@optave/codegraph 3.11.0 → 3.11.1

package/dist/domain/search/generator.js

@@ -43,48 +43,54 @@ function initEmbeddingsSchema(db) {
   `);
 }
 /**
- * Build embeddings for all functions/methods/classes in the graph.
+ * Resolve the repo root for embedding. Prefer the root recorded at build time;
+ * fall back to `<dbParent>` only when the DB lives at the conventional
+ * `<root>/.codegraph/graph.db` layout — otherwise trust the caller's rootDir.
  */
-export async function buildEmbeddings(rootDir, modelKey, customDbPath, options = {}) {
-    const strategy = options.strategy || 'structured';
-    const dbPath = customDbPath || findDbPath(undefined);
-    if (!fs.existsSync(dbPath)) {
-        throw new DbError(`No codegraph database found at ${dbPath}.\nRun "codegraph build" first to analyze your codebase.`, { file: dbPath });
-    }
-    const db = openDb(dbPath);
-    initEmbeddingsSchema(db);
-    // Prefer the repo root recorded at build time — embed may be invoked from a
-    // different cwd (e.g. `codegraph embed --db /abs/path/graph.db`) and the
-    // positional rootDir will be wrong in that case. For legacy DBs without
-    // root_dir metadata, fall back to `<dbParent>` only when the DB lives at
-    // the conventional `<root>/.codegraph/graph.db` layout — otherwise trust
-    // the caller-provided rootDir (which may be an explicit positional arg).
-    // `path.dirname(...)` is always non-empty (`'.'` at minimum), so the
-    // conventional-layout check is required to keep the rootDir path reachable.
+function resolveRoot(db, dbPath, rootDir) {
     const metaRoot = getBuildMeta(db, 'root_dir');
     const resolvedDbPath = path.resolve(dbPath);
     const dbDirName = path.basename(path.dirname(resolvedDbPath));
     const dbParent = dbDirName === '.codegraph' ? path.dirname(path.dirname(resolvedDbPath)) : undefined;
-    const resolvedRoot = metaRoot || dbParent || rootDir;
+    return metaRoot || dbParent || rootDir;
+}
+/** Reset embedding tables and load eligible symbols grouped by file. */
+function loadNodesByFile(db) {
     db.exec('DELETE FROM embeddings');
     db.exec('DELETE FROM embedding_meta');
     db.exec('DELETE FROM fts_index');
     const nodes = db
         .prepare(`SELECT * FROM nodes WHERE kind IN ('function', 'method', 'class') ORDER BY file, line`)
         .all();
-    console.log(`Building embeddings for ${nodes.length} symbols (strategy: ${strategy})...`);
     const byFile = new Map();
     for (const node of nodes) {
         if (!byFile.has(node.file))
             byFile.set(node.file, []);
         byFile.get(node.file)?.push(node);
     }
+    return byFile;
+}
+/** Build embedding text for a single node, truncating if it would overflow. */
+function buildNodeText(node, file, lines, db, strategy, contextWindow) {
+    let text = strategy === 'structured'
+        ? buildStructuredText(node, file, lines, db)
+        : buildSourceText(node, file, lines);
+    const tokens = estimateTokens(text);
+    if (tokens > contextWindow) {
+        text = text.slice(0, contextWindow * 4);
+        return { text, overflowed: true };
+    }
+    return { text, overflowed: false };
+}
+/**
+ * Walk files in the graph, read source, and produce parallel arrays of
+ * texts / nodeIds / nodeNames / previews ready for embedding.
+ */
+function prepareEmbeddingTexts(byFile, db, resolvedRoot, strategy, contextWindow) {
     const texts = [];
     const nodeIds = [];
     const nodeNames = [];
     const previews = [];
-    const config = getModelConfig(modelKey);
-    const contextWindow = config.contextWindow;
     let overflowCount = 0;
     let filesRead = 0;
     let filesSkipped = 0;
@@ -101,36 +107,20 @@ export async function buildEmbeddings(rootDir, modelKey, customDbPath, options =
             continue;
         }
         for (const node of fileNodes) {
-            let text = strategy === 'structured'
-                ? buildStructuredText(node, file, lines, db)
-                : buildSourceText(node, file, lines);
-            // Detect and handle context window overflow
-            const tokens = estimateTokens(text);
-            if (tokens > contextWindow) {
+            const { text, overflowed } = buildNodeText(node, file, lines, db, strategy, contextWindow);
+            if (overflowed)
                 overflowCount++;
-                const maxChars = contextWindow * 4;
-                text = text.slice(0, maxChars);
-            }
             texts.push(text);
             nodeIds.push(node.id);
             nodeNames.push(node.name);
             previews.push(`${node.name} (${node.kind}) -- ${file}:${node.line}`);
         }
     }
-    if (overflowCount > 0) {
-        warn(`${overflowCount} symbol(s) exceeded model context window (${contextWindow} tokens) and were truncated`);
-    }
-    // If there were symbols to embed but every file failed to read, the DB was
-    // almost certainly built from a different location than the current cwd.
-    // Surface this clearly instead of emitting a silent "Stored 0 embeddings".
-    if (byFile.size > 0 && filesRead === 0) {
-        closeDb(db);
-        throw new DbError(`embed: could not read any of the ${filesSkipped} source files recorded in the graph — the DB may have been built from a different location than the current working directory.\n` +
-            `Tried resolving against: ${resolvedRoot}\n` +
-            'Pass a positional <dir> argument pointing at the original repo root, or re-run "codegraph build" from that directory.', { file: dbPath });
-    }
-    console.log(`Embedding ${texts.length} symbols...`);
-    const { vectors, dim } = await embed(texts, modelKey);
+    return { texts, nodeIds, nodeNames, previews, overflowCount, filesRead, filesSkipped };
+}
+/** Persist vectors, FTS rows, and embedding metadata in a single transaction. */
+function persistEmbeddings(db, prepared, vectors, dim, modelName, strategy) {
+    const { nodeIds, nodeNames, previews, texts, overflowCount } = prepared;
     const insert = db.prepare('INSERT OR REPLACE INTO embeddings (node_id, vector, text_preview, full_text) VALUES (?, ?, ?, ?)');
     const insertFts = db.prepare('INSERT INTO fts_index(rowid, name, content) VALUES (?, ?, ?)');
     const insertMeta = db.prepare('INSERT OR REPLACE INTO embedding_meta (key, value) VALUES (?, ?)');
@@ -140,7 +130,7 @@ export async function buildEmbeddings(rootDir, modelKey, customDbPath, options =
             insert.run(nodeIds[i], Buffer.from(vec.buffer), previews[i], texts[i]);
             insertFts.run(nodeIds[i], nodeNames[i], texts[i]);
         }
-        insertMeta.run('model', config.name);
+        insertMeta.run('model', modelName);
         insertMeta.run('dim', String(dim));
         insertMeta.run('count', String(vectors.length));
         insertMeta.run('fts_count', String(vectors.length));
@@ -151,6 +141,39 @@ export async function buildEmbeddings(rootDir, modelKey, customDbPath, options =
         }
     });
     insertAll();
+}
+/**
+ * Build embeddings for all functions/methods/classes in the graph.
+ */
+export async function buildEmbeddings(rootDir, modelKey, customDbPath, options = {}) {
+    const strategy = options.strategy || 'structured';
+    const dbPath = customDbPath || findDbPath(undefined);
+    if (!fs.existsSync(dbPath)) {
+        throw new DbError(`No codegraph database found at ${dbPath}.\nRun "codegraph build" first to analyze your codebase.`, { file: dbPath });
+    }
+    const db = openDb(dbPath);
+    initEmbeddingsSchema(db);
+    const resolvedRoot = resolveRoot(db, dbPath, rootDir);
+    const byFile = loadNodesByFile(db);
+    const nodeCount = [...byFile.values()].reduce((acc, list) => acc + list.length, 0);
+    console.log(`Building embeddings for ${nodeCount} symbols (strategy: ${strategy})...`);
+    const config = getModelConfig(modelKey);
+    const prepared = prepareEmbeddingTexts(byFile, db, resolvedRoot, strategy, config.contextWindow);
+    if (prepared.overflowCount > 0) {
+        warn(`${prepared.overflowCount} symbol(s) exceeded model context window (${config.contextWindow} tokens) and were truncated`);
+    }
+    // If there were symbols to embed but every file failed to read, the DB was
+    // almost certainly built from a different location than the current cwd.
+    // Surface this clearly instead of emitting a silent "Stored 0 embeddings".
+    if (byFile.size > 0 && prepared.filesRead === 0) {
+        closeDb(db);
+        throw new DbError(`embed: could not read any of the ${prepared.filesSkipped} source files recorded in the graph — the DB may have been built from a different location than the current working directory.\n` +
+            `Tried resolving against: ${resolvedRoot}\n` +
+            'Pass a positional <dir> argument pointing at the original repo root, or re-run "codegraph build" from that directory.', { file: dbPath });
+    }
+    console.log(`Embedding ${prepared.texts.length} symbols...`);
+    const { vectors, dim } = await embed(prepared.texts, modelKey);
+    persistEmbeddings(db, prepared, vectors, dim, config.name, strategy);
     console.log(`\nStored ${vectors.length} embeddings (${dim}d, ${config.name}, strategy: ${strategy}) in graph.db`);
     closeDb(db);
 }

package/dist/domain/search/generator.js.map

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package/dist/domain/search/models.d.ts

@@ -20,6 +20,8 @@ export interface ModelConfig {
     contextWindow: number;
     desc: string;
     quantized: boolean;
+    /** Pooling strategy passed to the transformers pipeline. Defaults to 'mean'. */
+    pooling?: 'mean' | 'cls';
 }
 export declare const MODELS: Record<string, ModelConfig>;
 export declare const EMBEDDING_STRATEGIES: readonly string[];

package/dist/domain/search/models.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"models.d.ts","sourceRoot":"","sources":["../../../src/domain/search/models.ts"],"names":[],"mappings":"AASA;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,oBAAoB,IAAI,MAAM,GAAG,SAAS,CAWzD;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,GAAG,EAAE,MAAM,CAAC;IACZ,aAAa,EAAE,MAAM,CAAC;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,OAAO,CAAC;CACpB;AAUD,eAAO,MAAM,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,WAAW,CAkD9C,CAAC;AAEF,eAAO,MAAM,oBAAoB,EAAE,SAAS,MAAM,EAA6B,CAAC;AAEhF,eAAO,MAAM,aAAa,EAAE,MAAqB,CAAC;AAalD,sEAAsE;AACtE,wBAAgB,cAAc,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,WAAW,CAO7D;AAED;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CA0CnE;AAED;;;;;GAKG;AACH,wBAAsB,gBAAgB,IAAI,OAAO,CAAC,OAAO,CAAC,CAkBzD;AAED;;;GAGG;AACH,wBAAsB,YAAY,IAAI,OAAO,CAAC,IAAI,CAAC,CAMlD;AA2CD;;GAEG;AACH,wBAAsB,KAAK,CACzB,KAAK,EAAE,MAAM,EAAE,EACf,QAAQ,CAAC,EAAE,MAAM,GAChB,OAAO,CAAC;IAAE,OAAO,EAAE,YAAY,EAAE,CAAC;IAAC,GAAG,EAAE,MAAM,CAAA;CAAE,CAAC,CA6BnD"}
+{"version":3,"file":"models.d.ts","sourceRoot":"","sources":["../../../src/domain/search/models.ts"],"names":[],"mappings":"AASA;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,oBAAoB,IAAI,MAAM,GAAG,SAAS,CAWzD;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,GAAG,EAAE,MAAM,CAAC;IACZ,aAAa,EAAE,MAAM,CAAC;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,OAAO,CAAC;IACnB,gFAAgF;IAChF,OAAO,CAAC,EAAE,MAAM,GAAG,KAAK,CAAC;CAC1B;AAUD,eAAO,MAAM,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,WAAW,CAgF9C,CAAC;AAEF,eAAO,MAAM,oBAAoB,EAAE,SAAS,MAAM,EAA6B,CAAC;AAEhF,eAAO,MAAM,aAAa,EAAE,MAAgB,CAAC;AAiB7C,sEAAsE;AACtE,wBAAgB,cAAc,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,WAAW,CAO7D;AAED;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CA0CnE;AAED;;;;;GAKG;AACH,wBAAsB,gBAAgB,IAAI,OAAO,CAAC,OAAO,CAAC,CAkBzD;AAED;;;GAGG;AACH,wBAAsB,YAAY,IAAI,OAAO,CAAC,IAAI,CAAC,CAMlD;AA2CD;;GAEG;AACH,wBAAsB,KAAK,CACzB,KAAK,EAAE,MAAM,EAAE,EACf,QAAQ,CAAC,EAAE,MAAM,GAChB,OAAO,CAAC;IAAE,OAAO,EAAE,YAAY,EAAE,CAAC;IAAC,GAAG,EAAE,MAAM,CAAA;CAAE,CAAC,CA6BnD"}

package/dist/domain/search/models.js

@@ -77,7 +77,7 @@ export const MODELS = {
         name: 'nomic-ai/nomic-embed-text-v1.5',
         dim: 768,
         contextWindow: 8192,
-        desc: 'Improved nomic (~137MB). Matryoshka dimensions, 8192 context.',
+        desc: 'Matryoshka MRL trained (~137MB). 8192 context. Codegraph stores full 768d (no truncation); v1 scores higher on our benchmark.',
         quantized: false,
     },
     'bge-large': {
@@ -87,9 +87,39 @@ export const MODELS = {
         desc: 'Best general retrieval (~335MB). Top MTEB scores.',
         quantized: false,
     },
+    'mxbai-xsmall': {
+        name: 'mixedbread-ai/mxbai-embed-xsmall-v1',
+        dim: 384,
+        contextWindow: 4096,
+        desc: 'Tiny model with long context (~50MB). 4096 ctx.',
+        quantized: false,
+        pooling: 'cls',
+    },
+    'mxbai-large': {
+        name: 'mixedbread-ai/mxbai-embed-large-v1',
+        dim: 1024,
+        contextWindow: 512,
+        desc: 'Top MTEB BERT-large, Matryoshka dimensions (~400MB). 512 ctx.',
+        quantized: false,
+        pooling: 'cls',
+    },
+    'bge-m3': {
+        name: 'Xenova/bge-m3',
+        dim: 1024,
+        contextWindow: 8192,
+        desc: 'Multilingual, multi-task (~600MB). 100+ languages, 8192 context.',
+        quantized: false,
+    },
+    modernbert: {
+        name: 'nomic-ai/modernbert-embed-base',
+        dim: 768,
+        contextWindow: 8192,
+        desc: 'ModernBERT base (~150MB). Newer architecture, 8192 ctx, English.',
+        quantized: false,
+    },
 };
 export const EMBEDDING_STRATEGIES = ['structured', 'source'];
-export const DEFAULT_MODEL = 'nomic-v1.5';
+export const DEFAULT_MODEL = 'nomic';
 const NPM_BIN = process.platform === 'win32' ? 'npm.cmd' : 'npm';
 const BATCH_SIZE_MAP = {
     minilm: 32,
@@ -99,6 +129,10 @@ const BATCH_SIZE_MAP = {
     nomic: 8,
     'nomic-v1.5': 8,
     'bge-large': 4,
+    'mxbai-xsmall': 32,
+    'mxbai-large': 4,
+    'bge-m3': 4,
+    modernbert: 8,
 };
 const DEFAULT_BATCH_SIZE = 32;
 /** @internal Used by generator.js — not part of the public barrel. */
@@ -233,7 +267,7 @@ export async function embed(texts, modelKey) {
     for (let i = 0; i < texts.length; i += batchSize) {
         const batch = texts.slice(i, i + batchSize);
         const output = (await // biome-ignore lint/complexity/noBannedTypes: dynamically loaded extractor is untyped
-         ext(batch, { pooling: 'mean', normalize: true }));
+         ext(batch, { pooling: config.pooling ?? 'mean', normalize: true }));
         for (let j = 0; j < batch.length; j++) {
             const start = j * dim;
             const vec = new Float32Array(dim);

package/dist/domain/search/models.js.map

@@ -1 +1 @@
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package/dist/domain/search/search/hybrid.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"hybrid.d.ts","sourceRoot":"","sources":["../../../../src/domain/search/search/hybrid.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,eAAe,CAAC;AAGxD,UAAU,YAAY;IACpB,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;IACvB,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;IACxB,GAAG,EAAE,MAAM,CAAC;IACZ,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;IACxB,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;CAC7B;AAED,MAAM,WAAW,kBAAkB;IACjC,OAAO,EAAE,YAAY,EAAE,CAAC;CACzB;AAsJD,wBAAsB,gBAAgB,CACpC,KAAK,EAAE,MAAM,EACb,YAAY,EAAE,MAAM,GAAG,SAAS,EAChC,IAAI,GAAE,kBAAuB,GAC5B,OAAO,CAAC,kBAAkB,GAAG,IAAI,CAAC,CAiBpC"}

package/dist/domain/search/search/hybrid.js

@@ -39,47 +39,40 @@ async function collectRankedLists(queries, customDbPath, opts, topK) {
     }
     return rankedLists;
 }
-/** Reciprocal Rank Fusion: merge ranked lists into a single scored result set. */
-function fuseResults(rankedLists, k, limit) {
-    const fusionMap = new Map();
-    for (const list of rankedLists) {
-        for (const item of list) {
-            if (!fusionMap.has(item.key)) {
-                fusionMap.set(item.key, {
-                    name: item.name,
-                    kind: item.kind,
-                    file: item.file,
-                    line: item.line,
-                    endLine: item.endLine ?? null,
-                    role: item.role ?? null,
-                    fileHash: item.fileHash ?? null,
-                    rrfScore: 0,
-                    bm25Score: null,
-                    bm25Rank: null,
-                    similarity: null,
-                    semanticRank: null,
-                });
-            }
-            const entry = fusionMap.get(item.key);
-            entry.rrfScore += 1 / (k + item.rank);
-            if (item.source === 'bm25') {
-                if (entry.bm25Rank === null || item.rank < entry.bm25Rank) {
-                    entry.bm25Score = item.bm25Score ?? null;
-                    entry.bm25Rank = item.rank;
-                }
-            }
-            else {
-                if (entry.semanticRank === null || item.rank < entry.semanticRank) {
-                    entry.similarity = item.similarity ?? null;
-                    entry.semanticRank = item.rank;
-                }
-            }
+/** Initialise a fusion entry seeded from the first ranked item we see for a key. */
+function createFusionEntry(item) {
+    return {
+        name: item.name,
+        kind: item.kind,
+        file: item.file,
+        line: item.line,
+        endLine: item.endLine ?? null,
+        role: item.role ?? null,
+        fileHash: item.fileHash ?? null,
+        rrfScore: 0,
+        bm25Score: null,
+        bm25Rank: null,
+        similarity: null,
+        semanticRank: null,
+    };
+}
+/** Merge a single ranked item into its fusion entry: update RRF and best per-source rank. */
+function mergeRankedItem(entry, item, k) {
+    entry.rrfScore += 1 / (k + item.rank);
+    if (item.source === 'bm25') {
+        if (entry.bm25Rank === null || item.rank < entry.bm25Rank) {
+            entry.bm25Score = item.bm25Score ?? null;
+            entry.bm25Rank = item.rank;
         }
     }
-    return [...fusionMap.values()]
-        .sort((a, b) => b.rrfScore - a.rrfScore)
-        .slice(0, limit)
-        .map((e) => ({
+    else if (entry.semanticRank === null || item.rank < entry.semanticRank) {
+        entry.similarity = item.similarity ?? null;
+        entry.semanticRank = item.rank;
+    }
+}
+/** Flatten a fusion entry into the public-facing hybrid result shape. */
+function toHybridResult(e) {
+    return {
         name: e.name,
         kind: e.kind,
         file: e.file,
@@ -92,7 +85,23 @@ function fuseResults(rankedLists, k, limit) {
         bm25Rank: e.bm25Rank,
         similarity: e.similarity,
         semanticRank: e.semanticRank,
-    }));
+    };
+}
+/** Reciprocal Rank Fusion: merge ranked lists into a single scored result set. */
+function fuseResults(rankedLists, k, limit) {
+    const fusionMap = new Map();
+    for (const list of rankedLists) {
+        for (const item of list) {
+            if (!fusionMap.has(item.key)) {
+                fusionMap.set(item.key, createFusionEntry(item));
+            }
+            mergeRankedItem(fusionMap.get(item.key), item, k);
+        }
+    }
+    return [...fusionMap.values()]
+        .sort((a, b) => b.rrfScore - a.rrfScore)
+        .slice(0, limit)
+        .map(toHybridResult);
 }
 export async function hybridSearchData(query, customDbPath, opts = {}) {
     const config = opts.config || loadConfig();

package/dist/domain/search/search/hybrid.js.map

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package/dist/domain/search/search/semantic.d.ts.map

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package/dist/domain/search/search/semantic.js

@@ -4,6 +4,19 @@ import { normalizeSymbol } from '../../queries.js';
 import { embed } from '../models.js';
 import { cosineSim } from '../stores/sqlite-blob.js';
 import { prepareSearch } from './prepare.js';
+/** Reconstitute a stored embedding row's vector blob into a Float32Array. */
+function rowVector(row) {
+    return new Float32Array(new Uint8Array(row.vector).buffer);
+}
+/** Warn when stored embeddings and the query model use different dimensions. */
+function checkDimensionMismatch(storedDim, dim) {
+    if (storedDim && dim !== storedDim) {
+        console.log(`Warning: query model dimension (${dim}) doesn't match stored embeddings (${storedDim}).`);
+        console.log(`  Re-run \`codegraph embed\` with the same model, or use --model to match.`);
+        return true;
+    }
+    return false;
+}
 export async function searchData(query, customDbPath, opts = {}) {
     const config = opts.config || loadConfig();
     const searchCfg = config.search || {};
@@ -15,16 +28,12 @@ export async function searchData(query, customDbPath, opts = {}) {
     const { db, rows, modelKey, storedDim } = prepared;
     try {
         const { vectors: [queryVec], dim, } = await embed([query], modelKey ?? undefined);
-        if (storedDim && dim !== storedDim) {
-            console.log(`Warning: query model dimension (${dim}) doesn't match stored embeddings (${storedDim}).`);
-            console.log(`  Re-run \`codegraph embed\` with the same model, or use --model to match.`);
+        if (checkDimensionMismatch(storedDim, dim))
             return null;
-        }
         const hc = new Map();
         const results = [];
         for (const row of rows) {
-            const vec = new Float32Array(new Uint8Array(row.vector).buffer);
-            const sim = cosineSim(queryVec, vec);
+            const sim = cosineSim(queryVec, rowVector(row));
             if (sim >= minScore) {
                 results.push({
                     ...normalizeSymbol(row, db, hc),
@@ -39,62 +48,73 @@ export async function searchData(query, customDbPath, opts = {}) {
         db.close();
     }
 }
+/**
+ * Emit a warning for any query pair whose embeddings are nearly identical,
+ * since RRF would over-weight matches shared between them.
+ */
+function warnOnSimilarQueries(queries, queryVecs, threshold) {
+    for (let i = 0; i < queryVecs.length; i++) {
+        for (let j = i + 1; j < queryVecs.length; j++) {
+            const sim = cosineSim(queryVecs[i], queryVecs[j]);
+            if (sim >= threshold) {
+                warn(`Queries "${queries[i]}" and "${queries[j]}" are very similar ` +
+                    `(${(sim * 100).toFixed(0)}% cosine similarity). ` +
+                    `This may bias RRF results toward their shared matches. ` +
+                    `Consider using more distinct queries.`);
+            }
+        }
+    }
+}
+/** Rank stored rows for a single query, keeping only those above minScore. */
+function rankRowsForQuery(queryVec, rowVecs, minScore) {
+    const scored = [];
+    for (let ri = 0; ri < rowVecs.length; ri++) {
+        const sim = cosineSim(queryVec, rowVecs[ri]);
+        if (sim >= minScore) {
+            scored.push({ rowIndex: ri, similarity: sim });
+        }
+    }
+    scored.sort((a, b) => b.similarity - a.similarity);
+    return scored.map((item, rank) => ({ ...item, rank: rank + 1 }));
+}
+/** Reciprocal Rank Fusion across each query's ranked hits. */
+function fuseRankedHits(queries, perQueryRanked, k) {
+    const fusionMap = new Map();
+    for (let qi = 0; qi < queries.length; qi++) {
+        for (const item of perQueryRanked[qi]) {
+            if (!fusionMap.has(item.rowIndex)) {
+                fusionMap.set(item.rowIndex, { rrfScore: 0, queryScores: [] });
+            }
+            const entry = fusionMap.get(item.rowIndex);
+            entry.rrfScore += 1 / (k + item.rank);
+            entry.queryScores.push({
+                query: queries[qi],
+                similarity: item.similarity,
+                rank: item.rank,
+            });
+        }
+    }
+    return fusionMap;
+}
 export async function multiSearchData(queries, customDbPath, opts = {}) {
     const config = opts.config || loadConfig();
     const searchCfg = config.search || {};
     const limit = opts.limit ?? searchCfg.topK ?? 15;
     const minScore = opts.minScore ?? searchCfg.defaultMinScore ?? 0.2;
     const k = opts.rrfK ?? searchCfg.rrfK ?? 60;
+    const similarityWarnThreshold = searchCfg.similarityWarnThreshold ?? 0.85;
     const prepared = prepareSearch(customDbPath, opts);
     if (!prepared)
         return null;
     const { db, rows, modelKey, storedDim } = prepared;
     try {
         const { vectors: queryVecs, dim } = await embed(queries, modelKey ?? undefined);
-        const SIMILARITY_WARN_THRESHOLD = searchCfg.similarityWarnThreshold ?? 0.85;
-        for (let i = 0; i < queryVecs.length; i++) {
-            for (let j = i + 1; j < queryVecs.length; j++) {
-                const sim = cosineSim(queryVecs[i], queryVecs[j]);
-                if (sim >= SIMILARITY_WARN_THRESHOLD) {
-                    warn(`Queries "${queries[i]}" and "${queries[j]}" are very similar ` +
-                        `(${(sim * 100).toFixed(0)}% cosine similarity). ` +
-                        `This may bias RRF results toward their shared matches. ` +
-                        `Consider using more distinct queries.`);
-                }
-            }
-        }
-        if (storedDim && dim !== storedDim) {
-            console.log(`Warning: query model dimension (${dim}) doesn't match stored embeddings (${storedDim}).`);
-            console.log(`  Re-run \`codegraph embed\` with the same model, or use --model to match.`);
+        warnOnSimilarQueries(queries, queryVecs, similarityWarnThreshold);
+        if (checkDimensionMismatch(storedDim, dim))
             return null;
-        }
-        const rowVecs = rows.map((row) => new Float32Array(new Uint8Array(row.vector).buffer));
-        const perQueryRanked = queries.map((_query, qi) => {
-            const scored = [];
-            for (let ri = 0; ri < rows.length; ri++) {
-                const sim = cosineSim(queryVecs[qi], rowVecs[ri]);
-                if (sim >= minScore) {
-                    scored.push({ rowIndex: ri, similarity: sim });
-                }
-            }
-            scored.sort((a, b) => b.similarity - a.similarity);
-            return scored.map((item, rank) => ({ ...item, rank: rank + 1 }));
-        });
-        const fusionMap = new Map();
-        for (let qi = 0; qi < queries.length; qi++) {
-            for (const item of perQueryRanked[qi]) {
-                if (!fusionMap.has(item.rowIndex)) {
-                    fusionMap.set(item.rowIndex, { rrfScore: 0, queryScores: [] });
-                }
-                const entry = fusionMap.get(item.rowIndex);
-                entry.rrfScore += 1 / (k + item.rank);
-                entry.queryScores.push({
-                    query: queries[qi],
-                    similarity: item.similarity,
-                    rank: item.rank,
-                });
-            }
-        }
+        const rowVecs = rows.map(rowVector);
+        const perQueryRanked = queries.map((_q, qi) => rankRowsForQuery(queryVecs[qi], rowVecs, minScore));
+        const fusionMap = fuseRankedHits(queries, perQueryRanked, k);
         const hc = new Map();
         const results = [];
         for (const [rowIndex, entry] of fusionMap) {