential context around an observation, a canonical citation link, recent changes (the CLI side of the `mk_*` MCP read tools) |
@@ -63,6 +65,7 @@ Most-used commands (full list via `cmk --help`):
 | `cmk persona generate` | Run cross-project persona synthesis on demand (instead of waiting for the weekly pass) |
 | `cmk persona export <file>` / `import <file>` | Carry your cross-project persona (the user tier) to another of **your** machines — export to one portable bundle, import on the other (overwrites with backup + rollback). The persona stays private (never committed to a project) |
 | `cmk import-anthropic-memory [--dry-run] [--yes]` | Merge bullets from Anthropic's native auto-memory into MEMORY.md |
+| `cmk import-claude-md [file] [--dry-run] [--yes]` | Onboard from the rules you already own — parse an existing `CLAUDE.md` / `.cursorrules` / `AGENTS.md` into typed facts through the safe write path (Poison_Guard + sanitization + dedup) |
 
 ## Requirements
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@lh8ppl/claude-memory-kit",
-  "version": "0.3.0",
+  "version": "0.3.1",
   "description": "cmk — the CLI for claude-memory-kit. Per-project, in-repo memory system for Claude Code.",
   "type": "module",
   "bin": {

package/src/audit-log.mjs

@@ -33,6 +33,7 @@ export const REASON_CODES = Object.freeze({
   FACT_CREATED: 'fact-created', // writeFact: a new fact file was written (Task 123.A — the default create audit; callers emitting a richer code opt out via audit:false)
   DUPLICATE: 'duplicate', // writeFact: same path + same id
   DUPLICATE_ELSEWHERE: 'duplicate-elsewhere', // writeFact: different path + same id
+  INDEX_REBUILD_FAILED: 'index-rebuild-failed', // writeFact: the fact landed on disk but the best-effort INDEX.md rebuild threw (e.g. a detached auto-extract child killed mid-rebuild). Surfaces what was previously a SILENTLY swallowed catch (D-152) so a lagging committed INDEX is diagnosable; the next reindex/cmk reindex self-heals.
   USER_REQUESTED: 'user-requested', // forget: user-initiated tombstone
   CURATED_MERGE: 'curated-merge', // mergeFacts: explicit merge of A + B → C
   SCRATCHPAD_APPEND: 'scratchpad-append', // scratchpad: appendScratchpadBullet (Task 12)

package/src/auto-drain.mjs

@@ -22,6 +22,7 @@
 
 import { resolveReviewQueue } from './review-queue.mjs';
 import { resolveConflictQueue } from './conflict-queue.mjs';
+import { resolvePersonaReviewQueue } from './auto-persona.mjs';
 import { mergeFacts } from './merge-facts.mjs';
 
 // Stateless optimistic resolvers (no per-entry judgement — that's the point).
@@ -55,5 +56,20 @@ export async function autoDrainQueues({ tier = 'P', projectRoot, userDir, scratc
     mergeFn: mergeFacts, // never invoked under KEEP_OLD; wired for correctness
   });
 
-  return { review, conflict };
+  // Persona-review queue (D-154): the medium-confidence cross-project persona
+  // candidates that were ROUTED here with the promise of an auto-drain that was
+  // never implemented — so they stranded (the v0.3.1 cold-open found the user's
+  // architecture philosophy stuck here). Drain it optimistically like the review
+  // queue (sync; userDir-scoped so it runs regardless of `tier`). Best-effort: a
+  // persona-drain hiccup must not fail the project-tier review/conflict drain.
+  let persona = { promoted: 0, drained: 0, queuePath: null };
+  if (userDir) {
+    try {
+      persona = resolvePersonaReviewQueue({ userDir });
+    } catch {
+      // best-effort; the queue file survives for the next pass
+    }
+  }
+
+  return { review, conflict, persona };
 }

package/src/auto-extract.mjs

@@ -48,8 +48,8 @@ import {
   appendFileSync,
 } from 'node:fs';
 import { join, dirname } from 'node:path';
-import { createHash } from 'node:crypto';
 import { generateId } from '@lh8ppl/cmk-canonicalize';
+import { hashContent } from './content-hash.mjs';
 import { memoryWrite } from './memory-write.mjs';
 import { writeFact } from './write-fact.mjs';
 import { buildRichFactBody, slugifyFact } from './rich-fact.mjs';
@@ -663,10 +663,9 @@ function routeRichFact({ candidate, projectRoot, ts }) {
     sourceFile: 'auto-extract',
     sourceLine: 1,
     // Content fingerprint for the provenance field — NOT a security context.
-    // Matches the kit's sha1-of-content convention (write-fact.mjs caller in
-    // subcommands.runRememberRich, memory-write.mjs); writeFact dedups by the
-    // content-addressed id, this is just source_sha1. // NOSONAR
-    sourceSha1: createHash('sha1').update(body).digest('hex'), // NOSONAR
+    // Routes through the shared hashContent (SHA-256, D-149); writeFact dedups
+    // by the content-addressed id, this is just source_sha1 metadata.
+    sourceSha1: hashContent(body),
     createdAt: ts,
     projectRoot,
   });

package/src/auto-persona.mjs

@@ -38,7 +38,7 @@
 // promotion primitive), audit-log, result-shapes, cooldown, compressor.
 // Per design §16.16 + §6.2 (conflict) + §6.8 (auto-drain) + §8.3 + tasks.md 45.
 
-import { readFileSync, appendFileSync, mkdirSync, existsSync, readdirSync } from 'node:fs';
+import { readFileSync, writeFileSync, appendFileSync, mkdirSync, existsSync, readdirSync } from 'node:fs';
 import { join, dirname } from 'node:path';
 import { generateId } from '@lh8ppl/cmk-canonicalize';
 import { ERROR_CATEGORIES, errorResult } from './result-shapes.mjs';
@@ -425,6 +425,91 @@ export function appendPersonaReviewQueue({ userDir, entries, now }) {
   return queuePath;
 }
 
+// Parse persona-review.md back into candidate objects. The queue lines are
+//   - (U-XXXXXXXX) [TARGET § SECTION] <text>
+//     <!-- target: TARGET, section: SECTION, confidence: C, reason: ..., ... -->
+// The HTML comment is authoritative for target/section/confidence (the bracket
+// prefix is human-readable redundancy); fall back to the bracket if absent.
+// ReDoS-safe: NEGATED character classes (not lazy `.+?...+?` pairs) so the regex
+// is linear — each group matches "anything but the delimiter that ends it", which
+// cannot backtrack across that delimiter (the canonicalize stripTrailingPunct
+// lesson — Task 140 / D-143 — applied at write).
+const PERSONA_QUEUE_LINE_RE = /^- \([UPL]-[^)]+\)\s+\[([^§\]]+)§([^\]]+)\]\s+(\S.*)$/;
+// No `\s*` sits adjacent to a `[^,]+` capture: `\s*` and `[^,]+` both match a
+// space, and that overlap is the super-linear-backtracking ambiguity Sonar
+// flags. Each value is captured by `[^,]+` (which absorbs leading/trailing
+// space — we `.trim()` below), with the `,` and label as fixed delimiters.
+const PERSONA_QUEUE_META_RE = /target:([^,]+),\s*section:([^,]+),\s*confidence:\s*(\w+)/;
+export function parsePersonaReviewQueue(text) {
+  const lines = (text ?? '').split(/\r?\n/);
+  const candidates = [];
+  for (let i = 0; i < lines.length; i++) {
+    const m = PERSONA_QUEUE_LINE_RE.exec(lines[i].trim());
+    if (!m) continue;
+    let [, target, section, body] = m;
+    let confidence = 'medium';
+    const meta = PERSONA_QUEUE_META_RE.exec(lines[i + 1] ?? '');
+    if (meta) {
+      target = meta[1].trim();
+      section = meta[2].trim();
+      confidence = meta[3].trim().toLowerCase();
+    }
+    candidates.push({ target: target.trim(), section: section.trim(), confidence, text: body.trim() });
+  }
+  return candidates;
+}
+
+/**
+ * Auto-drain the persona-review queue (the down-payment for Task 151 / D-154).
+ *
+ * The medium-confidence persona candidates were ROUTED to persona-review.md with
+ * the documented promise that "the daily/weekly auto-drain acts on them" — but
+ * that drain was never implemented, so they STRANDED (the v0.3.1 cold-open found
+ * the user's architecture philosophy stuck here, never reaching the persona).
+ * This makes the promise real: the same optimistic auto-promote the review queue
+ * already gets (D-6) — trust the synthesis, mistakes self-correct via `cmk forget`
+ * (the post-hoc-reversibility model every surveyed memory system uses instead of
+ * a pre-promotion human gate). NOT a manual command: runs inside autoDrainQueues
+ * on the daily/weekly maintenance passes. The full recurrence-scored redesign is
+ * Task 151 (v0.4); this just stops the stranding.
+ *
+ * @returns {{promoted: number, drained: number, queuePath: string|null}}
+ */
+export function resolvePersonaReviewQueue({ userDir, now, settings } = {}) {
+  const userTierRoot = resolveTierRoot({ tier: 'U', userDir });
+  const queuePath = join(userTierRoot, 'queues', 'persona-review.md');
+  let text;
+  try {
+    text = readFileSync(queuePath, 'utf8');
+  } catch {
+    return { promoted: 0, drained: 0, queuePath: null }; // no queue → nothing to drain
+  }
+  const candidates = parsePersonaReviewQueue(text);
+  if (candidates.length === 0) return { promoted: 0, drained: 0, queuePath };
+
+  // Re-feed through the SAME promote path the synthesis uses (home-path sanitize
+  // + Poison_Guard + dedup + audit all inherited). OPTIMISTIC AUTO-DRAIN: these
+  // candidates already SURVIVED a synthesis pass without being superseded; the
+  // drain IS the decision to promote them (the field-standard "auto-promote then
+  // post-hoc revert via cmk forget" posture — see the persona-promotion research
+  // note). So force confidence:'high' to clear promoteCandidatesToUserTier's
+  // confidence gate — otherwise they'd re-queue forever (the gate that stranded
+  // them in the first place). The full recurrence-scored model is Task 151 (v0.4).
+  const promotable = candidates.map((c) => ({ ...c, confidence: 'high' }));
+  const r = promoteCandidatesToUserTier({ candidates: promotable, userDir, now, settings });
+  const promoted = r.promoted?.length ?? 0;
+
+  // Clear the queue — the candidates are now resolved (promoted or de-duped into
+  // existing persona). Leave a tombstone header so the file isn't silently empty.
+  const ts = now ?? new Date().toISOString().replace(/\.\d{3}Z$/, 'Z');
+  writeFileSync(
+    queuePath,
+    `<!-- persona-review queue — auto-drained ${ts}: ${candidates.length} candidate(s) promoted to the persona. -->\n`,
+    'utf8',
+  );
+  return { promoted, drained: candidates.length, queuePath };
+}
+
 export function promoteCandidatesToUserTier({ candidates, userDir, now, settings, trust = 'medium', source = 'persona-synthesis' }) {
   // `trust`/`source` default to the AUTO-persona posture (medium, system-derived
   // — 45.6). The EXPLICIT path (`cmk lessons promote`) passes trust:'high' +

package/src/capture-prompt.mjs

@@ -63,7 +63,8 @@ export function buildMemoryHint({ projectRoot, prompt } = {}) {
   }
   return (
     '[claude-memory-kit] Recorded memory available beyond the session snapshot — ' +
-    'use the memory-search skill when the answer may already be recorded (prior decisions, history, conventions).'
+    'use the memory-search skill when the answer may already be recorded (prior decisions, history, conventions, ' +
+    'project structure/architecture, where things live). Recall it; do not re-read the code to reconstruct it.'
   );
 }
 

package/src/config-core.mjs

@@ -0,0 +1,161 @@
+// `cmk config get/set/--show-origin` core (Task 129, D-121).
+//
+// The v0.1.0 stub became real the day `--with-semantic` shipped:
+// context/settings.json now carries a user-facing setting
+// (search.default_mode) and hand-editing JSON was the only path. This is
+// the read-merge-write surface over the kit's settings files.
+//
+// Settings live in `<tier-root>/settings.json` for each of the three tiers
+// (resolveTierRoot — the shared module, not re-derived). Resolution
+// precedence mirrors the kit's memory model + git config semantics:
+//   local (context.local/) > project (context/) > user (~/.claude-memory-kit/)
+// A `get` returns the highest-precedence tier that defines the dotted key;
+// `--show-origin` lists every tier that defines it (winner + shadowed), the
+// direnv lesson (design §7.2: "without --show-origin, users rage-quit when
+// settings appear from nowhere"). `set` writes one tier (project default),
+// preserving every sibling key (the mergeProjectSettings discipline,
+// generalized per tier).
+//
+// Scope (D-121): the kit's own JSON settings files. NOT the richer
+// settings-or-observation `--show-origin` sketch in design §7.2's example
+// (observations have their own provenance/shadowed_by surface, §6); this is
+// the concrete settings half the semantic default forced into existence.
+
+import { existsSync, mkdirSync, readFileSync, writeFileSync } from 'node:fs';
+import { dirname, join } from 'node:path';
+import { resolveTierRoot } from './tier-paths.mjs';
+
+// Highest-precedence first.
+const TIERS = Object.freeze([
+  { name: 'local', tier: 'L' },
+  { name: 'project', tier: 'P' },
+  { name: 'user', tier: 'U' },
+]);
+
+// Keys that would pollute the prototype chain — rejected on both read and
+// write. `cmk config set __proto__.x y` must never reach Object.prototype
+// (skill-review blocking finding); a key path containing any of these is
+// invalid, not a silent no-op.
+const FORBIDDEN_KEYS = new Set(['__proto__', 'constructor', 'prototype']);
+function hasForbiddenSegment(dottedKey) {
+  return dottedKey.split('.').some((p) => FORBIDDEN_KEYS.has(p));
+}
+
+function settingsPathFor(tierName, { projectRoot, userDir }) {
+  const tier = TIERS.find((t) => t.name === tierName)?.tier;
+  return join(resolveTierRoot({ tier, projectRoot, userDir }), 'settings.json');
+}
+
+function readSettings(path) {
+  if (!existsSync(path)) return null;
+  try {
+    return JSON.parse(readFileSync(path, 'utf8'));
+  } catch {
+    // A malformed settings file is treated as absent for resolution — never
+    // throw on a read (a hand-broken JSON shouldn't crash `cmk config get`).
+    return null;
+  }
+}
+
+// Walk a dotted path; returns {found, value}. `found` distinguishes a key
+// set to `undefined`-ish from a key that isn't there (the honesty contract).
+function dig(obj, dottedKey) {
+  if (obj == null || typeof obj !== 'object') return { found: false };
+  const parts = dottedKey.split('.');
+  let cur = obj;
+  for (const p of parts) {
+    if (cur == null || typeof cur !== 'object' || !(p in cur)) return { found: false };
+    cur = cur[p];
+  }
+  return { found: true, value: cur };
+}
+
+/**
+ * Resolve a dotted setting key across tiers (local > project > user).
+ *
+ * @returns {{found: boolean, value?: *, tier?: 'local'|'project'|'user'}}
+ */
+export function configGet(key, { projectRoot, userDir } = {}) {
+  if (!key || !String(key).trim()) return { found: false };
+  if (hasForbiddenSegment(key)) return { found: false };
+  for (const { name } of TIERS) {
+    const settings = readSettings(settingsPathFor(name, { projectRoot, userDir }));
+    const hit = dig(settings, key);
+    if (hit.found) return { found: true, value: hit.value, tier: name };
+  }
+  return { found: false };
+}
+
+/** Scalar coercion: true/false/null → primitives, integer/float strings →
+ *  numbers, everything else stays a string. JSON settings are typed, and a
+ *  CLI arg is always a string — `cmk config set x true` should write a bool. */
+function coerce(raw) {
+  if (raw === 'true') return true;
+  if (raw === 'false') return false;
+  if (raw === 'null') return null;
+  if (/^-?\d+$/.test(raw)) return Number.parseInt(raw, 10);
+  if (/^-?\d*\.\d+$/.test(raw)) return Number.parseFloat(raw);
+  return raw;
+}
+
+function setDeep(obj, dottedKey, value) {
+  const parts = dottedKey.split('.');
+  let cur = obj;
+  for (let i = 0; i < parts.length - 1; i++) {
+    const p = parts[i];
+    if (cur[p] == null || typeof cur[p] !== 'object' || Array.isArray(cur[p])) cur[p] = {};
+    cur = cur[p];
+  }
+  cur[parts[parts.length - 1]] = value;
+}
+
+/**
+ * Set a dotted key in one tier's settings.json (project default), preserving
+ * every sibling key (read-merge-write).
+ *
+ * @returns {{ok: boolean, tier?: string, path?: string, error?: string}}
+ */
+export function configSet(key, rawValue, { projectRoot, userDir, tier = 'project' } = {}) {
+  if (!key || !String(key).trim()) return { ok: false, error: 'key is required (dotted path)' };
+  if (hasForbiddenSegment(key)) {
+    return { ok: false, error: `key contains a forbidden segment (${[...FORBIDDEN_KEYS].join('/')}) — prototype-pollution guard` };
+  }
+  if (!TIERS.some((t) => t.name === tier)) {
+    return { ok: false, error: `tier must be one of local/project/user (got ${tier})` };
+  }
+  const path = settingsPathFor(tier, { projectRoot, userDir });
+  try {
+    const current = readSettings(path) ?? {};
+    setDeep(current, key, coerce(String(rawValue)));
+    mkdirSync(dirname(path), { recursive: true });
+    writeFileSync(path, JSON.stringify(current, null, 2) + '\n', 'utf8');
+    return { ok: true, tier, path };
+  } catch (err) {
+    return { ok: false, error: err?.message ?? String(err) };
+  }
+}
+
+/**
+ * Every tier that defines the key, highest-precedence first. The winner is
+ * the first; the rest carry `shadowedBy` = the winning tier (the direnv
+ * "where did this come from?" surface).
+ *
+ * @returns {{found: boolean, entries: Array<{tier, value, path, winner, shadowedBy?}>}}
+ */
+export function configShowOrigin(key, { projectRoot, userDir } = {}) {
+  const entries = [];
+  if (!key || !String(key).trim()) return { found: false, entries };
+  if (hasForbiddenSegment(key)) return { found: false, entries };
+  for (const { name } of TIERS) {
+    const path = settingsPathFor(name, { projectRoot, userDir });
+    const hit = dig(readSettings(path), key);
+    if (hit.found) entries.push({ tier: name, value: hit.value, path });
+  }
+  if (entries.length === 0) return { found: false, entries: [] };
+  const winnerTier = entries[0].tier;
+  for (let i = 0; i < entries.length; i++) {
+    entries[i].winner = i === 0;
+    if (i > 0) entries[i].shadowedBy = winnerTier;
+  }
+  return { found: true, entries };
+}

package/src/conflict-queue.mjs

@@ -50,7 +50,7 @@ import {
 import { join } from 'node:path';
 import { resolveTierRoot, VALID_TIERS } from './tier-paths.mjs';
 import { writeBullet } from './provenance.mjs';
-import { createHash } from 'node:crypto';
+import { hashContent } from './content-hash.mjs';
 import { nowIso, appendAuditEntry, REASON_CODES } from './audit-log.mjs';
 import { ERROR_CATEGORIES, errorResult } from './result-shapes.mjs';
 import { generateId } from '@lh8ppl/cmk-canonicalize';
@@ -792,7 +792,7 @@ export function mergeScratchpadBullets({
   // no `write:` key, so the first reindex after a merge-both resolution hit
   // the NOT-NULL observations.write_source constraint. Canonical shape via
   // the shared builder; the merged_from trail lives in the audit entry below.
-  const sha1 = createHash('sha1').update(combinedText, 'utf8').digest('hex');
+  const sha1 = hashContent(combinedText);
   const formatted = writeBullet({
     id: newId,
     text: combinedText,

package/src/content-hash.mjs

@@ -0,0 +1,30 @@
+// Content-fingerprint helper — the single home for the kit's content hash.
+//
+// Every "fingerprint this text/file content" site (provenance source_sha1,
+// the `files` checkpoint diff key, transcript dedup, conflict-merge keys)
+// MUST route through hashContent so the algorithm is defined in exactly one
+// place. Eight modules previously rolled their own `createHash('sha1')`,
+// which (a) let the algorithm drift per-site and (b) tripped CodeQL's
+// js/weak-cryptographic-algorithm on each one independently.
+//
+// SHA-256, not SHA-1: the digests are non-cryptographic content fingerprints
+// (dedup + change-detection), so SHA-1 was never a security flaw here — but a
+// weak-hash sink on every site is noise that hides real findings, and the
+// whole-convention move to SHA-256 (the user's call, D-149) removes the sink
+// kit-wide while keeping the digest consistent across writers. The on-disk
+// FIELD name stays `source_sha1` / `sha1` for back-compat (renaming the YAML
+// key + db column would break existing fact files + checkpoints); only the
+// algorithm changes. Existing `files`-table checkpoints mismatch once on the
+// first boot after upgrade and self-heal via the normal reindex.
+
+import { createHash } from 'node:crypto';
+
+/**
+ * Hash text/file content to a hex digest used as a non-cryptographic
+ * fingerprint (dedup, drift-detection, provenance). UTF-8 input.
+ * @param {string} content
+ * @returns {string} 64-char lowercase hex SHA-256 digest
+ */
+export function hashContent(content) {
+  return createHash('sha256').update(content, 'utf8').digest('hex');
+}

package/src/doctor.mjs

@@ -1,4 +1,4 @@
-// `cmk doctor` — health checks HC-1..HC-7 (Task 37, T-031; memsearch HC-1/HC-7 removed in Task 120).
+// `cmk doctor` — health checks HC-1..HC-8 (Task 37, T-031; memsearch HC-1/HC-7 removed in Task 120; HC-8 native bindings added in Task 141a).
 //
 // Public boundary:
 //   async runDoctor({projectRoot, userDir, now, promptUser?, ...overrides})
@@ -44,6 +44,8 @@ import { nowIso } from './audit-log.mjs';
 import { detectStaleLocks } from './lock-discipline.mjs';
 import { cronSentinelPath } from './lazy-compress.mjs';
 import { getNativeAutoMemoryState } from './native-memory.mjs';
+import { checkKitBinding, checkEmbedderBinding } from './native-binding.mjs';
+import { resolveDefaultSearchMode } from './semantic-backend.mjs';
 
 const TWO_DAYS_MS = 2 * 24 * 60 * 60 * 1000;
 const THREE_DAYS_MS = 3 * 24 * 60 * 60 * 1000;
@@ -470,13 +472,67 @@ function hc7StaleLocks({ projectRoot, userDir }) {
   };
 }
 
+// --- HC-8: native bindings present (npm 12 readiness, Task 141a) -------
+// The BACKSTOP, not the primary UX: `cmk install` probes + asks inline
+// (the user's 2026-06-12 steer); HC-8 catches the after-the-fact states
+// (npm upgraded later, package reinstalled without the allow flag).
+// The repair is an `npm install -g` → requiresInstall per the design §14
+// ask-before-install rule.
+async function hc8NativeBindings({ projectRoot, kitBindingProbe, embedderBindingProbe }) {
+  const kitProbe = kitBindingProbe ?? checkKitBinding;
+  const kit = kitProbe();
+  if (!kit.ok) {
+    return {
+      id: 'HC-8',
+      name: 'Native bindings present (npm 12 readiness)',
+      status: 'fail',
+      message: `better-sqlite3 native binding unavailable (${kit.reason}) — most common cause: npm 12 blocks dependency install scripts by default, so a fresh install skips the binding build (a Node major upgrade is the other); search/reindex will crash until it is rebuilt`,
+      recoveryCommand: kit.remedy,
+      requiresInstall: true,
+    };
+  }
+  // The embedder matters only when this project actually defaults to it.
+  const mode = resolveDefaultSearchMode({ projectRoot });
+  if (mode === 'keyword') {
+    return {
+      id: 'HC-8',
+      name: 'Native bindings present (npm 12 readiness)',
+      status: 'pass',
+      message: 'better-sqlite3 binding healthy (semantic not configured — embedder not checked)',
+    };
+  }
+  const embedderProbe = embedderBindingProbe ?? checkEmbedderBinding;
+  const embedder = await embedderProbe();
+  if (!embedder.ok) {
+    const state = embedder.installed
+      ? `installed but its native binding failed (${embedder.reason}) — npm 12 blocks onnxruntime-node's install script by default`
+      : `not installed, but search.default_mode is '${mode}'`;
+    return {
+      id: 'HC-8',
+      name: 'Native bindings present (npm 12 readiness)',
+      status: 'fail',
+      message: `semantic embedder ${state}; searches degrade to keyword until fixed`,
+      recoveryCommand: embedder.remedy,
+      requiresInstall: true,
+    };
+  }
+  return {
+    id: 'HC-8',
+    name: 'Native bindings present (npm 12 readiness)',
+    status: 'pass',
+    message: `better-sqlite3 binding healthy; embedder import OK (default mode: ${mode}; the deep pipeline check runs at --with-semantic warm)`,
+  };
+}
+
 /**
- * Run the full 7-check health audit.
+ * Run the full 8-check health audit.
  *
  * @param {object} opts
  * @param {string} opts.projectRoot
  * @param {string} [opts.userDir]
  * @param {string} [opts.now]
+ * @param {Function} [opts.kitBindingProbe] - HC-8 test seam.
+ * @param {Function} [opts.embedderBindingProbe] - HC-8 test seam.
  * @returns {Promise<{action, checks, duration_ms}>}
  *
  * Note: M3 fix (skill-review 2026-05-28) dropped the v0.1.0 `promptUser`
@@ -489,6 +545,8 @@ export async function runDoctor({
   projectRoot,
   userDir,
   now,
+  kitBindingProbe,
+  embedderBindingProbe,
 } = {}) {
   const t0 = Date.now();
   if (!projectRoot) {
@@ -510,10 +568,11 @@ export async function runDoctor({
   const c5 = hc5CronRegistered({ projectRoot });
   const c6 = hc6NativeAutoMemory({ projectRoot, now: ts });
   const c7 = hc7StaleLocks({ projectRoot, userDir: resolvedUserDir });
+  const c8 = await hc8NativeBindings({ projectRoot, kitBindingProbe, embedderBindingProbe });
 
   return {
     action: 'completed',
-    checks: [c1, c2, c3, c4, c5, c6, c7],
+    checks: [c1, c2, c3, c4, c5, c6, c7, c8],
     duration_ms: Date.now() - t0,
   };
 }

package/src/import-anthropic-memory.mjs

@@ -40,7 +40,7 @@ import {
 } from './audit-log.mjs';
 import { ERROR_CATEGORIES, errorResult } from './result-shapes.mjs';
 import { writeBullet } from './provenance.mjs';
-import { createHash } from 'node:crypto';
+import { hashContent } from './content-hash.mjs';
 
 const MEMORY_REL = ['context', 'MEMORY.md'];
 
@@ -236,7 +236,7 @@ export async function importAnthropicMemory({
   // an import failed and search degraded to the stale index (cut-gate9 F-13).
   const bulletLines = proposals
     .map((p) => {
-      const sha1 = createHash('sha1').update(p.text, 'utf8').digest('hex');
+      const sha1 = hashContent(p.text);
       const formatted = writeBullet({
         id: p.id,
         text: p.text,