diff --git a/.opencode/package.json b/.opencode/package.json
index 5ffa908..b9c3f07 100644
--- a/.opencode/package.json
+++ b/.opencode/package.json
@@ -3,4 +3,4 @@
   "dependencies": {
     "@opencode-ai/plugin": "1.3.17"
   }
-}
\ No newline at end of file
+}
diff --git a/src/agent-tools/graphExplorer.ts b/src/agent-tools/graphExplorer.ts
index 009478c..75d4976 100644
--- a/src/agent-tools/graphExplorer.ts
+++ b/src/agent-tools/graphExplorer.ts
@@ -42,7 +42,7 @@ export function createGraphExplorerTool(graph: Graph) {
         if (nodeAttr.file) result += `- File: ${nodeAttr.file}\n`;
         result += `\nConnected parts:\n`;
 
-        neighbors.forEach((neighbor) => {
+        neighbors.forEach((neighbor: string) => {
           const attr = graph.getNodeAttributes(neighbor);
           const edges = graph.edges(nodeId, neighbor);
           const edgeAttr = graph.getEdgeAttributes(edges[0]);
diff --git a/src/agent-tools/reranker.ts b/src/agent-tools/reranker.ts
index 19c9376..022ba7a 100644
--- a/src/agent-tools/reranker.ts
+++ b/src/agent-tools/reranker.ts
@@ -3,7 +3,7 @@
  * Uses Ollama's reranker API to score documents against a query.
  */
 
-import { RERANKER_MODEL } from "../constants";
+import { RERANKER_MODEL } from "../constants.js";
 
 const OLLAMA_HOST = process.env.OLLAMA_HOST || "http://localhost:11434";
 
diff --git a/src/agent.ts b/src/agent.ts
index 1763664..c26451e 100644
--- a/src/agent.ts
+++ b/src/agent.ts
@@ -11,13 +11,13 @@ import {
   createGetSectionContentTool,
   createGraphExplorerTool,
   createSearchSpecSectionsTool,
-} from "./agent-tools";
+} from "./agent-tools/index.js";
 import {
   CONFIG_FILE,
   EMBEDDING_MODEL,
   GRAPH_FILE,
   STORAGE_DIR,
-} from "./constants";
+} from "./constants.js";
 
 const embeddings = new OllamaEmbeddings({
   model: EMBEDDING_MODEL,
diff --git a/src/setup/ingest.ts b/src/setup/ingest.ts
index da11d64..bb4a75c 100644
--- a/src/setup/ingest.ts
+++ b/src/setup/ingest.ts
@@ -8,9 +8,9 @@ import { OllamaEmbeddings } from "@langchain/ollama";
 import * as cheerio from "cheerio";
 import { glob } from "glob";
 import ora from "ora";
-import { EMBEDDING_MODEL, SPEC_DIR, STORAGE_DIR } from "../constants";
-import { HTMLTextSplitter } from "./text-splitters";
-import { formatForIngestion } from "./utils/formatHTMLForIngestion";
+import { EMBEDDING_MODEL, SPEC_DIR, STORAGE_DIR } from "../constants.js";
+import { HTMLTextSplitter } from "./text-splitters/index.js";
+import { formatForIngestion } from "./utils/formatHTMLForIngestion.js";
 
 const embeddings = new OllamaEmbeddings({
   model: EMBEDDING_MODEL,
diff --git a/src/setup/text-splitters/HtmlTextSplitter.test.ts b/src/setup/text-splitters/HtmlTextSplitter.test.ts
index df2ea4c..8948d94 100644
--- a/src/setup/text-splitters/HtmlTextSplitter.test.ts
+++ b/src/setup/text-splitters/HtmlTextSplitter.test.ts
@@ -1,6 +1,6 @@
 import { describe, expect, test } from "bun:test";
 import { Document } from "@langchain/core/documents";
-import { HTMLTextSplitter } from "./index";
+import { HTMLTextSplitter } from "./index.js";
 
 describe("HTMLTextSplitter", () => {
   test("keeps small HTML in a single chunk", async () => {
diff --git a/src/setup/text-splitters/index.ts b/src/setup/text-splitters/index.ts
index d9d4edf..aaf48ec 100644
--- a/src/setup/text-splitters/index.ts
+++ b/src/setup/text-splitters/index.ts
@@ -1 +1 @@
-export * from "./HtmlTextSplitter";
+export * from "./HtmlTextSplitter.js";
diff --git a/src/setup/utils/formatHTMLForIngestion.test.ts b/src/setup/utils/formatHTMLForIngestion.test.ts
index 93ab052..8c91a1f 100644
--- a/src/setup/utils/formatHTMLForIngestion.test.ts
+++ b/src/setup/utils/formatHTMLForIngestion.test.ts
@@ -9,7 +9,7 @@ import {
   convertTablesToMarkdown,
   DEFAULT_CONFIG,
   formatForIngestion,
-} from "./formatHTMLForIngestion";
+} from "./formatHTMLForIngestion.js";
 
 describe("formatHTMLForIngestion", () => {
   describe("convertLinksToMarkdown", () => {
diff --git a/src/test/manual/test-search-spec-sections.ts b/src/test/manual/test-search-spec-sections.ts
index d3c7584..a02ae52 100644
--- a/src/test/manual/test-search-spec-sections.ts
+++ b/src/test/manual/test-search-spec-sections.ts
@@ -13,8 +13,8 @@
 
 import * as lancedbSdk from "@lancedb/lancedb";
 import { OllamaEmbeddings } from "@langchain/ollama";
-import { createSearchSpecSectionsTool } from "../../agent-tools";
-import { EMBEDDING_MODEL, STORAGE_DIR } from "../../constants";
+import { createSearchSpecSectionsTool } from "../../agent-tools/index.js";
+import { EMBEDDING_MODEL, STORAGE_DIR } from "../../constants.js";
 
 async function main() {
   // Get query from command line or use default
@@ -43,7 +43,7 @@ async function main() {
     console.log("✓ Tool created\n");
 
     console.log("Executing tool...\n");
-    const result = await searchSpecSectionsTool.func({ query });
+    const result = await searchSpecSectionsTool({ query });
 
     console.log("=== TOOL OUTPUT ===");
     console.log(result);
diff --git a/src/test/manual/verify-db.ts b/src/test/manual/verify-db.ts
index ab52558..b73b034 100644
--- a/src/test/manual/verify-db.ts
+++ b/src/test/manual/verify-db.ts
@@ -21,7 +21,7 @@ import type { Table } from "@lancedb/lancedb";
 import * as lancedbSdk from "@lancedb/lancedb";
 import { OllamaEmbeddings } from "@langchain/ollama";
 import { Command } from "commander";
-import { EMBEDDING_MODEL, STORAGE_DIR } from "../../constants";
+import { EMBEDDING_MODEL, STORAGE_DIR } from "../../constants.js";
 
 const embeddings = new OllamaEmbeddings({
   model: EMBEDDING_MODEL,