nlm-memory 0.11.1 → 0.13.0

package/README.md

@@ -335,7 +335,7 @@ recall: prompt / query
 | `NLM_MCP_TOKEN` | auto-generated | 256-bit bearer for `/api/*` (non-browser) and `/mcp` |
 | `NLM_MCP_CONFIG` | `~/.mcp.json` | Path the `connect`/`disconnect` commands modify |
 | `NLM_CLASSIFIER` | `ollama` | `ollama` (local, default), `deepseek`, `openai`, `anthropic`, `openrouter`, or `openai-compatible` |
-| `NLM_CLASSIFIER_MODEL` | `qwen3:4b-instruct-2507-q4_K_M` | Model id for the chosen provider. See [classifier bench](reports/classifier-comparison/2026-06-02-deepseek-v4-vs-qwen3.md) for why this is the recommended local default. |
+| `NLM_CLASSIFIER_MODEL` | `qwen3.5:4b` | Model id for the chosen provider. `qwen3.5:4b` (Q4_K_M, 4.7B) is the recommended local default — scored 74.4% decision-precision vs 58.7% for `qwen3:4b-instruct-2507-q4_K_M` (task #320, 2026-06-12). |
 | `NLM_OLLAMA_URL` | `http://localhost:11434` | Override Ollama endpoint |
 | `NLM_ADAPTERS` | all | Comma-separated allowlist of adapters to enable |
 | `DEEPSEEK_API_KEY` | — | Required only when classifier=deepseek |

package/dist/cli/classify-parity.js

@@ -29,7 +29,7 @@ function parseArgs(argv) {
     const limit = Number.parseInt(flag("--limit", "10") ?? "10", 10);
     const providerRaw = (flag("--provider", "deepseek") ?? "deepseek").toLowerCase();
     const provider = providerRaw === "ollama" ? "ollama" : "deepseek";
-    const defaultModel = provider === "deepseek" ? "deepseek-v4-flash" : "qwen3:4b-instruct-2507-q4_K_M";
+    const defaultModel = provider === "deepseek" ? "deepseek-v4-flash" : "qwen3.5:4b";
     return {
         limit: Number.isFinite(limit) && limit > 0 ? limit : 10,
         dbPath: flag("--db", process.env["NLM_DB_PATH"] ?? resolve(homedir(), ".nlm/canonical.sqlite")) ??

package/dist/cli/classify-parity.js.map

@@ -1 +1 @@
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package/dist/cli/nlm.js

@@ -26,7 +26,7 @@
 import { fileURLToPath } from "node:url";
 import { dirname, resolve, join } from "node:path";
 import { homedir } from "node:os";
-import { mkdirSync, readFileSync, writeFileSync, existsSync, rmSync } from "node:fs";
+import { mkdirSync, readFileSync, writeFileSync, existsSync, rmSync, copyFileSync } from "node:fs";
 import { execFileSync, spawn, spawnSync } from "node:child_process";
 import { Command } from "commander";
 import pkg from "../../package.json" with { type: "json" };
@@ -35,23 +35,24 @@ import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js"
 import { FactRecallService } from "../core/recall-facts/fact-recall-service.js";
 import { RecallService } from "../core/recall/recall-service.js";
 import { ProviderRegistry } from "../core/providers/provider-registry.js";
-import { SourceRegistry } from "../core/sources/source-registry.js";
 import { SqliteStorage } from "../core/storage/sqlite-storage.js";
 import { PgStorage } from "../core/storage/pg-storage.js";
-import { PgSourceRegistry } from "../core/sources/source-registry.js";
-import { PgProviderRegistry } from "../core/providers/provider-registry.js";
-import { applyPendingRestore } from "../core/storage/db-restore.js";
+import { applyPendingRestore, stageRestore } from "../core/storage/db-restore.js";
+import { listBackupDates, resolveBackup, runRollingBackup } from "../core/storage/backup-rotation.js";
 import { createApp } from "../http/app.js";
 import { createMcpServer } from "../mcp/server.js";
 import { ClassifierBox } from "../llm/classifier-box.js";
 import { DeepSeekClient } from "../llm/deepseek-client.js";
 import { OllamaClient } from "../llm/ollama-client.js";
+import { OllamaCodeEmbedder } from "../llm/ollama-code-embedder.js";
 import { autoloadEnv } from "../llm/env-autoload.js";
 import { addHook, buildHookCommand, removeHook } from "../core/hook/claude-settings.js";
-import { codexBinaryAvailable, connectCodex, disconnectCodex, pluginScriptsDir, } from "../install/codex.js";
+import { codexBinaryAvailable, connectCodex, disconnectCodex, repairCodex, pluginScriptsDir, } from "../install/codex.js";
 import { connectClaudeCode, disconnectClaudeCode, installClaudeCodeHooks, mcpConfigPath } from "../install/claude-code.js";
+import { evaluateInstallHealth, evaluateModelHealth, evaluateRecallSmoke } from "../install/health.js";
+import { codexConfigPath } from "../install/codex.js";
 import { hardenNlmDirPermissions } from "../install/nlm-dir-perms.js";
-import { ensureMcpToken } from "../install/ollama.js";
+import { embeddingModelPresent, ensureMcpToken, ollamaModelPresent } from "../install/ollama.js";
 import { connectCursor, disconnectCursor } from "../install/cursor.js";
 import { describeRemove, describeUpsert, installCursorRules, installOpencodeRules, installWindsurfRules, uninstallCursorRules, uninstallOpencodeRules, uninstallWindsurfRules, } from "../install/rules-install.js";
 import { runSupersedeCommand } from "./supersede.js";
@@ -98,17 +99,17 @@ function ollamaUrl() {
     return process.env["NLM_OLLAMA_URL"] ?? "http://localhost:11434";
 }
 function buildClassifier() {
-    // qwen3:4b-instruct-2507-q4_K_M is the recommended local classifier per the
-    // 2026-06-02 head-to-head bench (reports/classifier-comparison/2026-06-02-deepseek-v4-vs-qwen3.md):
-    // statistical tie with DeepSeek V4 Flash on schema validity and entity/decision
-    // counts, with better open-question coverage (100% vs 75%). Ollama is the
-    // default to keep the daemon local-first and key-free; DeepSeek remains
-    // available via NLM_CLASSIFIER=deepseek for users who prioritize speed.
+    // qwen3.5:4b is the production classifier as of 2026-06-12 (NLM task #320).
+    // Scored 74.4% decision-precision vs qwen3:4b-instruct-2507-q4_K_M's 58.7% in
+    // the 2026-06-11 eval. Requires think:false (handled by ClassifierBox via
+    // classifierNeedsThinkDisabled) to stay within the 180s classify timeout.
+    // Ollama is the default to keep the daemon local-first and key-free; DeepSeek
+    // remains available via NLM_CLASSIFIER=deepseek for users who prioritize speed.
     const provider = (process.env["NLM_CLASSIFIER"] ?? "ollama").toLowerCase();
     if (provider !== "ollama")
         autoloadEnv();
     const model = process.env["NLM_CLASSIFIER_MODEL"]
-        ?? (provider === "ollama" ? "qwen3:4b-instruct-2507-q4_K_M" : "deepseek-v4-flash");
+        ?? (provider === "ollama" ? "qwen3.5:4b" : "deepseek-v4-flash");
     return new ClassifierBox({ provider, model, ollamaUrl: ollamaUrl() });
 }
 async function buildAdapters(sources) {
@@ -163,17 +164,14 @@ async function buildStack() {
     const facts = storage.facts;
     const signals = storage.signals;
     const scope = installScope();
-    // TODO(#215a): replace storage.rawDb() with port methods
-    const sources = storage instanceof PgStorage
-        ? new PgSourceRegistry(storage.pgPool())
-        : new SourceRegistry(storage.rawDb());
+    const sources = storage.sources;
     await sources.seedDefaults();
-    // TODO(#215a): replace storage.rawDb() with port methods
-    const providers = storage instanceof PgStorage
-        ? new PgProviderRegistry(storage.pgPool())
-        : new ProviderRegistry(storage.rawDb());
+    const providers = storage.providers;
+    // Provider seeding is SQLite-only: it bridges from the local DEEPSEEK_API_KEY
+    // env, which is wrong for a hosted multi-tenant PG. PgProviderRegistry has no
+    // seedDefaults (not on ProviderRegistryPort), so this narrows to the SQLite case.
     if (providers instanceof ProviderRegistry)
-        providers.seedDefaults();
+        await providers.seedDefaults();
     // Recall only uses embed(). Embeddings live on Ollama; DeepSeek doesn't
     // expose them. Classifier is wired separately for Phase D ingest.
     const embedder = new OllamaClient({ baseUrl: ollamaUrl() });
@@ -213,17 +211,19 @@ program
         classifier,
         sources,
         providers,
-        // TODO(#215a): PgStorage ingest port; cast until then
-        ...(!(storage instanceof PgStorage) ? {
-            ingest: {
-                classifier,
-                embedder,
-                store: store,
-                ...(facts ? { factStore: facts } : {}),
-            },
-        } : {}),
+        ingest: {
+            classifier,
+            embedder,
+            store,
+            ...(facts ? { factStore: facts } : {}),
+        },
         signalStore: signals,
         installScope: scope,
+        // Code-exemplar lane. The store + code embedder are always wired; the
+        // NLM_CODE_EXEMPLARS_ENABLED flag gates capture (POST /api/signal) and
+        // the /api/exemplar + /api/recall-code routes at request time.
+        exemplarStore: storage.exemplars,
+        codeEmbedder: new OllamaCodeEmbedder({ baseUrl: ollamaUrl() }),
         embedderInfo: { provider: "ollama", model: "nomic-embed-text", dims: 768 },
         ...(existsSync(UI_DIST) ? { uiDist: UI_DIST } : {}),
         // Wire POST /mcp only when NLM_MCP_TOKEN is present. Absent = route never
@@ -294,15 +294,14 @@ program
     const memoSweep = new MemoSweepScheduler();
     memoSweep.start();
     console.error("  memo sweep: dormant cleanup every 5m (threshold 24h)");
-    if (opts.scheduler !== false && !(storage instanceof PgStorage)) {
+    if (opts.scheduler !== false) {
         const adapters = await buildAdapters(sources);
         if (adapters.length === 0) {
             console.error("  scheduler: no adapters detected (set NLM_ADAPTERS to force-enable)");
         }
         else {
             const scheduler = new ScanScheduler({
-                // TODO(#215a): PgStorage scheduler port; SQLite-only until then
-                store: store,
+                store,
                 adapters,
                 classifier,
                 embedder,
@@ -378,6 +377,58 @@ program
         await storage.close();
     }
 });
+program
+    .command("recall-code")
+    .description("Semantic search over code exemplars (requires NLM_CODE_EXEMPLARS_ENABLED=1)")
+    .argument("<query>", "natural-language description of the task you are about to implement")
+    .option("-r, --repo <path>", "filter by repository path")
+    .option("-l, --lang <lang>", "filter by language (ts, py, go, ...)")
+    .option("-k <n>", "max results", (v) => Number.parseInt(v, 10), 5)
+    .option("--no-negatives", "exclude fail/exhausted exemplars from results")
+    .option("--json", "emit the raw JSON result")
+    .action(async (query, opts) => {
+    if (process.env["NLM_CODE_EXEMPLARS_ENABLED"] !== "1") {
+        process.stderr.write("recall-code requires NLM_CODE_EXEMPLARS_ENABLED=1\n");
+        process.exit(1);
+    }
+    const { storage } = await buildStack();
+    const { OllamaCodeEmbedder } = await import("../llm/ollama-code-embedder.js");
+    const { recallCode } = await import("../core/exemplars/recall-code.js");
+    const { installScope: getScope } = await import("../core/signals/install-scope.js");
+    try {
+        const embedder = new OllamaCodeEmbedder();
+        const result = await recallCode({
+            query,
+            installScope: getScope(),
+            ...(opts.repo ? { repo: opts.repo } : {}),
+            ...(opts.lang ? { lang: opts.lang } : {}),
+            k: opts.k ?? 5,
+            includeNegatives: opts.negatives !== false,
+        }, storage.exemplars, embedder, null);
+        if (opts.json) {
+            process.stdout.write(JSON.stringify(result, null, 2) + "\n");
+        }
+        else {
+            const printHits = (label, hits) => {
+                if (hits.length === 0)
+                    return;
+                process.stdout.write(`\n── ${label} ──\n`);
+                for (const h of hits) {
+                    process.stdout.write(`[${h.outcome}] ${h.taskContext} (${h.repo}, dist=${h.distance.toFixed(4)})\n`);
+                    process.stdout.write(h.code.slice(0, 400) + (h.code.length > 400 ? "\n…" : "") + "\n\n");
+                }
+            };
+            printHits("Positives (pass / fix)", result.positives);
+            printHits("Negatives (fail / exhausted) — avoid these patterns", result.negatives);
+            if (result.positives.length === 0 && result.negatives.length === 0) {
+                process.stdout.write("(no exemplars found)\n");
+            }
+        }
+    }
+    finally {
+        await storage.close();
+    }
+});
 program
     .command("misses")
     .description("Show sessions the agent explicitly fetched but the hook never surfaced (recall miss log)")
@@ -430,15 +481,17 @@ program
         process.stdout.write(`${JSON.stringify({ ...result, perSource, unmeasurableSources: unmeasurable }, null, 2)}\n`);
         return;
     }
+    console.log(`Recall precision@k — last ${opts.days} day(s)`);
     if (result.precisionAtK === null) {
-        console.log("No scoreable conversations in the last " + opts.days + " day(s).");
-        console.log("  Precision joins hook-surfaced sessions (hook-log.jsonl) against explicit");
-        console.log("  citations (citation-log.jsonl). If citations are empty, run: nlm help close-loop");
-        return;
+        console.log("  Blended: no hook-lane conversations to score (hook-log.jsonl empty for this window).");
+        if (citationEntries.length === 0) {
+            console.log("  No citations recorded — run: nlm help close-loop");
+        }
+    }
+    else {
+        const pct = (result.precisionAtK * 100).toFixed(1);
+        console.log(`  Blended: ${pct}%  (${result.conversationCount} conversations scored)`);
     }
-    const pct = (result.precisionAtK * 100).toFixed(1);
-    console.log(`Recall precision@k — last ${opts.days} day(s)`);
-    console.log(`  Blended: ${pct}%  (${result.conversationCount} conversations scored)`);
     if (perSource.length > 0) {
         console.log("\n  Per source:");
         for (const row of perSource) {
@@ -478,11 +531,11 @@ program
     .description("Run TS classifier against ~/.nlm/canonical.sqlite and diff vs persisted Python output")
     .option("-l, --limit <n>", "sessions to sample", (v) => Number.parseInt(v, 10), 10)
     .option("-p, --provider <name>", "deepseek | ollama", "deepseek")
-    .option("-m, --model <name>", "model tag (default: deepseek-v4-flash for deepseek, qwen3:4b-instruct-2507-q4_K_M for ollama)")
+    .option("-m, --model <name>", "model tag (default: deepseek-v4-flash for deepseek, qwen3.5:4b for ollama)")
     .option("-v, --verbose", "per-session diff lines on stderr")
     .action(async (opts) => {
     const provider = opts.provider === "ollama" ? "ollama" : "deepseek";
-    const defaultModel = provider === "deepseek" ? "deepseek-v4-flash" : "qwen3:4b-instruct-2507-q4_K_M";
+    const defaultModel = provider === "deepseek" ? "deepseek-v4-flash" : "qwen3.5:4b";
     const report = await runParity({
         limit: opts.limit,
         dbPath: dbPath(),
@@ -530,8 +583,7 @@ program
     const { storage, store, facts, embedder, classifier } = await buildStack();
     try {
         const report = await backfillFacts({
-            // TODO(#215a): PgStorage backfill port; SQLite-only until then
-            store: store,
+            store,
             factStore: facts,
             classifier,
             embedder: opts.embed === false ? null : embedder,
@@ -574,8 +626,16 @@ program
     .command("mcp")
     .description("Run as an MCP stdio server (for ~/.mcp.json)")
     .action(async () => {
-    const { recall, store, facts, factRecall } = await buildStack();
-    const server = createMcpServer({ recall, store, factStore: facts, factRecall });
+    const { recall, store, facts, factRecall, storage, scope } = await buildStack();
+    const server = createMcpServer({
+        recall,
+        store,
+        factStore: facts,
+        factRecall,
+        exemplarStore: storage.exemplars,
+        codeEmbedder: new OllamaCodeEmbedder({ baseUrl: ollamaUrl() }),
+        installScope: scope,
+    });
     const transport = new StdioServerTransport();
     await server.connect(transport);
 });
@@ -1027,6 +1087,7 @@ connect
     .option("--source <source>", "marketplace source (owner/repo, git URL, or local path)", "pbmagnet4/nlm-memory")
     .option("--local", "shortcut for --source <repo-root>; use during dev")
     .option("--with-hooks", "additionally write absolute paths to ~/.codex/hooks.json (Codex Desktop fallback for openai/codex#16430)")
+    .option("--repair", "first strip a stale pre-rename nlm-memory-ts install (config block + plugin + marketplace), then connect")
     .option("--dry-run", "print what would happen without invoking codex")
     .action((opts) => {
     if (!opts.dryRun && !codexBinaryAvailable()) {
@@ -1034,8 +1095,19 @@ connect
         process.exit(1);
     }
     const source = opts.local ? REPO_ROOT : opts.source;
-    const report = connectCodex({ source, withHooks: Boolean(opts.withHooks), dryRun: Boolean(opts.dryRun) }, pluginScriptsDir(REPO_ROOT));
+    const connectOpts = { source, withHooks: Boolean(opts.withHooks), dryRun: Boolean(opts.dryRun) };
+    const repair = opts.repair
+        ? repairCodex(connectOpts, pluginScriptsDir(REPO_ROOT))
+        : null;
+    const report = repair ? repair.connect : connectCodex(connectOpts, pluginScriptsDir(REPO_ROOT));
+    if (repair && !repair.dryRun) {
+        console.error(repair.staleMcpRemovedFromConfig
+            ? "nlm connect codex --repair: stripped stale nlm-memory-ts MCP block from config.toml"
+            : "nlm connect codex --repair: no stale nlm-memory-ts MCP block found");
+    }
     if (report.dryRun) {
+        if (repair)
+            console.error("  --repair: would strip any stale nlm-memory-ts block, then:");
         console.error("nlm connect codex (dry run):");
         console.error(`  codex plugin marketplace add ${report.source}`);
         console.error(`  codex plugin add ${report.pluginName}@${report.marketplaceName}`);
@@ -1063,6 +1135,9 @@ connect
     if (report.mcpServerWritten) {
         console.error(`  Wrote [mcp_servers.nlm-memory] to ${report.mcpServerWritten}`);
     }
+    else if (report.mcpServerAlreadyPresent) {
+        console.error("  Left your existing [mcp_servers.nlm-memory] block in place (not overwriting it)");
+    }
     if (report.legacyHooksWritten) {
         console.error(`  Wrote hooks.json fallback to ${report.legacyHooksWritten}`);
     }
@@ -1148,9 +1223,7 @@ connect
     const storage = SqliteStorage.create({ dbPath: dbPath(), migrationsDir: MIGRATIONS_DIR });
     await storage.init();
     try {
-        // TODO(#215a): replace storage.rawDb() with port methods
-        const registry = new SourceRegistry(storage.rawDb());
-        const report = connectCursor(registry, {
+        const report = await connectCursor(storage.sources, {
             ...(opts.dbPath ? { dbPath: opts.dbPath } : {}),
             dryRun: Boolean(opts.dryRun),
         });
@@ -1182,9 +1255,7 @@ connect
     const storage = SqliteStorage.create({ dbPath: dbPath(), migrationsDir: MIGRATIONS_DIR });
     await storage.init();
     try {
-        // TODO(#215a): replace storage.rawDb() with port methods
-        const registry = new SourceRegistry(storage.rawDb());
-        const report = connectWindsurf(registry, {
+        const report = await connectWindsurf(storage.sources, {
             ...(opts.userDir ? { userDir: opts.userDir } : {}),
             dryRun: Boolean(opts.dryRun),
         });
@@ -1347,9 +1418,7 @@ disconnect
     const storage = SqliteStorage.create({ dbPath: dbPath(), migrationsDir: MIGRATIONS_DIR });
     await storage.init();
     try {
-        // TODO(#215a): replace storage.rawDb() with port methods
-        const registry = new SourceRegistry(storage.rawDb());
-        const report = disconnectCursor(registry, { dryRun: Boolean(opts.dryRun) });
+        const report = await disconnectCursor(storage.sources, { dryRun: Boolean(opts.dryRun) });
         if (opts.dryRun) {
             console.error("nlm disconnect cursor (dry run): disable Cursor source in registry");
             if (opts.withRules)
@@ -1377,9 +1446,7 @@ disconnect
     const storage = SqliteStorage.create({ dbPath: dbPath(), migrationsDir: MIGRATIONS_DIR });
     await storage.init();
     try {
-        // TODO(#215a): replace storage.rawDb() with port methods
-        const registry = new SourceRegistry(storage.rawDb());
-        const report = disconnectWindsurf(registry, { dryRun: Boolean(opts.dryRun) });
+        const report = await disconnectWindsurf(storage.sources, { dryRun: Boolean(opts.dryRun) });
         if (opts.dryRun) {
             console.error("nlm disconnect windsurf (dry run): disable Windsurf source in registry");
             if (opts.withRules)
@@ -1496,9 +1563,69 @@ program
         process.exit(1);
     }
 });
+async function gatherInstallProbe() {
+    autoloadEnv();
+    let reachable = false;
+    let version = null;
+    try {
+        const ctrl = new AbortController();
+        const timer = setTimeout(() => ctrl.abort(), 1_500);
+        const res = await fetch(`http://localhost:${port()}/api/health`, { signal: ctrl.signal });
+        clearTimeout(timer);
+        if (res.ok) {
+            const body = (await res.json());
+            reachable = true;
+            version = typeof body.version === "string" ? body.version : null;
+        }
+    }
+    catch {
+        // unreachable — reported as a FAIL by the evaluator
+    }
+    const mcpPath = mcpConfigPath();
+    let claudeMcp = false;
+    try {
+        if (existsSync(mcpPath)) {
+            const cfg = JSON.parse(readFileSync(mcpPath, "utf8"));
+            claudeMcp = Boolean(cfg.mcpServers && "nlm-memory" in cfg.mcpServers);
+        }
+    }
+    catch {
+        // malformed config → treat as unconfigured (connect will rewrite it)
+    }
+    const codexPath = codexConfigPath();
+    let codexPresent = false;
+    let codexMcp = false;
+    let codexStale = false;
+    if (existsSync(codexPath)) {
+        codexPresent = true;
+        const txt = readFileSync(codexPath, "utf8");
+        // Recognize the MCP table whether it's our managed (sentineled) block or a
+        // hand-authored bare one — both wire the server.
+        codexMcp = txt.split("\n").some((l) => l.trim() === "[mcp_servers.nlm-memory]");
+        // Match the marketplace suffix, not the bare name: a [projects."…/nlm-memory-ts"]
+        // trust entry is Codex's registry (not nlm's), so it must not trip this check.
+        codexStale = txt.includes("@nlm-memory-ts");
+    }
+    const envPath = join(homedir(), ".nlm", ".env");
+    return {
+        daemon: { reachable, version, expectedVersion: pkg.version },
+        env: {
+            path: envPath,
+            exists: existsSync(envPath),
+            hasMcpToken: Boolean(process.env["NLM_MCP_TOKEN"]),
+        },
+        claudeCode: { configPath: mcpPath, mcpConfigured: claudeMcp },
+        codex: {
+            configPath: codexPath,
+            configPresent: codexPresent,
+            mcpConfigured: codexMcp,
+            staleNlmMemoryTs: codexStale,
+        },
+    };
+}
 program
     .command("doctor")
-    .description("Check database integrity invariants and optionally repair safe violations")
+    .description("Check database integrity invariants and install/runtime health, optionally repair safe violations")
     .option("--fix", "repair mechanically safe violations: delete self-loop edges (I1), restore orphaned superseded/replaced sessions to closed (I2)")
     .action(async (opts) => {
     const storage = await buildStorage(dbPath());
@@ -1535,6 +1662,7 @@ program
     const ALL_CHECKS = ["I1", "I2", "I3", "I4", "I5a", "I5b", "I6"];
     const byId = new Map(violations.map((v) => [v.id, v]));
     let anyFail = false;
+    console.log("Database integrity:");
     for (const id of ALL_CHECKS) {
         const v = byId.get(id);
         if (v) {
@@ -1546,9 +1674,142 @@ program
             console.log(`PASS ${id}`);
         }
     }
+    console.log("\nInstall & runtime health:");
+    if (printHealthChecks(evaluateInstallHealth(await gatherInstallProbe())))
+        anyFail = true;
+    if (anyFail)
+        process.exit(1);
+});
+function printHealthChecks(checks) {
+    let anyFail = false;
+    for (const c of checks) {
+        if (c.status === "fail")
+            anyFail = true;
+        const label = c.status === "ok" ? "PASS" : c.status === "warn" ? "WARN" : "FAIL";
+        const fix = c.fix ? `\n  → fix: ${c.fix}` : "";
+        console.log(`${label} ${c.id}  ${c.detail}${fix}`);
+    }
+    return anyFail;
+}
+async function dbIntegrityCheck() {
+    const storage = await buildStorage(dbPath());
+    try {
+        const violations = storage instanceof PgStorage
+            ? await runChecksOnPg(storage.pgPool())
+            : runChecksOnSqlite(storage.rawDb());
+        if (violations.length === 0)
+            return { id: "db-integrity", status: "ok", detail: "all invariants hold" };
+        return {
+            id: "db-integrity",
+            status: "fail",
+            detail: `violations: ${violations.map((v) => v.id).join(", ")}`,
+            fix: "nlm doctor --fix",
+        };
+    }
+    finally {
+        await storage.close();
+    }
+}
+async function recallSmokeCheck() {
+    let reachable = false;
+    let status = null;
+    let wellFormed = false;
+    try {
+        const ctrl = new AbortController();
+        const timer = setTimeout(() => ctrl.abort(), 3_000);
+        const res = await fetch(`http://localhost:${port()}/api/recall?q=verify&limit=1`, { signal: ctrl.signal });
+        clearTimeout(timer);
+        reachable = true;
+        status = res.status;
+        const body = (await res.json().catch(() => null));
+        wellFormed = Boolean(body && Array.isArray(body.results));
+    }
+    catch {
+        // unreachable — evaluateRecallSmoke reports the fail
+    }
+    return evaluateRecallSmoke(reachable, status, wellFormed);
+}
+program
+    .command("verify")
+    .description("Release-gate: verify the install is wired and recall works end-to-end. Exit 1 on any failure.")
+    .action(async () => {
+    const provider = (process.env["NLM_CLASSIFIER"] ?? "ollama").toLowerCase();
+    const classifierModel = process.env["NLM_CLASSIFIER_MODEL"] ?? (provider === "ollama" ? "qwen3.5:4b" : "deepseek-v4-flash");
+    const classifierPresent = provider === "ollama" ? ollamaModelPresent(classifierModel) : true;
+    const checks = [
+        ...evaluateInstallHealth(await gatherInstallProbe()),
+        evaluateModelHealth(embeddingModelPresent(), classifierModel, classifierPresent),
+        await dbIntegrityCheck(),
+        await recallSmokeCheck(),
+    ];
+    const anyFail = printHealthChecks(checks);
+    const warns = checks.filter((c) => c.status === "warn").length;
+    console.log(anyFail ? "\nVERIFY: FAIL" : warns > 0 ? `\nVERIFY: PASS (${warns} warning(s))` : "\nVERIFY: PASS");
     if (anyFail)
         process.exit(1);
 });
+program
+    .command("backup")
+    .description("Write a dated snapshot to ~/.nlm/backups/ and prune ones past the retention window")
+    .option("--retention <days>", "keep snapshots from the last N days", "7")
+    .action(async (opts) => {
+    const retention = Number.parseInt(opts.retention, 10);
+    if (!Number.isFinite(retention) || retention < 1) {
+        console.error("nlm backup: --retention must be a positive integer");
+        process.exit(1);
+    }
+    const today = new Date().toISOString().slice(0, 10);
+    const storage = await buildStorage(dbPath());
+    try {
+        if (storage instanceof PgStorage) {
+            console.error("nlm backup: only the SQLite backend is supported (Postgres: use pg_dump)");
+            process.exit(1);
+        }
+        const result = runRollingBackup(storage.rawDb(), dbPath(), today, retention);
+        console.log(`Wrote ${result.written} (${(result.bytes / 1_048_576).toFixed(1)} MiB)`);
+        if (result.pruned.length > 0)
+            console.log(`Pruned ${result.pruned.length} snapshot(s) older than ${retention}d`);
+    }
+    finally {
+        await storage.close();
+    }
+});
+program
+    .command("restore")
+    .description("Stage a dated backup for restore on next daemon start (does not overwrite the live DB in place)")
+    .option("--from <date>", "backup date to restore (YYYY-MM-DD)")
+    .option("--list", "list available backup dates")
+    .action((opts) => {
+    if (opts.list || !opts.from) {
+        const dates = listBackupDates(dbPath());
+        if (dates.length === 0) {
+            console.log("No backups found. Run `nlm backup` (or wait for the daily job).");
+            return;
+        }
+        console.log("Available backups:");
+        for (const d of dates)
+            console.log(`  ${d}`);
+        if (!opts.from)
+            console.log("\nRestore one with: nlm restore --from <date>");
+        return;
+    }
+    const backup = resolveBackup(dbPath(), opts.from);
+    if (!backup) {
+        console.error(`nlm restore: no backup for ${opts.from}. Run \`nlm restore --list\` to see options.`);
+        process.exit(1);
+    }
+    // Copy (not move) the snapshot to a scratch candidate so the backup is
+    // preserved; stageRestore renames the candidate into the pending slot.
+    const candidate = `${dbPath()}.restore-candidate`;
+    copyFileSync(backup, candidate);
+    const validation = stageRestore(dbPath(), candidate);
+    if (!validation.ok) {
+        console.error(`nlm restore: ${opts.from} is not a usable backup: ${validation.error}`);
+        process.exit(1);
+    }
+    console.log(`Staged ${opts.from} (${validation.sessions} sessions, schema v${validation.schemaVersion}).`);
+    console.log("Run `nlm restart` to apply — the current DB is archived aside, not deleted.");
+});
 program.parseAsync().catch((e) => {
     console.error("nlm: fatal", e);
     process.exit(1);