diff --git a/AGENTS.md b/AGENTS.md
index 47d49c3..0b8528f 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -21,26 +21,27 @@ Users ask questions like: *"How does the if statement work?"* or *"Which functio
 
 ```
 ask262/
-├── agent.ts                  # Main ReAct agent - answers user queries
-├── agent-tools/              # Tool implementations (spec retriever, graph explorer)
-│   ├── index.ts              # Tool exports
-│   ├── specRetriever.ts      # Vector search tool
-│   ├── sectionRetriever.ts   # Section chunk retrieval tool
-│   ├── graphExplorer.ts      # Knowledge graph navigation tool
-│   └── reranker.ts           # Document reranking utility
-├── constants.ts              # Directory paths and model configs
+├── src/
+│   ├── agent.ts              # Main ReAct agent - answers user queries
+│   ├── constants.ts          # Directory paths and model configs
+│   ├── agent-tools/          # Tool implementations (spec retriever, graph explorer)
+│   │   ├── index.ts          # Tool exports
+│   │   ├── specRetriever.ts  # Vector search tool
+│   │   ├── sectionRetriever.ts   # Section chunk retrieval tool
+│   │   ├── graphExplorer.ts  # Knowledge graph navigation tool
+│   │   └── reranker.ts       # Document reranking utility
+│   └── setup/                # Data ingestion and graph building
+│       ├── ingest.ts         # Ingests spec HTML into vector index
+│       ├── buildGraph.ts     # Builds knowledge graph
+│       ├── stripSpecContainer.ts # Cleans spec HTML files
+│       ├── htmlAddInternalMethodLink.ts  # Adds internal method links
+│       ├── text-splitters/   # Text chunking utilities
+│       └── utils/            # Formatting utilities
+│   └── test/                 # Manual verification tests
+│       └── manual/
+│           ├── verify-db.ts  # Verify database contents
+│           └── test-spec-retriever.ts
 ├── config.json               # API keys and endpoints (user-created)
-├── setup/                    # Data ingestion and graph building
-│   ├── ingest.ts             # Ingests spec HTML into vector index
-│   ├── buildGraph.ts         # Builds knowledge graph
-│   ├── stripSpecContainer.ts # Cleans spec HTML files
-│   ├── htmlAddInternalMethodLink.ts  # Adds internal method links
-│   ├── text-splitters/         # Text chunking utilities
-│   └── utils/                  # Formatting utilities
-├── test/                     # Manual verification tests
-│   ├── manual/
-│   │   ├── verify-db.ts      # Verify database contents
-│   │   └── test-spec-retriever.ts
 ├── spec-built/multipage/     # ECMAScript spec HTML files
 ├── engine262/src/            # JavaScript engine implementation
 ├── storage/                  # Vector index persistence (LanceDB)
diff --git a/package.json b/package.json
index 7ef3447..45c1108 100644
--- a/package.json
+++ b/package.json
@@ -9,10 +9,10 @@
     "lint:fix": "biome check . --write",
     "lint:fix:unsafe": "biome check . --write --unsafe",
     "format:fix": "biome format . --write",
-    "ingest": "bun run setup/ingest.ts",
-    "verify-db": "bun run test/manual/verify-db.ts",
-    "agent": "bun run agent.ts",
-    "build": "bun run setup/buildGraph.ts",
+    "ingest": "bun run src/setup/ingest.ts",
+    "verify-db": "bun run src/test/manual/verify-db.ts",
+    "agent": "bun run src/agent.ts",
+    "build": "bun run src/setup/buildGraph.ts",
     "test": "bun test"
   },
   "keywords": [],
diff --git a/agent-tools/graphExplorer.ts b/src/agent-tools/graphExplorer.ts
similarity index 100%
rename from agent-tools/graphExplorer.ts
rename to src/agent-tools/graphExplorer.ts
diff --git a/agent-tools/index.ts b/src/agent-tools/index.ts
similarity index 100%
rename from agent-tools/index.ts
rename to src/agent-tools/index.ts
diff --git a/agent-tools/reranker.ts b/src/agent-tools/reranker.ts
similarity index 100%
rename from agent-tools/reranker.ts
rename to src/agent-tools/reranker.ts
diff --git a/agent-tools/sectionRetriever.ts b/src/agent-tools/sectionRetriever.ts
similarity index 100%
rename from agent-tools/sectionRetriever.ts
rename to src/agent-tools/sectionRetriever.ts
diff --git a/agent-tools/specRetriever.ts b/src/agent-tools/specRetriever.ts
similarity index 100%
rename from agent-tools/specRetriever.ts
rename to src/agent-tools/specRetriever.ts
diff --git a/agent.ts b/src/agent.ts
similarity index 95%
rename from agent.ts
rename to src/agent.ts
index e9430d7..766896e 100644
--- a/agent.ts
+++ b/src/agent.ts
@@ -11,13 +11,18 @@ import {
   createSectionRetrieverTool,
   createSpecRetrieverTool,
 } from "./agent-tools";
-import { EMBEDDING_MODEL, GRAPH_FILE, STORAGE_DIR } from "./constants";
+import {
+  CONFIG_FILE,
+  EMBEDDING_MODEL,
+  GRAPH_FILE,
+  STORAGE_DIR,
+} from "./constants";
 
 const embeddings = new OllamaEmbeddings({
   model: EMBEDDING_MODEL,
 });
 
-const config = JSON.parse(fs.readFileSync("./config.json", "utf-8"));
+const config = JSON.parse(fs.readFileSync(CONFIG_FILE, "utf-8"));
 const apiKey = config.NVIDIA_API_KEY;
 const baseURL = config.NVIDIA_API_BASE;
 
diff --git a/constants.ts b/src/constants.ts
similarity index 88%
rename from constants.ts
rename to src/constants.ts
index 124407e..597dbd8 100644
--- a/constants.ts
+++ b/src/constants.ts
@@ -2,6 +2,7 @@ export const STORAGE_DIR = "./storage";
 export const SPEC_DIR = "./spec-built/multipage";
 export const CODE_DIR = "./engine262/src";
 export const GRAPH_FILE = "./graphology/graph.json";
+export const CONFIG_FILE = "./config.json";
 
 // Model configurations
 export const EMBEDDING_MODEL = "qwen3-embedding:0.6b";
diff --git a/setup/buildGraph.ts b/src/setup/buildGraph.ts
similarity index 100%
rename from setup/buildGraph.ts
rename to src/setup/buildGraph.ts
diff --git a/setup/htmlAddInternalMethodLink.ts b/src/setup/htmlAddInternalMethodLink.ts
similarity index 100%
rename from setup/htmlAddInternalMethodLink.ts
rename to src/setup/htmlAddInternalMethodLink.ts
diff --git a/setup/ingest.ts b/src/setup/ingest.ts
similarity index 100%
rename from setup/ingest.ts
rename to src/setup/ingest.ts
diff --git a/setup/initEngine262.sh b/src/setup/initEngine262.sh
similarity index 100%
rename from setup/initEngine262.sh
rename to src/setup/initEngine262.sh
diff --git a/setup/stripSpecContainer.ts b/src/setup/stripSpecContainer.ts
similarity index 100%
rename from setup/stripSpecContainer.ts
rename to src/setup/stripSpecContainer.ts
diff --git a/setup/text-splitters/HtmlTextSplitter.test.ts b/src/setup/text-splitters/HtmlTextSplitter.test.ts
similarity index 100%
rename from setup/text-splitters/HtmlTextSplitter.test.ts
rename to src/setup/text-splitters/HtmlTextSplitter.test.ts
diff --git a/setup/text-splitters/HtmlTextSplitter.ts b/src/setup/text-splitters/HtmlTextSplitter.ts
similarity index 100%
rename from setup/text-splitters/HtmlTextSplitter.ts
rename to src/setup/text-splitters/HtmlTextSplitter.ts
diff --git a/setup/text-splitters/index.ts b/src/setup/text-splitters/index.ts
similarity index 100%
rename from setup/text-splitters/index.ts
rename to src/setup/text-splitters/index.ts
diff --git a/setup/utils/formatHTMLForIngestion.test.ts b/src/setup/utils/formatHTMLForIngestion.test.ts
similarity index 100%
rename from setup/utils/formatHTMLForIngestion.test.ts
rename to src/setup/utils/formatHTMLForIngestion.test.ts
diff --git a/setup/utils/formatHTMLForIngestion.ts b/src/setup/utils/formatHTMLForIngestion.ts
similarity index 100%
rename from setup/utils/formatHTMLForIngestion.ts
rename to src/setup/utils/formatHTMLForIngestion.ts
diff --git a/test/manual/test-spec-retriever.ts b/src/test/manual/test-spec-retriever.ts
similarity index 93%
rename from test/manual/test-spec-retriever.ts
rename to src/test/manual/test-spec-retriever.ts
index 0a54ea1..c221e40 100644
--- a/test/manual/test-spec-retriever.ts
+++ b/src/test/manual/test-spec-retriever.ts
@@ -1,6 +1,6 @@
 /**
  * Manual test script for spec_retriever agent tool
- * Usage: bun run test/manual/test-spec-retriever.ts "your search query"
+ * Usage: bun run src/test/manual/test-spec-retriever.ts "your search query"
  */
 
 import * as lancedbSdk from "@lancedb/lancedb";
diff --git a/test/manual/verify-db.ts b/src/test/manual/verify-db.ts
similarity index 93%
rename from test/manual/verify-db.ts
rename to src/test/manual/verify-db.ts
index a90b820..ab52558 100644
--- a/test/manual/verify-db.ts
+++ b/src/test/manual/verify-db.ts
@@ -3,17 +3,17 @@
  * Manual verification script for inspecting LanceDB documents/chunks.
  *
  * Usage:
- *   bun run test/manual/verify-db.ts                    # Show summary (default command)
- *   bun run test/manual/verify-db.ts summary            # Show database summary
- *   bun run test/manual/verify-db.ts list               # List all sections
- *   bun run test/manual/verify-db.ts section <id>       # Show chunks for a section
- *   bun run test/manual/verify-db.ts search "query"     # Search by vector similarity (semantic search)
- *   bun run test/manual/verify-db.ts tree               # Show full section hierarchy
- *   bun run test/manual/verify-db.ts tree sec-ecmascript-language-source-code  # Show subtree from section
- *   bun run test/manual/verify-db.ts sample             # Show random samples
- *   bun run test/manual/verify-db.ts large              # Show large documents
- *   bun run test/manual/verify-db.ts --help            # Show help
- *   bun run test/manual/verify-db.ts <command> --help  # Show help for specific command
+ *   bun run src/test/manual/verify-db.ts                    # Show summary (default command)
+ *   bun run src/test/manual/verify-db.ts summary            # Show database summary
+ *   bun run src/test/manual/verify-db.ts list               # List all sections
+ *   bun run src/test/manual/verify-db.ts section <id>       # Show chunks for a section
+ *   bun run src/test/manual/verify-db.ts search "query"     # Search by vector similarity (semantic search)
+ *   bun run src/test/manual/verify-db.ts tree               # Show full section hierarchy
+ *   bun run src/test/manual/verify-db.ts tree sec-ecmascript-language-source-code  # Show subtree from section
+ *   bun run src/test/manual/verify-db.ts sample             # Show random samples
+ *   bun run src/test/manual/verify-db.ts large              # Show large documents
+ *   bun run src/test/manual/verify-db.ts --help            # Show help
+ *   bun run src/test/manual/verify-db.ts <command> --help  # Show help for specific command
  */
 
 import fs from "node:fs";