@knowledgine/cli 0.6.2 → 0.6.4

package/dist/CLAUDE.md

@@ -0,0 +1,7 @@
+<claude-mem-context>
+# Recent Activity
+
+<!-- This section is auto-generated by claude-mem. Edit content outside the tags. -->
+
+*No recent activity*
+</claude-mem-context>

package/dist/commands/benchmark.d.ts

@@ -0,0 +1,6 @@
+export interface BenchmarkOptions {
+    path?: string;
+    semantic?: boolean;
+}
+export declare function benchmarkCommand(options: BenchmarkOptions): Promise<void>;
+//# sourceMappingURL=benchmark.d.ts.map

package/dist/commands/benchmark.d.ts.map

@@ -0,0 +1 @@
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package/dist/commands/benchmark.js

@@ -0,0 +1,136 @@
+import { resolve } from "path";
+import { existsSync } from "fs";
+import { createDatabase, Migrator, ALL_MIGRATIONS } from "@knowledgine/core";
+function cosineSimilarityFromL2(a, b) {
+    // L2-normalized vectors: cosine_similarity = 1 - L2_distance^2 / 2
+    let sumSq = 0;
+    for (let i = 0; i < a.length; i++) {
+        const diff = a[i] - b[i];
+        sumSq += diff * diff;
+    }
+    const l2dist = Math.sqrt(sumSq);
+    return Math.max(0, 1 - (l2dist * l2dist) / 2);
+}
+function sampleIndices(total, maxSamples) {
+    if (total <= maxSamples)
+        return Array.from({ length: total }, (_, i) => i);
+    const step = total / maxSamples;
+    return Array.from({ length: maxSamples }, (_, i) => Math.floor(i * step));
+}
+export async function benchmarkCommand(options) {
+    const rootPath = options.path ? resolve(options.path) : process.cwd();
+    const dbPath = resolve(rootPath, ".knowledgine", "index.sqlite");
+    if (!existsSync(dbPath)) {
+        console.error(`Error: Database not found at ${dbPath}`);
+        console.error("Run 'knowledgine init --path <dir>' first.");
+        process.exit(1);
+    }
+    if (!options.semantic) {
+        console.error("Use --semantic to run the semantic score distribution benchmark.");
+        process.exit(0);
+    }
+    let db;
+    try {
+        db = createDatabase(dbPath);
+        new Migrator(db, ALL_MIGRATIONS).migrate();
+    }
+    catch (err) {
+        console.error(`Error opening database: ${err instanceof Error ? err.message : String(err)}`);
+        process.exit(1);
+    }
+    const countRow = db.prepare("SELECT COUNT(*) AS count FROM note_embeddings").get();
+    const totalEmbeddings = countRow?.count ?? 0;
+    if (totalEmbeddings === 0) {
+        console.error("No embeddings found. Run 'knowledgine upgrade --semantic' first.");
+        db.close();
+        process.exit(0);
+    }
+    const MAX_SAMPLES = 50;
+    const indices = sampleIndices(totalEmbeddings, MAX_SAMPLES);
+    // Fetch only the sampled rows by offset to avoid loading all BLOBs.
+    const stmtOffset = db.prepare("SELECT note_id, embedding, dimensions FROM note_embeddings ORDER BY note_id LIMIT 1 OFFSET ?");
+    const sample = indices
+        .map((offset) => stmtOffset.get(offset))
+        .filter((row) => row !== undefined);
+    console.error(`\nSemantic Score Distribution Benchmark`);
+    console.error(`Total embeddings: ${totalEmbeddings}`);
+    console.error(`Sample size: ${sample.length}`);
+    console.error(`Computing pairwise cosine similarities...\n`);
+    const BYTES_PER_FLOAT32 = 4;
+    const scores = [];
+    let skippedPairs = 0;
+    for (let i = 0; i < sample.length; i++) {
+        const rowA = sample[i];
+        const dimsA = rowA.dimensions;
+        const maxFloatsA = rowA.embedding.byteLength / BYTES_PER_FLOAT32;
+        if (!Number.isInteger(dimsA) || dimsA <= 0 || dimsA > maxFloatsA)
+            continue;
+        const a = new Float32Array(rowA.embedding.buffer, rowA.embedding.byteOffset, dimsA);
+        for (let j = i + 1; j < sample.length; j++) {
+            const rowB = sample[j];
+            const dimsB = rowB.dimensions;
+            const maxFloatsB = rowB.embedding.byteLength / BYTES_PER_FLOAT32;
+            if (!Number.isInteger(dimsB) || dimsB <= 0 || dimsB > maxFloatsB || dimsB !== dimsA) {
+                skippedPairs++;
+                continue;
+            }
+            const b = new Float32Array(rowB.embedding.buffer, rowB.embedding.byteOffset, dimsB);
+            scores.push(cosineSimilarityFromL2(a, b));
+        }
+    }
+    if (scores.length === 0) {
+        console.error("Not enough samples to compute distribution (need at least 2 valid matching-dimension embeddings).");
+        if (skippedPairs > 0) {
+            console.error(`Note: Skipped ${skippedPairs} pair(s) due to invalid or mismatched dimensions.`);
+        }
+        db.close();
+        return;
+    }
+    if (skippedPairs > 0) {
+        console.error(`Note: Skipped ${skippedPairs} pair(s) with invalid or mismatched dimensions.`);
+    }
+    scores.sort((a, b) => a - b);
+    const n = scores.length;
+    const mean = scores.reduce((s, x) => s + x, 0) / n;
+    const variance = scores.reduce((s, x) => s + (x - mean) ** 2, 0) / n;
+    const stddev = Math.sqrt(variance);
+    const min = scores[0];
+    const max = scores[n - 1];
+    const p25 = scores[Math.floor(n * 0.25)];
+    const median = scores[Math.floor(n * 0.5)];
+    const p75 = scores[Math.floor(n * 0.75)];
+    const p90 = scores[Math.floor(n * 0.9)];
+    console.error(`Results (${n} pairs):`);
+    console.error(`  mean:   ${(mean * 100).toFixed(2)}%`);
+    console.error(`  stddev: ${(stddev * 100).toFixed(2)}%`);
+    console.error(`  min:    ${(min * 100).toFixed(2)}%`);
+    console.error(`  p25:    ${(p25 * 100).toFixed(2)}%`);
+    console.error(`  median: ${(median * 100).toFixed(2)}%`);
+    console.error(`  p75:    ${(p75 * 100).toFixed(2)}%`);
+    console.error(`  p90:    ${(p90 * 100).toFixed(2)}%`);
+    console.error(`  max:    ${(max * 100).toFixed(2)}%`);
+    console.error("");
+    if (stddev < 0.05) {
+        console.error("Warning: Low stddev indicates score flattening. Check embedding normalization.");
+    }
+    else {
+        console.error("Score distribution looks healthy (stddev >= 5%).");
+    }
+    console.error("");
+    // Also output as JSON to stdout for scripting
+    console.log(JSON.stringify({
+        totalEmbeddings: totalEmbeddings,
+        sampleSize: sample.length,
+        pairCount: n,
+        mean: parseFloat((mean * 100).toFixed(4)),
+        stddev: parseFloat((stddev * 100).toFixed(4)),
+        min: parseFloat((min * 100).toFixed(4)),
+        p25: parseFloat((p25 * 100).toFixed(4)),
+        median: parseFloat((median * 100).toFixed(4)),
+        p75: parseFloat((p75 * 100).toFixed(4)),
+        p90: parseFloat((p90 * 100).toFixed(4)),
+        max: parseFloat((max * 100).toFixed(4)),
+    }, null, 2));
+    db.close();
+}
+//# sourceMappingURL=benchmark.js.map

package/dist/commands/benchmark.js.map

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package/dist/commands/ingest.d.ts

@@ -15,6 +15,7 @@ export interface IngestOptions {
     observe?: boolean;
     observeLimit?: number;
     noEmbeddings?: boolean;
+    embedMissing?: boolean;
 }
 export declare function ingestCommand(options: IngestOptions): Promise<void>;
 //# sourceMappingURL=ingest.d.ts.map

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+{"version":3,"file":"ingest.d.ts","sourceRoot":"","sources":["../../src/commands/ingest.ts"],"names":[],"mappings":"AAmEA,MAAM,WAAW,aAAa;IAC5B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;IAC1B,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,YAAY,CAAC,EAAE,OAAO,CAAC;CACxB;AAED,wBAAsB,aAAa,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC,CA0dzE"}

package/dist/commands/ingest.js

@@ -44,6 +44,11 @@ export async function ingestCommand(options) {
     // --force is an alias for --full
     if (options.force)
         options.full = true;
+    // --embed-missing: generate embeddings for notes that are missing them (no normal ingest)
+    if (options.embedMissing) {
+        await embedMissingCommand(options);
+        return;
+    }
     // Validate mutually exclusive options
     if (options.source && options.all) {
         console.error(colors.error("Error: --source and --all cannot be used together"));
@@ -244,6 +249,31 @@ export async function ingestCommand(options) {
             ];
             const report = createSummaryReport("knowledgine ingest", entries);
             console.error("\n" + report);
+            // Show error details when errors occurred
+            if (summary.errors > 0 && summary.errorDetails && summary.errorDetails.length > 0) {
+                const displayCount = options.verbose
+                    ? summary.errorDetails.length
+                    : Math.min(5, summary.errorDetails.length);
+                console.error(`\n  ${symbols.warning} ${colors.warning(`${summary.errors} error(s) during ingest:`)}`);
+                for (let i = 0; i < displayCount; i++) {
+                    const e = summary.errorDetails[i];
+                    console.error(`    [${e.category}] ${e.sourceUri} — ${e.message}`);
+                }
+                if (!options.verbose && summary.errorDetails.length > 5) {
+                    console.error(`    ... and ${summary.errorDetails.length - 5} more (use --verbose to see all)`);
+                }
+                if (options.verbose) {
+                    // category breakdown
+                    const counts = {};
+                    for (const e of summary.errorDetails) {
+                        counts[e.category] = (counts[e.category] ?? 0) + 1;
+                    }
+                    const breakdown = Object.entries(counts)
+                        .map(([k, v]) => `${k}: ${v}`)
+                        .join(", ");
+                    console.error(`    Categories: ${breakdown}`);
+                }
+            }
             // Show skip reason when 0 events processed
             if (summary.processed === 0 && summary.skipReason) {
                 const reasons = {
@@ -411,4 +441,113 @@ export async function ingestCommand(options) {
         db.close();
     }
 }
+/** Maximum number of retry attempts for a failed embedding batch. */
+const MAX_EMBED_RETRIES = 2;
+/**
+ * Standalone flow for `knowledgine ingest --embed-missing`.
+ * Generates embeddings only for notes that currently have none — no ingest is performed.
+ */
+async function embedMissingCommand(options) {
+    const rootPath = resolveDefaultPath(options.path);
+    // Initialise DB (same pattern as the normal ingest flow)
+    const knowledgineDir = resolve(rootPath, ".knowledgine");
+    mkdirSync(knowledgineDir, { recursive: true });
+    const config = defineConfig({ rootPath });
+    const db = createDatabase(config.dbPath);
+    new Migrator(db, ALL_MIGRATIONS).migrate();
+    const repository = new KnowledgeRepository(db);
+    try {
+        const rcConfig = loadRcFile(rootPath);
+        const embeddingConfig = rcConfig?.embedding;
+        const embeddingEnabled = embeddingConfig?.enabled ?? rcConfig?.semantic ?? false;
+        if (!embeddingEnabled) {
+            console.error(`  ${symbols.warning} ${colors.warning("Semantic search is not enabled. Run 'knowledgine upgrade --semantic' first.")}`);
+            process.exitCode = 1;
+            return;
+        }
+        const modelManager = new ModelManager();
+        const modelName = embeddingConfig?.modelName ?? DEFAULT_MODEL_NAME;
+        if (!modelManager.isModelAvailable(modelName)) {
+            console.error(`  ${symbols.warning} ${colors.warning("Embedding model not available. Run 'knowledgine upgrade --semantic' to download.")}`);
+            process.exitCode = 1;
+            return;
+        }
+        const vecLoaded = await loadSqliteVecExtension(db);
+        if (!vecLoaded) {
+            console.error(`  ${symbols.warning} ${colors.warning("sqlite-vec extension could not be loaded. Embedding generation is unavailable.")}`);
+            process.exitCode = 1;
+            return;
+        }
+        const noteIdsNeedingEmbeddings = repository.getNotesWithoutEmbeddingIds();
+        const totalNotes = repository.getStats().totalNotes;
+        if (noteIdsNeedingEmbeddings.length === 0) {
+            const coverage = totalNotes > 0 ? 100 : 0;
+            console.error(`  ${symbols.success} ${colors.success(`All notes have embeddings (coverage: ${coverage}%)`)}`);
+            return;
+        }
+        const embeddingProvider = new OnnxEmbeddingProvider(modelName, modelManager);
+        const BATCH_SIZE = 20;
+        const total = noteIdsNeedingEmbeddings.length;
+        console.error(`\n  ${symbols.info} Generating embeddings for ${total} notes...`);
+        let generated = 0;
+        let failed = 0;
+        try {
+            for (let i = 0; i < noteIdsNeedingEmbeddings.length; i += BATCH_SIZE) {
+                const batchIds = noteIdsNeedingEmbeddings.slice(i, i + BATCH_SIZE);
+                const noteRows = repository.getNotesByIds(batchIds);
+                const noteMap = new Map(noteRows.map((n) => [n.id, n]));
+                const orderedNotes = batchIds
+                    .map((id) => noteMap.get(id))
+                    .filter((n) => n != null);
+                if (orderedNotes.length === 0)
+                    continue;
+                for (let attempt = 0; attempt <= MAX_EMBED_RETRIES; attempt++) {
+                    try {
+                        const embeddings = await embeddingProvider.embedBatch(orderedNotes.map((n) => n.content));
+                        const result = repository.saveEmbeddingBatch(orderedNotes.map((n, j) => ({
+                            noteId: n.id,
+                            embedding: embeddings[j],
+                            modelName,
+                        })));
+                        generated += result.saved;
+                        failed += result.failed;
+                        break;
+                    }
+                    catch {
+                        if (attempt === MAX_EMBED_RETRIES) {
+                            failed += orderedNotes.length;
+                        }
+                        else {
+                            await new Promise((r) => setTimeout(r, 1000 * Math.pow(2, attempt)));
+                        }
+                    }
+                }
+                const done = generated + failed;
+                const pct = Math.round((done / total) * 100);
+                process.stderr.write(`\r  ${symbols.info} Embeddings: ${done}/${total} (${pct}%)`);
+            }
+        }
+        finally {
+            await embeddingProvider.close();
+        }
+        process.stderr.write("\n");
+        // Calculate final coverage
+        const notesTotal = totalNotes > 0 ? totalNotes : total + generated;
+        const nowWithEmbeddings = notesTotal - repository.getNotesWithoutEmbeddingIds().length;
+        const coveragePct = notesTotal > 0 ? Math.round((nowWithEmbeddings / notesTotal) * 100) : 100;
+        if (failed > 0) {
+            console.error(`  ${symbols.warning} ${colors.warning(`Embeddings: ${generated} generated, ${failed} failed (coverage: ${coveragePct}%)`)}`);
+        }
+        else {
+            console.error(`  ${symbols.success} ${colors.success(`Embeddings: ${generated} generated, 0 failed (coverage: ${coveragePct}%)`)}`);
+        }
+    }
+    catch (error) {
+        console.error(colors.error(`Embed-missing failed: ${error instanceof Error ? error.message : String(error)}`));
+        process.exitCode = 1;
+    }
+    finally {
+        db.close();
+    }
+}
 //# sourceMappingURL=ingest.js.map

package/dist/commands/ingest.js.map

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package/dist/commands/init.d.ts

@@ -6,6 +6,7 @@ export interface InitOptions {
     force?: boolean;
     yes?: boolean;
     saveConfig?: boolean;
+    verbose?: boolean;
 }
 export declare function initCommand(options: InitOptions): Promise<void>;
 //# sourceMappingURL=init.d.ts.map

package/dist/commands/init.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../src/commands/init.ts"],"names":[],"mappings":"AA0BA,MAAM,WAAW,WAAW;IAC1B,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,UAAU,CAAC,EAAE,OAAO,CAAC;CACtB;AAqED,wBAAsB,WAAW,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CAwfrE"}
+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../src/commands/init.ts"],"names":[],"mappings":"AA0BA,MAAM,WAAW,WAAW;IAC1B,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,OAAO,CAAC,EAAE,OAAO,CAAC;CACnB;AA+ED,wBAAsB,WAAW,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CAgjBrE"}

package/dist/commands/init.js

@@ -73,6 +73,15 @@ async function getFreeDiskBytes(targetPath) {
 function sleep(ms) {
     return new Promise((resolve) => setTimeout(resolve, ms));
 }
+function formatSkipReason(reason) {
+    const labels = {
+        empty_content: "empty",
+        too_large: "too large",
+        excluded_pattern: "excluded",
+        read_error: "read error",
+    };
+    return labels[reason] ?? reason;
+}
 export async function initCommand(options) {
     const initStartTime = Date.now();
     let rootPath;
@@ -190,7 +199,10 @@ export async function initCommand(options) {
     const engine = new IngestEngine(registry, db, repository);
     let ingestSummary;
     try {
-        ingestSummary = await engine.ingest("markdown", rootPath, { full: true });
+        ingestSummary = await engine.ingest("markdown", rootPath, {
+            full: true,
+            verbose: options.verbose,
+        });
     }
     catch (err) {
         const message = err instanceof Error ? err.message : String(err);
@@ -230,6 +242,24 @@ export async function initCommand(options) {
     }
     if (ingestSummary.errors > 0) {
         stepProgress.warn(`${ingestSummary.errors} file(s) could not be indexed`);
+        if (ingestSummary.errorDetails && ingestSummary.errorDetails.length > 0) {
+            const displayCount = options.verbose
+                ? ingestSummary.errorDetails.length
+                : Math.min(5, ingestSummary.errorDetails.length);
+            for (let i = 0; i < displayCount; i++) {
+                const e = ingestSummary.errorDetails[i];
+                console.error(`    [${e.category}] ${e.sourceUri} — ${e.message}`);
+            }
+            if (!options.verbose && ingestSummary.errorDetails.length > 5) {
+                console.error(`    ... and ${ingestSummary.errorDetails.length - 5} more (use --verbose to see all)`);
+            }
+        }
+    }
+    if (options.verbose && ingestSummary.skipDetails && ingestSummary.skipDetails.length > 0) {
+        console.error(`  Skipped files:`);
+        for (const detail of ingestSummary.skipDetails) {
+            console.error(`    [${formatSkipReason(detail.reason)}] ${detail.path}`);
+        }
     }
     stepProgress.completeStep("Indexing markdown files");
     // Entity extraction (post-ingest batch)
@@ -366,24 +396,33 @@ export async function initCommand(options) {
                 const embProgress = createProgress(noteIds.length, "  Embeddings");
                 let generated = 0;
                 let failed = 0;
+                const MAX_EMBED_RETRIES = 2;
                 for (let i = 0; i < noteIds.length; i += BATCH_SIZE) {
                     const batchIds = noteIds.slice(i, i + BATCH_SIZE);
                     const noteRows = repository.getNotesByIds(batchIds);
                     // getNotesByIds の返り順は不定なので id→note Map で安全にマッピング
                     const noteMap = new Map(noteRows.map((n) => [n.id, n]));
                     const orderedNotes = batchIds.map((id) => noteMap.get(id)).filter((n) => n != null);
-                    try {
-                        const embeddings = await embeddingProvider.embedBatch(orderedNotes.map((n) => n.content));
-                        const result = repository.saveEmbeddingBatch(orderedNotes.map((n, j) => ({
-                            noteId: n.id,
-                            embedding: embeddings[j],
-                            modelName: config.embedding.modelName,
-                        })));
-                        generated += result.saved;
-                        failed += result.failed;
-                    }
-                    catch {
-                        failed += orderedNotes.length;
+                    for (let attempt = 0; attempt <= MAX_EMBED_RETRIES; attempt++) {
+                        try {
+                            const embeddings = await embeddingProvider.embedBatch(orderedNotes.map((n) => n.content));
+                            const result = repository.saveEmbeddingBatch(orderedNotes.map((n, j) => ({
+                                noteId: n.id,
+                                embedding: embeddings[j],
+                                modelName: config.embedding.modelName,
+                            })));
+                            generated += result.saved;
+                            failed += result.failed;
+                            break;
+                        }
+                        catch {
+                            if (attempt === MAX_EMBED_RETRIES) {
+                                failed += orderedNotes.length;
+                            }
+                            else {
+                                await new Promise((r) => setTimeout(r, 1000 * Math.pow(2, attempt)));
+                            }
+                        }
                     }
                     embProgress.update(generated + failed > noteIds.length ? noteIds.length : generated + failed);
                 }
@@ -427,20 +466,41 @@ export async function initCommand(options) {
     const notesWithoutEmb = repository.getNotesWithoutEmbeddings().length;
     const embeddingsGenerated = stats.totalNotes - notesWithoutEmb;
     const elapsed = formatDuration(Date.now() - initStartTime);
+    let skippedValue;
+    if (ingestSummary.skipped > 0) {
+        if (ingestSummary.skippedByReason && Object.keys(ingestSummary.skippedByReason).length > 0) {
+            const parts = Object.entries(ingestSummary.skippedByReason)
+                .filter(([, count]) => count && count > 0)
+                .map(([reason, count]) => `${count} ${formatSkipReason(reason)}`);
+            skippedValue = `${ingestSummary.skipped} files (${parts.join(", ")})`;
+        }
+        else {
+            skippedValue = `${ingestSummary.skipped} files`;
+        }
+    }
     const summaryEntries = [
         { label: "Notes:", value: `${stats.totalNotes} indexed` },
-        ...(ingestSummary.skipped > 0
-            ? [{ label: "Skipped:", value: `${ingestSummary.skipped} files (empty)` }]
-            : []),
+        ...(skippedValue !== undefined ? [{ label: "Skipped:", value: skippedValue }] : []),
         { label: "Patterns:", value: `${stats.totalPatterns} extracted` },
         { label: "Entities:", value: `${postSummary.totalEntities} extracted` },
         ...(enableSemantic && config.embedding.enabled
-            ? [
-                {
-                    label: "Embeddings:",
-                    value: embeddingsGenerated > 0 ? `${embeddingsGenerated} generated` : "none",
-                },
-            ]
+            ? (() => {
+                const coveragePct = stats.totalNotes > 0 ? Math.round((embeddingsGenerated / stats.totalNotes) * 100) : 100;
+                return [
+                    {
+                        label: "Embeddings:",
+                        value: embeddingsGenerated > 0 ? `${embeddingsGenerated} generated` : "none",
+                    },
+                    ...(coveragePct < 95 && stats.totalNotes > 0
+                        ? [
+                            {
+                                label: "Hint:",
+                                value: `Run 'knowledgine ingest --embed-missing' to complete embedding generation`,
+                            },
+                        ]
+                        : []),
+                ];
+            })()
             : [
                 { label: "Search:", value: "FTS5 full-text search (default)" },
                 {