@leanlabsinnov/codegraph 0.1.0 → 0.1.2

package/README.md

@@ -1,4 +1,4 @@
-# @cyrilc/codegraph
+# @leanlabsinnov/codegraph
 
 Live, queryable knowledge graph for your codebase. Indexes JS/TS into an embedded graph
 DB with vector embeddings, then exposes a local MCP server that Claude Code, Cursor, and
@@ -12,7 +12,7 @@ external services.
 ## Install
 
 ```bash
-npm i -g @cyrilc/codegraph
+npm i -g @leanlabsinnov/codegraph
 ```
 
 Requires Node 20+.
@@ -29,7 +29,7 @@ codegraph serve
 Then point Claude Code / Cursor / Windsurf at `http://127.0.0.1:3748/mcp` with the bearer
 token from `~/.codegraph/config.json`.
 
-See the full [README on GitHub](https://github.com/cyrilc/codegraph) for client setup, all
+See the full [README on GitHub](https://github.com/leanlabsinnov/codegraph) for client setup, all
 10 MCP tools, and troubleshooting.
 
 ## Commands

package/dist/bin.js

@@ -2,9 +2,9 @@
 import {
   buildProgram,
   renderError
-} from "./chunk-O4ZO6CP5.js";
+} from "./chunk-36AWRLQ6.js";
 import "./chunk-B2TIVKUB.js";
-import "./chunk-F5QKPRNW.js";
+import "./chunk-2TORJYBO.js";
 import "./chunk-XGPZDCQ4.js";
 
 // src/bin.ts

package/dist/{chunk-F5QKPRNW.js → chunk-2TORJYBO.js}

@@ -10,31 +10,38 @@ import { dirname, resolve } from "path";
 import * as kuzu from "kuzu";
 
 // ../graph-db/src/schema.ts
-var SYMBOL_COLUMNS = [
-  "id",
-  "kind",
-  "repoId",
-  "name",
-  "path",
-  "lineStart",
-  "lineEnd",
-  "signature",
-  "leadingComment",
-  "isExported",
+var SYMBOL_COLUMN_SPEC = {
+  id: "STRING",
+  kind: "STRING",
+  repoId: "STRING",
+  name: "STRING",
+  path: "STRING",
+  lineStart: "INT64",
+  lineEnd: "INT64",
+  signature: "STRING",
+  leadingComment: "STRING",
+  isExported: "BOOLEAN",
   // File-specific
-  "language",
-  "sizeBytes",
-  "contentHash",
+  language: "STRING",
+  sizeBytes: "INT64",
+  contentHash: "STRING",
   // Function-specific
-  "isAsync",
-  "isArrow",
+  isAsync: "BOOLEAN",
+  isArrow: "BOOLEAN",
   // Route-specific
-  "method",
-  "routePath",
-  "framework",
-  // Embedding
-  "embeddingNamespace"
-];
+  method: "STRING",
+  routePath: "STRING",
+  framework: "STRING",
+  // Embedding namespace tag
+  embeddingNamespace: "STRING"
+};
+var SYMBOL_COLUMNS = Object.keys(SYMBOL_COLUMN_SPEC);
+function defaultFor(column) {
+  const t = SYMBOL_COLUMN_SPEC[column];
+  if (t === "BOOLEAN") return false;
+  if (t === "INT64") return 0;
+  return "";
+}
 var EDGE_COLUMNS = ["line"];
 function buildSchemaStatements(opts) {
   const columnDefs = [
@@ -70,13 +77,7 @@ function buildSchemaStatements(opts) {
   }
   return statements;
 }
-function buildVectorIndexStatements() {
-  return [
-    "INSTALL VECTOR",
-    "LOAD EXTENSION VECTOR",
-    "CALL CREATE_VECTOR_INDEX('Symbol', 'embedding_idx', 'embedding', metric := 'cosine')"
-  ];
-}
+var SEMANTIC_SEARCH_MODE = "brute-force";
 var DEFAULT_EMBEDDING_DIMENSION = 1536;
 
 // ../graph-db/src/client.ts
@@ -88,7 +89,6 @@ var GraphDb = class {
   embeddingDimension;
   db = null;
   conn = null;
-  vectorIndexReady = false;
   /**
    * Cache of `conn.prepare()` results keyed by Cypher source. Kuzu's Node SDK requires a
    * prepared statement for any parameterized query - reusing the prepared object keeps
@@ -107,17 +107,8 @@ var GraphDb = class {
   }
   async close() {
     this.preparedCache.clear();
-    try {
-      this.conn?.close?.();
-    } catch {
-    }
-    try {
-      this.db?.close?.();
-    } catch {
-    }
     this.conn = null;
     this.db = null;
-    this.vectorIndexReady = false;
   }
   requireConn() {
     if (!this.conn) {
@@ -126,8 +117,11 @@ var GraphDb = class {
     return this.conn;
   }
   /**
-   * Idempotent migration. Runs all DDL through `IF NOT EXISTS` guards and tolerates the
-   * vector-index "already exists" error from re-runs.
+   * Idempotent migration: creates the `Symbol` node table and one REL table per
+   * `EdgeKind`. The `embedding FLOAT[N]` column lives on `Symbol` but we deliberately
+   * skip Kuzu's `CREATE_VECTOR_INDEX` - semantic search is brute-force via
+   * `array_cosine_similarity` to work around kuzudb/kuzu#5965 and kuzudb/kuzu#6040.
+   * See `schema.ts` for the full rationale.
    */
   async migrate() {
     await this.connect();
@@ -135,22 +129,6 @@ var GraphDb = class {
     for (const stmt of schemaStmts) {
       await this.exec(stmt);
     }
-    for (const stmt of buildVectorIndexStatements()) {
-      try {
-        await this.exec(stmt);
-      } catch (err) {
-        const message = err instanceof Error ? err.message : String(err);
-        if (isAlreadyExistsError(message)) continue;
-        if (/extension/i.test(message) && /(not found|missing|unsupported|disabled)/i.test(message)) {
-          console.warn(
-            `[codegraph] vector extension unavailable; semantic search disabled. Underlying: ${message}`
-          );
-          return;
-        }
-        throw new Error(`migrate failed on \`${stmt}\`: ${message}`);
-      }
-    }
-    this.vectorIndexReady = true;
   }
   /**
    * Typed Cypher escape hatch.
@@ -193,19 +171,39 @@ var GraphDb = class {
     return conn.execute(prepared, params);
   }
   /**
-   * Upserts nodes via batched UNWIND + MERGE. Kuzu requires every column we SET to exist
-   * in the schema, so each row is normalized to include every `SYMBOL_COLUMNS` field (NULL
-   * for fields not present).
+   * Inserts nodes via batched UNWIND + bare CREATE. The whole property map (including
+   * `embedding` when present) is set in the CREATE clause - we deliberately avoid `SET`
+   * because Kuzu rejects writes to an HNSW-indexed column even after the index is dropped
+   * (kuzudb/kuzu#6040). Callers must wipe pre-existing rows with `deleteByRepo` first.
+   *
+   * In-batch duplicates (same `id`) are coalesced to the last occurrence to keep CREATE
+   * from violating the primary-key uniqueness constraint.
    */
   async upsertNodes(nodes) {
     if (nodes.length === 0) return;
     await this.connect();
+    const deduped = dedupeById(nodes);
+    const withEmbedding = [];
+    const withoutEmbedding = [];
+    for (const n of deduped) {
+      if (Array.isArray(n.embedding) && n.embedding.length > 0) {
+        withEmbedding.push(n);
+      } else {
+        withoutEmbedding.push(n);
+      }
+    }
+    await this.createSymbolBatch(withoutEmbedding, false);
+    await this.createSymbolBatch(withEmbedding, true);
+  }
+  async createSymbolBatch(nodes, withEmbedding) {
+    if (nodes.length === 0) return;
     const BATCH = 200;
-    const setClause = SYMBOL_COLUMNS.filter((c) => c !== "id").map((c) => `n.${c} = r.${c}`).join(", ");
-    const cypher = `UNWIND $batch AS r MERGE (n:Symbol {id: r.id}) SET ${setClause}`;
+    const columns = [...SYMBOL_COLUMNS, ...withEmbedding ? ["embedding"] : []];
+    const propMap = columns.map((c) => `${c}: r.${c}`).join(", ");
+    const cypher = `UNWIND $batch AS r CREATE (n:Symbol {${propMap}})`;
     for (let i = 0; i < nodes.length; i += BATCH) {
       const slice = nodes.slice(i, i + BATCH);
-      const payload = slice.map(buildSymbolRow);
+      const payload = slice.map((n) => buildSymbolRow(n, withEmbedding, this.embeddingDimension));
       await this.exec(cypher, { batch: payload });
     }
   }
@@ -233,7 +231,7 @@ var GraphDb = class {
         const payload = slice.map((e) => ({
           fromId: e.fromId,
           toId: e.toId,
-          line: typeof e.line === "number" ? e.line : null
+          line: typeof e.line === "number" ? e.line : 0
         }));
         await this.exec(cypher, { batch: payload });
       }
@@ -292,22 +290,38 @@ var GraphDb = class {
     const coverage = total === 0 ? 0 : embedded / total;
     return { nodes, edges, embeddingCoverage: coverage };
   }
-  /** True once `migrate()` confirmed the vector extension is loaded. */
+  /**
+   * v0.1.x never creates an HNSW index - semantic search is brute-force via
+   * `array_cosine_similarity`. Always returns `false`. Kept on the surface so callers
+   * (e.g. `codegraph doctor`) can branch on a single boolean once the upstream Kuzu
+   * fixes ship and we flip the index back on.
+   */
   hasVectorIndex() {
-    return this.vectorIndexReady;
+    return false;
   }
 };
-function buildSymbolRow(node) {
+function buildSymbolRow(node, withEmbedding, embeddingDimension) {
   const src = node;
   const row = {};
   for (const col of SYMBOL_COLUMNS) {
     const value = src[col];
-    row[col] = value === void 0 ? null : value;
+    row[col] = value === void 0 || value === null ? defaultFor(col) : value;
   }
   row.id = node.id;
   row.kind = node.kind;
+  if (withEmbedding) {
+    const vec = node.embedding;
+    row.embedding = Array.isArray(vec) && vec.length === embeddingDimension ? vec : new Array(embeddingDimension).fill(0);
+  }
   return row;
 }
+function dedupeById(nodes) {
+  const seen = /* @__PURE__ */ new Map();
+  for (const n of nodes) {
+    seen.set(n.id, n);
+  }
+  return Array.from(seen.values());
+}
 function normalizeRow(row) {
   if (row instanceof Map) {
     const out = {};
@@ -343,17 +357,16 @@ async function collectAll(result) {
   if (typeof getAll !== "function") return [];
   return getAll.call(target);
 }
-function isAlreadyExistsError(message) {
-  return /already exists/i.test(message) || /already loaded/i.test(message) || /already installed/i.test(message) || /duplicate (table|index)/i.test(message);
-}
 
 export {
+  SYMBOL_COLUMN_SPEC,
   SYMBOL_COLUMNS,
+  defaultFor,
   EDGE_COLUMNS,
   buildSchemaStatements,
-  buildVectorIndexStatements,
+  SEMANTIC_SEARCH_MODE,
   DEFAULT_EMBEDDING_DIMENSION,
   defaultDbPath,
   GraphDb
 };
-//# sourceMappingURL=chunk-F5QKPRNW.js.map
+//# sourceMappingURL=chunk-2TORJYBO.js.map

package/dist/chunk-2TORJYBO.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../../graph-db/src/client.ts","../../graph-db/src/schema.ts"],"sourcesContent":["import { mkdir } from \"node:fs/promises\";\nimport { homedir } from \"node:os\";\nimport { dirname, resolve } from \"node:path\";\nimport { EDGE_KINDS, NODE_KINDS, type EdgeKind } from \"@codegraph/shared\";\nimport * as kuzu from \"kuzu\";\nimport {\n  DEFAULT_EMBEDDING_DIMENSION,\n  SYMBOL_COLUMNS,\n  buildSchemaStatements,\n  defaultFor,\n} from \"./schema.js\";\nimport type { QueryResult, UpsertEdgeInput, UpsertNodeInput } from \"./types.js\";\n\nexport interface GraphDbOptions {\n  /** Directory where Kuzu stores its on-disk database files. Defaults to `~/.codegraph/graph`. */\n  dbPath?: string;\n  /**\n   * Legacy `url` option kept for back-compat with Phase-1 callers. Ignored at runtime -\n   * Kuzu is embedded - but accepted so existing call sites compile while the rest of the\n   * codebase migrates to `dbPath`.\n   */\n  url?: string;\n  /** Vector dimension for the `Symbol.embedding` column. Baked into the schema at create time. */\n  embeddingDimension?: number;\n}\n\n/** Default on-disk location for the embedded graph. */\nexport function defaultDbPath(): string {\n  return resolve(homedir(), \".codegraph\", \"graph\");\n}\n\n/**\n * Thin, typed wrapper around the embedded Kuzu database.\n *\n * Public surface (intentionally identical to the Phase-1 FalkorDB client so callers don't\n * change): connect / close / migrate / query / upsertNodes / upsertEdges / deleteByRepo /\n * stats. Internals are pure Kuzu.\n */\nexport class GraphDb {\n  private readonly dbPath: string;\n  private readonly embeddingDimension: number;\n  private db: kuzu.Database | null = null;\n  private conn: kuzu.Connection | null = null;\n  /**\n   * Cache of `conn.prepare()` results keyed by Cypher source. Kuzu's Node SDK requires a\n   * prepared statement for any parameterized query - reusing the prepared object keeps\n   * UNWIND-batched upserts fast.\n   */\n  private preparedCache = new Map<string, kuzu.PreparedStatement>();\n\n  constructor(opts: GraphDbOptions = {}) {\n    this.dbPath = opts.dbPath ?? defaultDbPath();\n    this.embeddingDimension = opts.embeddingDimension ?? DEFAULT_EMBEDDING_DIMENSION;\n  }\n\n  async connect(): Promise<void> {\n    if (this.conn) return;\n    await mkdir(dirname(this.dbPath), { recursive: true });\n    this.db = new kuzu.Database(this.dbPath);\n    this.conn = new kuzu.Connection(this.db);\n  }\n\n  async close(): Promise<void> {\n    // We deliberately do NOT call `conn.close()` / `db.close()` on Kuzu's Node bindings.\n    // In 0.11.x those native handles are also disposed by the binding's process-exit hook,\n    // and double-disposing can SIGSEGV the worker on cleanup. Dropping references is\n    // enough for the GC to release the underlying memory before the process exits.\n    this.preparedCache.clear();\n    this.conn = null;\n    this.db = null;\n  }\n\n  private requireConn(): kuzu.Connection {\n    if (!this.conn) {\n      throw new Error(\"GraphDb not connected. Call connect() first.\");\n    }\n    return this.conn;\n  }\n\n  /**\n   * Idempotent migration: creates the `Symbol` node table and one REL table per\n   * `EdgeKind`. The `embedding FLOAT[N]` column lives on `Symbol` but we deliberately\n   * skip Kuzu's `CREATE_VECTOR_INDEX` - semantic search is brute-force via\n   * `array_cosine_similarity` to work around kuzudb/kuzu#5965 and kuzudb/kuzu#6040.\n   * See `schema.ts` for the full rationale.\n   */\n  async migrate(): Promise<void> {\n    await this.connect();\n    const schemaStmts = buildSchemaStatements({ embeddingDimension: this.embeddingDimension });\n    for (const stmt of schemaStmts) {\n      await this.exec(stmt);\n    }\n  }\n\n  /**\n   * Typed Cypher escape hatch.\n   *\n   * Kuzu returns BIGINT columns as native BigInt; we coerce to plain `number` when safe so\n   * downstream JSON serialization (MCP responses, snapshot tests) does not need bespoke\n   * handling.\n   */\n  async query<T = Record<string, unknown>>(\n    cypher: string,\n    params: Record<string, unknown> = {},\n  ): Promise<QueryResult<T>> {\n    const result = await this.runQuery(cypher, params);\n    const raw = await collectAll(result);\n    const data = raw.map((row) => normalizeRow(row)) as T[];\n    const headers = raw.length > 0 ? Object.keys(raw[0] ?? {}) : [];\n    return { data, headers, metadata: [] };\n  }\n\n  /** Fire-and-forget DDL/exec. */\n  private async exec(cypher: string, params: Record<string, unknown> = {}): Promise<void> {\n    await this.runQuery(cypher, params);\n  }\n\n  /**\n   * Bridge to Kuzu's two execution paths:\n   * - `conn.query(stmt)` for unparameterized statements (the second positional arg is a\n   *   `progressCallback`, NOT params - mistaking that is the #1 way to confuse the API).\n   * - `conn.prepare(stmt) + conn.execute(prepared, params)` for anything with `$name`\n   *   placeholders. We cache the prepared statement so UNWIND batches reuse it.\n   */\n  private async runQuery(cypher: string, params: Record<string, unknown>): Promise<unknown> {\n    const conn = this.requireConn();\n    if (Object.keys(params).length === 0) {\n      return conn.query(cypher);\n    }\n    let prepared = this.preparedCache.get(cypher);\n    if (!prepared) {\n      prepared = await conn.prepare(cypher);\n      if (!prepared.isSuccess()) {\n        throw new Error(prepared.getErrorMessage());\n      }\n      this.preparedCache.set(cypher, prepared);\n    }\n    // Cast through `unknown`: Kuzu's bindings advertise a strict `KuzuValue` union, but\n    // we can pass through any JSON-serializable value the embedded engine accepts (nested\n    // structs and lists are converted at the native layer).\n    return conn.execute(prepared, params as unknown as Parameters<kuzu.Connection[\"execute\"]>[1]);\n  }\n\n  /**\n   * Inserts nodes via batched UNWIND + bare CREATE. The whole property map (including\n   * `embedding` when present) is set in the CREATE clause - we deliberately avoid `SET`\n   * because Kuzu rejects writes to an HNSW-indexed column even after the index is dropped\n   * (kuzudb/kuzu#6040). Callers must wipe pre-existing rows with `deleteByRepo` first.\n   *\n   * In-batch duplicates (same `id`) are coalesced to the last occurrence to keep CREATE\n   * from violating the primary-key uniqueness constraint.\n   */\n  async upsertNodes(nodes: UpsertNodeInput[]): Promise<void> {\n    if (nodes.length === 0) return;\n    await this.connect();\n    const deduped = dedupeById(nodes);\n    const withEmbedding: UpsertNodeInput[] = [];\n    const withoutEmbedding: UpsertNodeInput[] = [];\n    for (const n of deduped) {\n      if (Array.isArray(n.embedding) && n.embedding.length > 0) {\n        withEmbedding.push(n);\n      } else {\n        withoutEmbedding.push(n);\n      }\n    }\n    await this.createSymbolBatch(withoutEmbedding, false);\n    await this.createSymbolBatch(withEmbedding, true);\n  }\n\n  private async createSymbolBatch(\n    nodes: UpsertNodeInput[],\n    withEmbedding: boolean,\n  ): Promise<void> {\n    if (nodes.length === 0) return;\n    const BATCH = 200;\n    const columns = [...SYMBOL_COLUMNS, ...(withEmbedding ? ([\"embedding\"] as const) : [])];\n    const propMap = columns.map((c) => `${c}: r.${c}`).join(\", \");\n    const cypher = `UNWIND $batch AS r CREATE (n:Symbol {${propMap}})`;\n    for (let i = 0; i < nodes.length; i += BATCH) {\n      const slice = nodes.slice(i, i + BATCH);\n      const payload = slice.map((n) => buildSymbolRow(n, withEmbedding, this.embeddingDimension));\n      await this.exec(cypher, { batch: payload });\n    }\n  }\n\n  /**\n   * Upserts edges. Both endpoints must already exist as `Symbol` nodes; rows where the\n   * MATCH fails are silently dropped, matching Cypher semantics.\n   *\n   * Uses CREATE because the orchestrator wipes the repo's slice before writing, so\n   * duplicates can't pre-exist within a single index pass.\n   */\n  async upsertEdges(edges: UpsertEdgeInput[]): Promise<void> {\n    if (edges.length === 0) return;\n    await this.connect();\n    const byKind = new Map<EdgeKind, UpsertEdgeInput[]>();\n    for (const e of edges) {\n      const bucket = byKind.get(e.kind);\n      if (bucket) bucket.push(e);\n      else byKind.set(e.kind, [e]);\n    }\n    const BATCH = 500;\n    for (const [kind, batch] of byKind) {\n      const cypher = `UNWIND $batch AS r MATCH (a:Symbol {id: r.fromId}) MATCH (b:Symbol {id: r.toId}) CREATE (a)-[e:${kind} {line: r.line}]->(b)`;\n      for (let i = 0; i < batch.length; i += BATCH) {\n        const slice = batch.slice(i, i + BATCH);\n        // Use 0 (not null) for missing line numbers so Kuzu can infer the struct field\n        // as INT64 even when an entire batch happens to have no `line` set.\n        const payload = slice.map((e) => ({\n          fromId: e.fromId,\n          toId: e.toId,\n          line: typeof e.line === \"number\" ? e.line : 0,\n        }));\n        await this.exec(cypher, { batch: payload });\n      }\n    }\n  }\n\n  /**\n   * Deletes all nodes (and incident edges via DETACH DELETE) for a repo. If `paths` is\n   * provided, restricts the delete to nodes whose `path` is in the list - used by\n   * incremental re-indexing.\n   */\n  async deleteByRepo(repoId: string, paths?: string[]): Promise<void> {\n    await this.connect();\n    if (paths && paths.length > 0) {\n      await this.exec(\n        \"MATCH (n:Symbol) WHERE n.repoId = $repoId AND n.path IN $paths DETACH DELETE n\",\n        { repoId, paths },\n      );\n      return;\n    }\n    await this.exec(\"MATCH (n:Symbol) WHERE n.repoId = $repoId DETACH DELETE n\", { repoId });\n  }\n\n  /**\n   * Returns counts of nodes (per kind) and edges (per kind) for a repo, plus the share of\n   * non-File nodes that carry an embedding.\n   */\n  async stats(repoId: string): Promise<{\n    nodes: Record<string, number>;\n    edges: Record<string, number>;\n    embeddingCoverage: number;\n  }> {\n    await this.connect();\n    const nodes: Record<string, number> = {};\n    for (const kind of NODE_KINDS) {\n      const r = await this.query<{ count: number }>(\n        \"MATCH (n:Symbol) WHERE n.repoId = $repoId AND n.kind = $kind RETURN count(n) AS count\",\n        { repoId, kind },\n      );\n      nodes[kind] = Number(r.data[0]?.count ?? 0);\n    }\n    const edges: Record<string, number> = {};\n    for (const kind of EDGE_KINDS) {\n      const r = await this.query<{ count: number }>(\n        `MATCH (a:Symbol)-[r:${kind}]->(b:Symbol)\n           WHERE a.repoId = $repoId AND b.repoId = $repoId\n           RETURN count(r) AS count`,\n        { repoId },\n      );\n      edges[kind] = Number(r.data[0]?.count ?? 0);\n    }\n    const cov = await this.query<{ total: number | bigint; embedded: number | bigint }>(\n      `MATCH (n:Symbol)\n         WHERE n.repoId = $repoId AND n.kind <> 'File'\n         RETURN count(n) AS total,\n                count(n.embedding) AS embedded`,\n      { repoId },\n    );\n    const row = cov.data[0];\n    const total = Number(row?.total ?? 0);\n    const embedded = Number(row?.embedded ?? 0);\n    const coverage = total === 0 ? 0 : embedded / total;\n    return { nodes, edges, embeddingCoverage: coverage };\n  }\n\n  /**\n   * v0.1.x never creates an HNSW index - semantic search is brute-force via\n   * `array_cosine_similarity`. Always returns `false`. Kept on the surface so callers\n   * (e.g. `codegraph doctor`) can branch on a single boolean once the upstream Kuzu\n   * fixes ship and we flip the index back on.\n   */\n  hasVectorIndex(): boolean {\n    return false;\n  }\n}\n\n/**\n * Build a fully-populated row for a Kuzu UNWIND batch. Every column in `SYMBOL_COLUMNS`\n * is present (typed default when missing) so Kuzu can infer a homogeneous struct schema\n * for the batch parameter. When `withEmbedding` is true the `embedding` field is also\n * populated - we either use the provided vector or a zero-vector of the configured\n * dimension so the struct schema stays uniform across the batch.\n */\nfunction buildSymbolRow(\n  node: UpsertNodeInput,\n  withEmbedding: boolean,\n  embeddingDimension: number,\n): Record<string, unknown> {\n  const src = node as unknown as Record<string, unknown>;\n  const row: Record<string, unknown> = {};\n  for (const col of SYMBOL_COLUMNS) {\n    const value = src[col];\n    row[col] = value === undefined || value === null ? defaultFor(col) : value;\n  }\n  row.id = node.id;\n  row.kind = node.kind;\n  if (withEmbedding) {\n    const vec = node.embedding;\n    row.embedding =\n      Array.isArray(vec) && vec.length === embeddingDimension\n        ? vec\n        : new Array<number>(embeddingDimension).fill(0);\n  }\n  return row;\n}\n\n/**\n * Coalesce same-id rows down to the last occurrence. Required because we now use bare\n * CREATE (not MERGE) for inserts and Kuzu rejects primary-key collisions inside a single\n * UNWIND batch.\n */\nfunction dedupeById(nodes: UpsertNodeInput[]): UpsertNodeInput[] {\n  const seen = new Map<string, UpsertNodeInput>();\n  for (const n of nodes) {\n    seen.set(n.id, n);\n  }\n  return Array.from(seen.values());\n}\n\n/** Convert Kuzu's row representation (Map or plain object) into a plain JSON object. */\nfunction normalizeRow(row: unknown): Record<string, unknown> {\n  if (row instanceof Map) {\n    const out: Record<string, unknown> = {};\n    for (const [k, v] of row) {\n      out[String(k)] = coerceValue(v);\n    }\n    return out;\n  }\n  if (row && typeof row === \"object\") {\n    const src = row as Record<string, unknown>;\n    const out: Record<string, unknown> = {};\n    for (const k of Object.keys(src)) {\n      out[k] = coerceValue(src[k]);\n    }\n    return out;\n  }\n  return { value: coerceValue(row) };\n}\n\n/**\n * Kuzu returns BIGINT columns as JS BigInt. Coerce to `number` when within Number.MAX_SAFE\n * for JSON-friendly downstream consumption.\n */\nfunction coerceValue(value: unknown): unknown {\n  if (typeof value === \"bigint\") {\n    if (value <= BigInt(Number.MAX_SAFE_INTEGER) && value >= BigInt(Number.MIN_SAFE_INTEGER)) {\n      return Number(value);\n    }\n    return value.toString();\n  }\n  if (Array.isArray(value)) return value.map(coerceValue);\n  return value;\n}\n\n/** Drain a Kuzu QueryResult (or array of them) into an array of row objects. */\nasync function collectAll(result: unknown): Promise<unknown[]> {\n  // Multi-statement queries return an array; we keep only the last one (matches how the\n  // final statement is the one that carries a `RETURN`).\n  const target = Array.isArray(result) ? result[result.length - 1] : result;\n  if (!target) return [];\n  const getAll = (target as { getAll?: () => Promise<unknown[]> }).getAll;\n  if (typeof getAll !== \"function\") return [];\n  return getAll.call(target);\n}\n\n","import { EDGE_KINDS } from \"@codegraph/shared\";\n\n/**\n * Kuzu is schema-first. Unlike FalkorDB which is schema-less, every column we ever want to\n * SET on a node must exist up-front. We use ONE `Symbol` node table with a `kind` column\n * (Kuzu does not support multi-labels), and one REL table per `EdgeKind`.\n *\n * Columns are the union of every field across the `GraphNode` discriminated union in\n * `@codegraph/shared` plus the two embedding-namespace fields. Fields that are not\n * relevant to a given kind stay NULL.\n */\n\n/**\n * Per-column metadata so the upserter can build batches with explicit typed defaults.\n *\n * Kuzu's struct parameter type inference fails when a column is null on every row in a\n * batch (it defaults to STRING and rejects assignment to a BOOL/INT64 column). Concrete\n * defaults keep inference deterministic and let us skip clunky CAST() clauses.\n *\n * Convention: optional booleans default to `false`, optional ints to `0`, optional strings\n * to `\"\"`. We never check `WHERE n.foo IS NULL` in queries, so the lost null-distinction\n * is acceptable for v0.1.0.\n */\nexport const SYMBOL_COLUMN_SPEC = {\n  id: \"STRING\",\n  kind: \"STRING\",\n  repoId: \"STRING\",\n  name: \"STRING\",\n  path: \"STRING\",\n  lineStart: \"INT64\",\n  lineEnd: \"INT64\",\n  signature: \"STRING\",\n  leadingComment: \"STRING\",\n  isExported: \"BOOLEAN\",\n  // File-specific\n  language: \"STRING\",\n  sizeBytes: \"INT64\",\n  contentHash: \"STRING\",\n  // Function-specific\n  isAsync: \"BOOLEAN\",\n  isArrow: \"BOOLEAN\",\n  // Route-specific\n  method: \"STRING\",\n  routePath: \"STRING\",\n  framework: \"STRING\",\n  // Embedding namespace tag\n  embeddingNamespace: \"STRING\",\n} as const;\n\nexport type SymbolColumn = keyof typeof SYMBOL_COLUMN_SPEC;\n\nexport const SYMBOL_COLUMNS = Object.keys(SYMBOL_COLUMN_SPEC) as SymbolColumn[];\n\n/** Return the typed default for an unset optional column. */\nexport function defaultFor(column: SymbolColumn): unknown {\n  const t = SYMBOL_COLUMN_SPEC[column];\n  if (t === \"BOOLEAN\") return false;\n  if (t === \"INT64\") return 0;\n  return \"\";\n}\n\n/** Optional per-edge metadata. Currently only `line`. */\nexport const EDGE_COLUMNS = [\"line\"] as const;\n\nexport type EdgeColumn = (typeof EDGE_COLUMNS)[number];\n\n/**\n * DDL statements that bring an empty Kuzu database to the codegraph schema.\n * `IF NOT EXISTS` makes `migrate()` idempotent so it can run on every connect.\n *\n * `embedding` is a fixed-dimension column - dimension is configured at migrate time and\n * baked into the schema. If a user later switches to an embedding provider with a\n * different dimension they must delete the on-disk graph directory to recreate it. The\n * embedding-namespace tag ensures we never silently mix dimensions.\n */\nexport function buildSchemaStatements(opts: { embeddingDimension: number }): string[] {\n  const columnDefs = [\n    \"id STRING\",\n    \"kind STRING\",\n    \"repoId STRING\",\n    \"name STRING\",\n    \"path STRING\",\n    \"lineStart INT64\",\n    \"lineEnd INT64\",\n    \"signature STRING\",\n    \"leadingComment STRING\",\n    \"isExported BOOLEAN\",\n    \"language STRING\",\n    \"sizeBytes INT64\",\n    \"contentHash STRING\",\n    \"isAsync BOOLEAN\",\n    \"isArrow BOOLEAN\",\n    \"method STRING\",\n    \"routePath STRING\",\n    \"framework STRING\",\n    \"embeddingNamespace STRING\",\n    `embedding FLOAT[${opts.embeddingDimension}]`,\n    \"PRIMARY KEY (id)\",\n  ];\n  const statements: string[] = [\n    `CREATE NODE TABLE IF NOT EXISTS Symbol(${columnDefs.join(\", \")})`,\n  ];\n  for (const kind of EDGE_KINDS) {\n    statements.push(\n      `CREATE REL TABLE IF NOT EXISTS ${kind}(FROM Symbol TO Symbol, line INT64)`,\n    );\n  }\n  return statements;\n}\n\n/**\n * Semantic search in v0.1.x is intentionally brute-force via Kuzu's built-in\n * `array_cosine_similarity` function - we do NOT create an HNSW vector index.\n *\n * Why: Kuzu 0.11.x has two open issues that make the HNSW path unusable for a\n * mutable graph workload:\n *  - kuzudb/kuzu#5965: SET on a vector-indexed column is rejected with\n *    \"Cannot set property vec in table embeddings because it is used in one or more\n *    indexes\". The Kuzu team's own recommended workaround in that thread is\n *    \"delay creation of the index itself\".\n *  - kuzudb/kuzu#6040: DROP_VECTOR_INDEX leaves stale on-disk metadata, so once a\n *    column has ever been indexed it becomes permanently un-writable - even fresh\n *    CREATEs fail with \"Catalog exception: _N_<index>_UPPER does not exist\".\n *\n * `array_cosine_similarity` is a core Kuzu function (not part of the vector extension)\n * and runs in microseconds for the corpus sizes Phase 1 targets. We will switch back\n * to `CALL CREATE_VECTOR_INDEX` / `QUERY_VECTOR_INDEX` once the upstream fixes ship.\n */\nexport const SEMANTIC_SEARCH_MODE = \"brute-force\" as const;\n\n/** Default embedding dimension when none is supplied. 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package/dist/{chunk-O4ZO6CP5.js → chunk-36AWRLQ6.js}

@@ -5,7 +5,7 @@ import {
 import {
   GraphDb,
   defaultDbPath
-} from "./chunk-F5QKPRNW.js";
+} from "./chunk-2TORJYBO.js";
 import {
   DEFAULT_CONFIG,
   LLM_PRESETS,
@@ -433,16 +433,19 @@ async function selfTestKuzu(dbPath, embeddingDimension) {
   try {
     await db.connect();
     await db.migrate();
-    const result = await db.query("RETURN 1 AS result");
+    const result = await db.query(
+      `RETURN array_cosine_similarity([1.0, 0.0], [1.0, 0.0]) AS similarity, true AS ok`
+    );
     await db.close();
-    if (result.data[0]?.result === 1) {
-      return {
-        name: "kuzu round-trip",
-        status: db.hasVectorIndex() ? "ok" : "warn",
-        detail: db.hasVectorIndex() ? "ok (vector index ready)" : "ok (vector extension missing; semantic search disabled)"
-      };
+    const row = result.data[0];
+    if (row?.ok !== true || typeof row.similarity !== "number") {
+      return { name: "kuzu round-trip", status: "fail", detail: "unexpected result" };
     }
-    return { name: "kuzu round-trip", status: "fail", detail: "unexpected result" };
+    return {
+      name: "kuzu round-trip",
+      status: "ok",
+      detail: "ok (brute-force semantic search ready)"
+    };
   } catch (err) {
     await db.close().catch(() => {
     });
@@ -1327,19 +1330,25 @@ async function indexRepo(opts) {
     edges: allEdges,
     knownFilePaths
   });
-  await opts.graphDb.deleteByRepo(opts.repoId);
-  await opts.graphDb.upsertNodes(allNodes);
-  await opts.graphDb.upsertEdges(resolved);
-  opts.onProgress?.({ type: "upsert", nodes: allNodes.length, edges: resolved.length });
-  let embeddingCount = 0;
+  let embeddedById = /* @__PURE__ */ new Map();
   if (!opts.skipEmbeddings && opts.router) {
     const embedded = await embedNodes(allNodes, {
       router: opts.router,
       onBatch: ({ embedded: embedded2, total }) => opts.onProgress?.({ type: "embed", embedded: embedded2, total })
     });
-    await persistEmbeddings(opts.graphDb, embedded);
-    embeddingCount = embedded.length;
+    embeddedById = new Map(embedded.map((e) => [e.id, e]));
   }
+  const nodePayload = allNodes.map((n) => {
+    const e = embeddedById.get(n.id);
+    const base = n;
+    if (!e) return base;
+    return { ...base, embedding: e.embedding, embeddingNamespace: e.embeddingNamespace };
+  });
+  await opts.graphDb.deleteByRepo(opts.repoId);
+  await opts.graphDb.upsertNodes(nodePayload);
+  await opts.graphDb.upsertEdges(resolved);
+  opts.onProgress?.({ type: "upsert", nodes: allNodes.length, edges: resolved.length });
+  const embeddingCount = embeddedById.size;
   return {
     durationMs: Date.now() - start,
     parsedFiles: parsedCount - failed,
@@ -1350,22 +1359,6 @@ async function indexRepo(opts) {
     droppedEdges: dropped
   };
 }
-async function persistEmbeddings(graphDb, embedded) {
-  if (embedded.length === 0) return;
-  const BATCH = 100;
-  for (let i = 0; i < embedded.length; i += BATCH) {
-    const batch = embedded.slice(i, i + BATCH);
-    await graphDb.query(
-      `
-        UNWIND $batch AS e
-        MATCH (n:Symbol { id: e.id })
-        SET n.embedding = e.embedding,
-            n.embeddingNamespace = e.embeddingNamespace
-      `,
-      { batch }
-    );
-  }
-}
 async function runWithConcurrency(items, concurrency, fn) {
   let cursor = 0;
   const runners = Array.from({ length: Math.min(concurrency, items.length) }, async () => {
@@ -2004,14 +1997,16 @@ var searchSemanticTool = {
       );
     }
     const namespace = `${deps.llm.embeddingNamespace.provider}:${deps.llm.embeddingNamespace.model}:${deps.llm.embeddingNamespace.dimension}`;
+    const dim = deps.llm.embeddingNamespace.dimension;
     return cachedJsonResult("search_semantic", { description, k, namespace }, deps, async () => {
       const rows = await deps.graph.query(
-        `CALL QUERY_VECTOR_INDEX('Symbol', 'embedding_idx', $vec, $k)
-           WITH node, distance
-           WHERE node.embeddingNamespace = $ns
-           RETURN node.id AS id, node.name AS name, node.kind AS kind, node.path AS path,
-                  node.lineStart AS line, node.signature AS signature, distance AS score
-           ORDER BY distance ASC`,
+        `MATCH (s:Symbol)
+           WHERE s.embeddingNamespace = $ns
+           RETURN s.id AS id, s.name AS name, s.kind AS kind, s.path AS path,
+                  s.lineStart AS line, s.signature AS signature,
+                  array_cosine_similarity(s.embedding, CAST($vec AS FLOAT[${dim}])) AS score
+           ORDER BY score DESC
+           LIMIT $k`,
         { vec: embedding, k, ns: namespace }
       );
       return { description, k, namespace, count: rows.length, matches: rows };
@@ -2299,7 +2294,7 @@ async function startMcpServer(portOrOptions) {
 async function loadGraphClient(dbPath) {
   let mod;
   try {
-    mod = await import("./src-467W2KXC.js");
+    mod = await import("./src-PDNTANJD.js");
   } catch (err) {
     throw new Error(
       `Failed to import @codegraph/graph-db. Run \`pnpm -r build\` first. Underlying error: ${err instanceof Error ? err.message : String(err)}`
@@ -2336,8 +2331,10 @@ async function loadLlmRouter(configPath2) {
     throw new Error("@codegraph/llm-router has no `createLlmRouter` export.");
   }
   const fileConfig = await readCodegraphConfig(configPath2);
+  const llmConfig = fileConfig.llm ?? void 0;
+  const effectiveConfig = llmConfig && llmConfig.generation && llmConfig.embeddings ? llmConfig : DEFAULT_CONFIG.llm;
   const router = await createLlmRouter2({
-    config: fileConfig.llm ?? void 0,
+    config: effectiveConfig,
     configPath: configPath2
   });
   return adaptLlmRouter(router);
@@ -2397,7 +2394,7 @@ shutting down (${signal})...
 // src/program.ts
 function buildProgram() {
   const program = new Command();
-  program.name("codegraph").description("Live, queryable knowledge graph for your codebase").version("0.1.0").option("--verbose", "Print full stack traces on error").hook("preAction", (thisCommand) => {
+  program.name("codegraph").description("Live, queryable knowledge graph for your codebase").version("0.1.2").option("--verbose", "Print full stack traces on error").hook("preAction", (thisCommand) => {
     const opts = thisCommand.optsWithGlobals();
     if (opts.verbose) process.env.CODEGRAPH_VERBOSE = "1";
   });
@@ -2443,4 +2440,4 @@ export {
   renderError,
   buildProgram
 };
-//# sourceMappingURL=chunk-O4ZO6CP5.js.map
+//# sourceMappingURL=chunk-36AWRLQ6.js.map