npm - @dzhechkov/harness-core - Versions diffs - 0.3.39 → 0.3.41 - Mend

@dzhechkov/harness-core 0.3.39 → 0.3.41

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Files changed (19) hide show

package/dist/setup.js CHANGED Viewed

@@ -4,46 +4,117 @@
  * Unlike `dz init` (skills only), `dz setup` configures the complete
  * self-learning environment:
  * 1. Skills installation (via init)
- * 2. Claude Code hooks (session-start/end for memory)
- * 3. Memory database initialization (.dz/memory.db)
+ * 2. Claude Code session hooks (start/end) — with `--memory agentdb`, a real vector-store
+ *    write via `.dz/agentdb-writer.mjs`; otherwise a `.dz/sessions.jsonl` marker
+ * 3. Memory store: `.dz/agentdb.db` (agentdb, shared with the MCP server via AGENTDB_PATH)
+ *    or `.dz/sessions.jsonl` + `.dz/patterns.jsonl` (jsonl default)
  * 4. Pretrain (project analysis → auto-recommend)
  *
  * All operations are additive — never overwrites existing files.
  *
  * @packageDocumentation
  */
-import { existsSync, mkdirSync, writeFileSync, readFileSync } from 'node:fs';
+import { existsSync, mkdirSync, writeFileSync, readFileSync, rmSync } from 'node:fs';
 import { join } from 'node:path';
+import { execSync } from 'node:child_process';
+/** Absolute path to the agentdb store shared by the hook writer and the MCP server. */
+function agentdbStorePath(projectRoot) {
+    return join(projectRoot, '.dz', 'agentdb.db');
+}
+/**
+ * Version of the generated `.dz/agentdb-writer.mjs`. Bump on ANY change to
+ * {@link generateAgentdbWriter}'s output — setup regenerates deployed writers whose
+ * `dz-writer-version` stamp is older, WITHOUT requiring `--force` (audit gap G4: generated code
+ * must not fossilize outside the package lifecycle).
+ */
+export const AGENTDB_WRITER_VERSION = 2;
+/**
+ * Generate the `.dz/agentdb-writer.mjs` helper invoked by the session hooks.
+ *
+ * v2 (ADR-002, audit gaps G3 + code#1 + code#4): session markers are **metadata-only telemetry** —
+ * a plain row in the `dz_session_events` table inside the SAME shared `.dz/agentdb.db` the MCP
+ * server is pinned to (`AGENTDB_PATH`). No embedding, no model load, no `successRate`:
+ * - ~ms latency (v1 loaded a ~90 MB transformers model → 12 s cold-timeout losing the marker);
+ * - zero pollution of the HNSW index real learnings live in (those enter via `agentdb_*` MCP tools);
+ * - uses better-sqlite3 DIRECTLY (WAL + busy_timeout) — if it is unavailable the writer falls back
+ *   to the jsonl marker instead of ever touching the sql.js in-memory backend, whose
+ *   last-write-wins semantics were the design's one real corruption vector.
+ *
+ * Best-effort and never throws: any failure degrades to a `.dz/sessions.jsonl` line labelled
+ * `jsonl-fallback` (with the error), so the hook always exits 0 and never blocks a session.
+ */
+export function generateAgentdbWriter(projectRoot) {
+    const dbPath = agentdbStorePath(projectRoot);
+    const sessionsPath = join(projectRoot, '.dz', 'sessions.jsonl');
+    return `#!/usr/bin/env node
+// dz-writer-version: ${AGENTDB_WRITER_VERSION}
+// Auto-generated by \`dz setup --memory agentdb\`. Do not edit — re-run \`dz setup\` to upgrade
+// (setup regenerates automatically when this version stamp is outdated; --force not required).
+// Writes a metadata-only session-event row into the shared AgentDB store (.dz/agentdb.db — the
+// same file the agentdb MCP server is pinned to via AGENTDB_PATH). Real learnings go into the
+// vector index via the agentdb_* MCP tools; this is deliberately non-semantic telemetry.
+// Best-effort: on ANY error it appends a .dz/sessions.jsonl marker and exits 0 — never throws,
+// never blocks the session.
+import { appendFileSync } from 'node:fs';
+const event = process.argv[2] === 'end' ? 'end' : 'start';
+const ts = new Date().toISOString();
+const DB = process.env.AGENTDB_PATH || ${JSON.stringify(dbPath)};
+const SESSIONS = ${JSON.stringify(sessionsPath)};
+function fallback(err) {
+  try {
+    appendFileSync(
+      SESSIONS,
+      JSON.stringify({ event, ts, backend: 'jsonl-fallback', error: String((err && err.message) || err) }) + '\\n',
+    );
+  } catch { /* last resort: swallow */ }
+}
+try {
+  // Native better-sqlite3 ONLY (prebuilt; synchronous; WAL). Never the sql.js fallback — its
+  // whole-file-in-memory persistence is unsafe against a concurrently-writing MCP server.
+  const { default: Database } = await import('better-sqlite3');
+  const db = new Database(DB);
+  db.pragma('journal_mode = WAL');
+  db.pragma('busy_timeout = 5000'); // wait out a brief MCP-server write lock instead of failing
+  db.exec('CREATE TABLE IF NOT EXISTS dz_session_events (id INTEGER PRIMARY KEY AUTOINCREMENT, event TEXT NOT NULL, ts TEXT NOT NULL, source TEXT NOT NULL DEFAULT \\'dz-session-hook\\')');
+  db.prepare('INSERT INTO dz_session_events (event, ts) VALUES (?, ?)').run(event, ts);
+  db.close();
+} catch (err) {
+  fallback(err);
+}
+`;
+}
+/** Parse the `dz-writer-version` stamp from a deployed writer file ('' or absent → 0). */
+export function writerVersionOf(content) {
+    const m = /^\/\/ dz-writer-version:\s*(\d+)/m.exec(content);
+    return m ? parseInt(m[1] ?? '0', 10) : 0;
+}
 /** Generate Claude Code hooks configuration for self-learning. */
-function generateHooksConfig(projectRoot, backend) {
+export function generateHooksConfig(projectRoot, backend) {
     const dzDir = join(projectRoot, '.dz');
     if (backend === 'agentdb') {
-        // agentdb backend: hooks use agentdb CLI to store patterns
-        const rvfPath = join(dzDir, 'memory.rvf');
+        // agentdb backend: hooks invoke the generated writer, which does a REAL vector-store write
+        // (ReasoningBank.storePattern) into the AGENTDB_PATH store the MCP server shares. The writer
+        // self-degrades to a sessions.jsonl marker on any failure, so no hook ever throws.
+        const writer = join(dzDir, 'agentdb-writer.mjs');
         return JSON.stringify({
             hooks: {
-                SessionStart: [{
-                        type: 'command',
-                        command: `node -e "const fs=require('fs');const d=new Date().toISOString();try{require('child_process').execSync('npx agentdb add \\'${rvfPath}\\' \\'session-start: '+d+'\\'',{stdio:'pipe'})}catch{fs.appendFileSync('${dzDir}/sessions.jsonl',JSON.stringify({event:'start',ts:d,backend:'agentdb'})+'\\n')}"`,
-                    }],
-                SessionEnd: [{
-                        type: 'command',
-                        command: `node -e "const fs=require('fs');const d=new Date().toISOString();try{require('child_process').execSync('npx agentdb add \\'${rvfPath}\\' \\'session-end: '+d+'\\'',{stdio:'pipe'})}catch{fs.appendFileSync('${dzDir}/sessions.jsonl',JSON.stringify({event:'end',ts:d,backend:'agentdb'})+'\\n')}"`,
-                    }],
+                SessionStart: [{ type: 'command', command: `node ${JSON.stringify(writer)} start` }],
+                SessionEnd: [{ type: 'command', command: `node ${JSON.stringify(writer)} end` }],
             },
         }, null, 2);
     }
-    // JSONL backend (default)
+    // JSONL backend (default) — honest session bookkeeping, no vector store involved.
+    // Use a RELATIVE path (Claude Code runs hooks from the project root): interpolating the absolute
+    // ${dzDir} into a single-quoted JS literal inside shell double-quotes breaks on Windows backslash
+    // paths (\U, \b…) and on any path containing a quote. `.dz/sessions.jsonl` sidesteps all of it.
+    const jsonlCmd = (event) => `node -e "const fs=require('fs');const d=new Date().toISOString();fs.appendFileSync('.dz/sessions.jsonl',JSON.stringify({event:'${event}',ts:d,backend:'jsonl'})+'\\n')"`;
     return JSON.stringify({
         hooks: {
-            SessionStart: [{
-                    type: 'command',
-                    command: `node -e "const fs=require('fs');const d=new Date().toISOString();fs.appendFileSync('${dzDir}/sessions.jsonl',JSON.stringify({event:'start',ts:d})+'\\n')"`,
-                }],
-            SessionEnd: [{
-                    type: 'command',
-                    command: `node -e "const fs=require('fs');const d=new Date().toISOString();fs.appendFileSync('${dzDir}/sessions.jsonl',JSON.stringify({event:'end',ts:d})+'\\n')"`,
-                }],
+            SessionStart: [{ type: 'command', command: jsonlCmd('start') }],
+            SessionEnd: [{ type: 'command', command: jsonlCmd('end') }],
         },
     }, null, 2);
 }
@@ -70,12 +141,18 @@ function generateDzConfig(target, preset, backend) {
         },
         memory: {
             backend,
-            path: backend === 'agentdb' ? '.dz/memory.rvf' : '.dz/sessions.jsonl',
+            // agentdb: the native SQLite vector store shared by the session-hook writer and the
+            // agentdb MCP server (both pinned via AGENTDB_PATH). Real ReasoningBank patterns land here.
+            path: backend === 'agentdb' ? '.dz/agentdb.db' : '.dz/sessions.jsonl',
             maxSizeMb: backend === 'agentdb' ? 100 : 10,
             agentdb: backend === 'agentdb' ? {
                 learning: true,
                 vectorDim: 384,
                 mcpServer: 'agentdb',
+                // Both the hook writer and the MCP server read/write THIS path (env AGENTDB_PATH).
+                storePath: '.dz/agentdb.db',
+                embeddingModel: 'Xenova/all-MiniLM-L6-v2',
+                sessionHookWrites: true,
             } : undefined,
         },
         hooks: {
@@ -84,11 +161,52 @@ function generateDzConfig(target, preset, backend) {
         },
     }, null, 2);
 }
-/** Check if agentdb is available. */
-function isAgentdbAvailable() {
+/** True if `agentdb` resolves from the project's node_modules (the hook writer needs it there). */
+function isAgentdbInstalledLocally(projectRoot) {
+    return existsSync(join(projectRoot, 'node_modules', 'agentdb', 'package.json'));
+}
+/**
+ * The exact agentdb version installed in the project, or `'latest'` as a fallback. Used to pin the
+ * MCP server spec (`agentdb@<version>`) so the long-running MCP server and the hook writer — which
+ * imports the on-disk local copy — run the SAME schema against the shared DB (agentdb is alpha;
+ * `@latest` could drift the MCP server's schema away from what the hook wrote).
+ */
+function installedAgentdbSpec(projectRoot) {
     try {
-        require('child_process').execSync('npx agentdb --version', { stdio: 'pipe', timeout: 10000 });
+        const pkg = JSON.parse(readFileSync(join(projectRoot, 'node_modules', 'agentdb', 'package.json'), 'utf-8'));
+        return pkg.version ? `agentdb@${pkg.version}` : 'agentdb@latest';
+    }
+    catch {
+        return 'agentdb@latest';
+    }
+}
+/**
+ * Install `agentdb` + `better-sqlite3` as LOCAL project deps so the session-hook writer can
+ * `import('agentdb')` and get a native SQLite store (better-sqlite3 ships prebuilt binaries — no
+ * build tools — and gives true cross-process WAL concurrency so the hook and the MCP server share
+ * one live store). Best-effort: returns false (caller degrades to jsonl) if install fails.
+ */
+function installAgentdbLocally(projectRoot) {
+    if (isAgentdbInstalledLocally(projectRoot))
         return true;
+    try {
+        // Anchor npm to THIS project: without a package.json here, npm's prefix walk-up would
+        // install into (and mutate the lockfile of) the nearest ANCESTOR project (audit code#2).
+        const pkgJsonPath = join(projectRoot, 'package.json');
+        if (!existsSync(pkgJsonPath)) {
+            writeFileSync(pkgJsonPath, JSON.stringify({ name: 'dz-harness-project', private: true, version: '0.0.0' }, null, 2) + '\n');
+        }
+        // NB: use the ESM-imported execSync — `require()` is undefined in this ESM module (the
+        // original agentdb hooks failed silently for exactly this reason). stdio:'ignore' (not
+        // 'pipe') avoids execSync's 1 MB maxBuffer aborting the child on npm's verbose output.
+        // --save-exact: agentdb is alpha; a semver range would let a later `npm update` drift the
+        // local copy away from the version the MCP registration pins (audit gap G7).
+        execSync('npm install agentdb better-sqlite3 --save-exact --no-audit --no-fund --loglevel=error', {
+            cwd: projectRoot,
+            stdio: 'ignore',
+            timeout: 300000,
+        });
+        return isAgentdbInstalledLocally(projectRoot);
     }
     catch {
         return false;
@@ -216,15 +334,20 @@ export function runSetup(opts) {
     const steps = [];
     const dzDir = join(opts.projectRoot, '.dz');
     const backend = opts.memory ?? 'jsonl';
-    // Step 0: Check agentdb availability if requested
+    // Step 0: Install agentdb + better-sqlite3 locally so the session-hook writer can import them
+    // and share a native store with the MCP server. Best-effort — the writer self-degrades to a
+    // jsonl marker (and self-heals once the deps exist) if this fails.
     if (backend === 'agentdb') {
-        const available = isAgentdbAvailable();
-        if (available) {
-            steps.push({ name: 'AgentDB check', status: 'done', detail: 'agentdb available' });
+        const ready = installAgentdbLocally(opts.projectRoot);
+        if (ready) {
+            steps.push({ name: 'Install agentdb + better-sqlite3', status: 'done', detail: 'local deps for real vector writes' });
         }
         else {
-            steps.push({ name: 'AgentDB check', status: 'error', detail: 'not found — install: npm i -g agentdb' });
-            // Fall through — will still create config, hooks will fallback to JSONL
+            steps.push({
+                name: 'Install agentdb + better-sqlite3',
+                status: 'error',
+                detail: 'install failed — hooks log to sessions.jsonl until you run: npm i agentdb better-sqlite3',
+            });
         }
     }
     // Step 1: Create .dz directory
@@ -255,24 +378,27 @@ export function runSetup(opts) {
     }
     // Step 4: Initialize memory store
     if (backend === 'agentdb') {
-        // Initialize .rvf via agentdb CLI
-        const rvfPath = join(dzDir, 'memory.rvf');
-        if (!existsSync(rvfPath)) {
-            try {
-                const { execSync } = require('child_process');
-                execSync(`npx agentdb init "${rvfPath}"`, { stdio: 'pipe', timeout: 30000 });
-                steps.push({ name: 'Initialize memory.rvf', status: 'done', detail: 'agentdb vector memory' });
-            }
-            catch {
-                // Fallback: create empty file, agentdb will init on first use
-                writeFileSync(rvfPath, '');
-                steps.push({ name: 'Initialize memory.rvf', status: 'done', detail: 'placeholder (agentdb will init on first use)' });
-            }
+        // Write the session-hook writer. The agentdb.db store itself is auto-created on first write
+        // by createDatabase() (both the writer and the MCP server init the schema), so there is no
+        // orphan placeholder file — the writer targets the real, shared native store.
+        const writerPath = join(dzDir, 'agentdb-writer.mjs');
+        // Regenerate when missing, forced, OR the deployed stamp is older than the current
+        // generator — deployed writers must not fossilize outside the package lifecycle (gap G4).
+        const deployedVersion = existsSync(writerPath) ? writerVersionOf(readFileSync(writerPath, 'utf-8')) : -1;
+        if (deployedVersion === -1 || opts.force || deployedVersion < AGENTDB_WRITER_VERSION) {
+            writeFileSync(writerPath, generateAgentdbWriter(opts.projectRoot));
+            steps.push({
+                name: 'Write agentdb-writer.mjs',
+                status: 'done',
+                detail: deployedVersion > -1 && deployedVersion < AGENTDB_WRITER_VERSION
+                    ? `upgraded v${deployedVersion} → v${AGENTDB_WRITER_VERSION}`
+                    : `session telemetry writer v${AGENTDB_WRITER_VERSION}`,
+            });
         }
         else {
-            steps.push({ name: 'Initialize memory.rvf', status: 'skipped', detail: 'already exists' });
+            steps.push({ name: 'Write agentdb-writer.mjs', status: 'skipped', detail: `current (v${deployedVersion})` });
         }
-        // Also create JSONL fallback
+        // Keep the jsonl fallback log available for the writer's degraded path.
         const sessionsPath = join(dzDir, 'sessions.jsonl');
         if (!existsSync(sessionsPath))
             writeFileSync(sessionsPath, '');
@@ -296,74 +422,166 @@ export function runSetup(opts) {
             steps.push({ name: 'Initialize patterns.jsonl', status: 'skipped', detail: 'already exists' });
         }
     }
-    // Step 5: Configure hooks (write to .claude/settings.json)
+    // Step 5: Configure hooks (write to .claude/settings.json) — EVENT-LEVEL merge (gap G2):
+    // dz-generated entries (recognized by signature, incl. the broken legacy `agentdb add` hooks
+    // this feature fixes) are replaced in place WITHOUT --force; the user's own hooks and every
+    // other settings key are preserved. Full-file overwrite happens only when the file is absent.
     if (!opts.noHooks) {
         const settingsDir = join(opts.projectRoot, '.claude');
         const settingsPath = join(settingsDir, 'settings.json');
-        if (!existsSync(settingsPath) || opts.force) {
+        const generated = JSON.parse(generateHooksConfig(opts.projectRoot, backend));
+        if (!existsSync(settingsPath)) {
             mkdirSync(settingsDir, { recursive: true });
-            writeFileSync(settingsPath, generateHooksConfig(opts.projectRoot, backend));
+            writeFileSync(settingsPath, JSON.stringify({ hooks: generated.hooks }, null, 2));
             steps.push({ name: 'Configure hooks', status: 'done', detail: `${backend} session hooks` });
         }
         else {
             try {
                 const existing = JSON.parse(readFileSync(settingsPath, 'utf-8'));
-                if (!existing['hooks']) {
-                    const hooks = JSON.parse(generateHooksConfig(opts.projectRoot, backend));
-                    existing['hooks'] = hooks.hooks;
+                const hooks = (existing['hooks'] ?? {});
+                let changed = false;
+                let replacedLegacy = false;
+                for (const event of Object.keys(generated.hooks)) {
+                    const current = Array.isArray(hooks[event]) ? hooks[event] : [];
+                    // Drop dz-generated entries (any vintage) — keep the user's own hooks untouched.
+                    const kept = current.filter((entry) => {
+                        const cmd = String(entry?.command ?? '');
+                        const isDz = cmd.includes('agentdb add') || cmd.includes('agentdb-writer.mjs') || cmd.includes('sessions.jsonl');
+                        if (isDz && !cmd.includes('agentdb-writer.mjs'))
+                            replacedLegacy = true;
+                        return !isDz;
+                    });
+                    const next = [...kept, ...generated.hooks[event]];
+                    if (JSON.stringify(next) !== JSON.stringify(current))
+                        changed = true;
+                    hooks[event] = next;
+                }
+                if (changed) {
+                    existing['hooks'] = hooks;
                     writeFileSync(settingsPath, JSON.stringify(existing, null, 2));
-                    steps.push({ name: 'Configure hooks', status: 'done', detail: `merged ${backend} hooks` });
+                    steps.push({
+                        name: 'Configure hooks',
+                        status: 'done',
+                        detail: replacedLegacy ? `replaced legacy dz hooks with ${backend} hooks` : `merged ${backend} hooks (user hooks preserved)`,
+                    });
                 }
                 else {
-                    steps.push({ name: 'Configure hooks', status: 'skipped', detail: 'hooks already configured' });
+                    steps.push({ name: 'Configure hooks', status: 'skipped', detail: 'hooks already current' });
                 }
             }
             catch {
-                steps.push({ name: 'Configure hooks', status: 'skipped', detail: 'could not parse existing settings' });
+                steps.push({ name: 'Configure hooks', status: 'error', detail: 'could not parse existing settings.json — fix it and re-run' });
             }
         }
     }
     else {
         steps.push({ name: 'Configure hooks', status: 'skipped', detail: '--no-hooks' });
     }
-    // Step 5.5: Register agentdb MCP server (if agentdb backend)
+    // Step 5.5: Register agentdb MCP server (if agentdb backend) in **`.mcp.json` at the project
+    // root** — the project-scope location Claude Code actually loads (gap G5: the previously used
+    // `.claude/mcp.json` is NOT read by Claude Code, so the server never got AGENTDB_PATH and the
+    // shared-store invariant silently failed). READ-MERGE-WRITE: only the `agentdb` entry is
+    // managed; every other registered server is preserved (audit code#5 — never clobber).
     if (backend === 'agentdb') {
-        const mcpConfigPath = join(opts.projectRoot, '.claude', 'mcp.json');
-        if (!existsSync(mcpConfigPath) || opts.force) {
-            const mcpConfig = {
-                mcpServers: {
-                    agentdb: {
-                        command: 'npx',
-                        args: ['agentdb@latest', 'mcp', 'start'],
-                    },
-                },
-            };
-            mkdirSync(join(opts.projectRoot, '.claude'), { recursive: true });
-            writeFileSync(mcpConfigPath, JSON.stringify(mcpConfig, null, 2));
-            steps.push({ name: 'Register agentdb MCP', status: 'done', detail: '41 tools available' });
+        const agentdbEntry = {
+            command: 'npx',
+            // Pin to the INSTALLED agentdb version (not @latest) so the MCP server and the hook
+            // writer run the same alpha schema against one DB.
+            args: [installedAgentdbSpec(opts.projectRoot), 'mcp', 'start'],
+            // Pin the store to the SAME native DB the session-hook writer targets, so hook telemetry
+            // and agentdb_* pattern/reflexion data live in one shared store.
+            env: { AGENTDB_PATH: agentdbStorePath(opts.projectRoot) },
+        };
+        const mcpConfigPath = join(opts.projectRoot, '.mcp.json');
+        try {
+            const mcpConfig = (existsSync(mcpConfigPath)
+                ? JSON.parse(readFileSync(mcpConfigPath, 'utf-8'))
+                : {});
+            const servers = mcpConfig.mcpServers ?? {};
+            const before = JSON.stringify(servers['agentdb']);
+            servers['agentdb'] = agentdbEntry;
+            mcpConfig.mcpServers = servers;
+            if (before !== JSON.stringify(agentdbEntry)) {
+                writeFileSync(mcpConfigPath, JSON.stringify(mcpConfig, null, 2));
+                steps.push({ name: 'Register agentdb MCP', status: 'done', detail: '.mcp.json: 41 tools, store pinned to .dz/agentdb.db' });
+            }
+            else {
+                steps.push({ name: 'Register agentdb MCP', status: 'skipped', detail: 'already registered and current' });
+            }
         }
-        else {
-            steps.push({ name: 'Register agentdb MCP', status: 'skipped', detail: 'mcp.json already exists' });
+        catch {
+            steps.push({ name: 'Register agentdb MCP', status: 'error', detail: '.mcp.json unparseable — fix it and re-run' });
+        }
+        // Migrate off the legacy location: `.claude/mcp.json` is not loaded by Claude Code. If it
+        // holds ONLY our old agentdb registration, remove the file; otherwise leave it and warn.
+        const legacyPath = join(opts.projectRoot, '.claude', 'mcp.json');
+        if (existsSync(legacyPath)) {
+            try {
+                const legacy = JSON.parse(readFileSync(legacyPath, 'utf-8'));
+                const keys = Object.keys(legacy.mcpServers ?? {});
+                if (keys.length === 1 && keys[0] === 'agentdb') {
+                    rmSync(legacyPath);
+                    steps.push({ name: 'Migrate legacy .claude/mcp.json', status: 'done', detail: 'removed (not loaded by Claude Code); registration now in .mcp.json' });
+                }
+                else {
+                    steps.push({ name: 'Migrate legacy .claude/mcp.json', status: 'error', detail: 'contains other servers — Claude Code does NOT load this file; move them to .mcp.json' });
+                }
+            }
+            catch {
+                steps.push({ name: 'Migrate legacy .claude/mcp.json', status: 'error', detail: 'unparseable legacy file — Claude Code does not load it; review manually' });
+            }
         }
     }
-    // Step 6: Update .gitignore
-    const gitignorePath = join(opts.projectRoot, '.gitignore');
-    const dzIgnoreEntry = backend === 'agentdb'
-        ? '\n# DZ Harness learning data\n.dz/memory.rvf\n.dz/sessions.jsonl\n'
-        : '\n# DZ Harness learning data\n.dz/sessions.jsonl\n.dz/patterns.jsonl\n';
-    if (existsSync(gitignorePath)) {
-        const content = readFileSync(gitignorePath, 'utf-8');
-        if (!content.includes('.dz/sessions.jsonl')) {
-            writeFileSync(gitignorePath, content + dzIgnoreEntry);
-            steps.push({ name: 'Update .gitignore', status: 'done', detail: 'added .dz/sessions.jsonl + patterns.jsonl' });
+    // Step 5.9: agentdb wiring invariant check (audit code#3). Skip-branches across repeated runs
+    // can leave inconsistent combinations (e.g. writer+MCP present but hooks still jsonl). Verify
+    // the three-way invariant explicitly and surface a loud error step instead of silent "skipped"s.
+    if (backend === 'agentdb' && !opts.noHooks) {
+        const problems = [];
+        if (!isAgentdbInstalledLocally(opts.projectRoot))
+            problems.push('deps missing (npm i agentdb better-sqlite3)');
+        try {
+            const settings = JSON.parse(readFileSync(join(opts.projectRoot, '.claude', 'settings.json'), 'utf-8'));
+            const refs = ['SessionStart', 'SessionEnd'].every((ev) => (settings.hooks?.[ev] ?? []).some((h) => String(h?.command ?? '').includes('agentdb-writer.mjs')));
+            if (!refs)
+                problems.push('hooks do not invoke the writer');
         }
-        else {
-            steps.push({ name: 'Update .gitignore', status: 'skipped', detail: 'already ignoring .dz data' });
+        catch {
+            problems.push('settings.json unreadable');
+        }
+        try {
+            const mcp = JSON.parse(readFileSync(join(opts.projectRoot, '.mcp.json'), 'utf-8'));
+            if (mcp.mcpServers?.['agentdb']?.env?.['AGENTDB_PATH'] !== agentdbStorePath(opts.projectRoot)) {
+                problems.push('.mcp.json agentdb missing or not pinned to .dz/agentdb.db');
+            }
         }
+        catch {
+            problems.push('.mcp.json unreadable');
+        }
+        steps.push(problems.length === 0
+            ? { name: 'agentdb wiring', status: 'done', detail: 'hooks → writer → .dz/agentdb.db ← MCP (one shared store)' }
+            : { name: 'agentdb wiring', status: 'error', detail: `INCOMPLETE: ${problems.join('; ')}` });
+    }
+    // Step 6: Update .gitignore. Append only the ENTRIES that are actually missing — a single
+    // sentinel check (e.g. sessions.jsonl, present in both backends) would skip agentdb.db/-wal/-shm
+    // on the documented jsonl→agentdb `--force` switch, leaking the binary store into git.
+    const gitignorePath = join(opts.projectRoot, '.gitignore');
+    const dzIgnoreLines = backend === 'agentdb'
+        ? ['.dz/agentdb.db', '.dz/agentdb.db-wal', '.dz/agentdb.db-shm', '.dz/sessions.jsonl']
+        : ['.dz/sessions.jsonl', '.dz/patterns.jsonl'];
+    const existing = existsSync(gitignorePath) ? readFileSync(gitignorePath, 'utf-8') : '';
+    const missing = dzIgnoreLines.filter((line) => !existing.split(/\r?\n/).includes(line));
+    if (missing.length > 0) {
+        const prefix = existing === '' ? '' : (existing.endsWith('\n') ? '' : '\n');
+        const block = `${prefix}\n# DZ Harness learning data\n${missing.join('\n')}\n`;
+        writeFileSync(gitignorePath, existing + block);
+        steps.push({
+            name: existsSync(gitignorePath) && existing !== '' ? 'Update .gitignore' : 'Create .gitignore',
+            status: 'done',
+            detail: `added ${missing.join(', ')}`,
+        });
     }
     else {
-        writeFileSync(gitignorePath, dzIgnoreEntry);
-        steps.push({ name: 'Create .gitignore', status: 'done', detail: 'with .dz entries' });
+        steps.push({ name: 'Update .gitignore', status: 'skipped', detail: 'already ignoring .dz data' });
     }
     // Step 7: Install the CLI-driver skill + agent docs (--install-driver)
     if (opts.installDriver) {

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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@dzhechkov/harness-core",
-  "version": "0.3.39",
+  "version": "0.3.41",
   "description": "Shared harness logic - skill loading, additive apply, and the init/sync/verify/doctor operations.",
   "type": "module",
   "license": "MIT",
@@ -31,8 +31,8 @@
     "@dzhechkov/adapter-opencode": "^0.2.0",
     "yaml": "^2.0.0",
     "@dzhechkov/adapter-copilot": "0.1.1",
-    "@dzhechkov/core": "0.2.4",
-    "@dzhechkov/memory": "0.2.5"
+    "@dzhechkov/memory": "0.2.5",
+    "@dzhechkov/core": "0.2.4"
   },
   "devDependencies": {
     "@types/node": "^25.6.0",

package/src/index.ts CHANGED Viewed

@@ -27,7 +27,7 @@ export { recommend } from './recommend.js';
 export { pretrain } from './pretrain.js';
 export { loadPatterns, loadSessions, computePatternBoost, readLearningConfig, BOOST_CAP, recordPattern, loadStorePatternsSync, patternToRecord, recordToPattern, consolidateSessions, recallPatterns } from './patterns.js';
 export type { PatternRecord, SessionRecord, LearningConfig, LoadOptions, ConsolidateResult, ConsolidateOptions, SqliteBackendMode, RecallHit, SessionsSource } from './patterns.js';
-export { runSetup } from './setup.js';
+export { runSetup, generateHooksConfig, generateAgentdbWriter, writerVersionOf, AGENTDB_WRITER_VERSION } from './setup.js';
 export { generatePlugin } from './plugin.js';
 export type { PluginManifest } from './plugin.js';
 export type { SetupOptions, SetupResult, SetupStep } from './setup.js';