diff --git a/apps/server/src/index.ts b/apps/server/src/index.ts
index b89469b3..65971d15 100644
--- a/apps/server/src/index.ts
+++ b/apps/server/src/index.ts
@@ -27,7 +27,6 @@ import { createGitRoutes } from "./routes/git.js";
 import { createSetupRoutes } from "./routes/setup.js";
 import { createSuggestionsRoutes } from "./routes/suggestions.js";
 import { createModelsRoutes } from "./routes/models.js";
-import { createSpecRegenerationRoutes } from "./routes/spec-regeneration.js";
 import { createRunningAgentsRoutes } from "./routes/running-agents.js";
 import { createWorkspaceRoutes } from "./routes/workspace.js";
 import { createTemplatesRoutes } from "./routes/templates.js";
@@ -41,6 +40,7 @@ import { AgentService } from "./services/agent-service.js";
 import { FeatureLoader } from "./services/feature-loader.js";
 import { AutoModeService } from "./services/auto-mode-service.js";
 import { getTerminalService } from "./services/terminal-service.js";
+import { createSpecRegenerationRoutes } from "./routes/app-spec/index.js";
 
 // Load environment variables
 dotenv.config();
diff --git a/apps/server/src/routes/spec-regeneration.ts b/apps/server/src/routes/spec-regeneration.ts
deleted file mode 100644
index 313054d2..00000000
--- a/apps/server/src/routes/spec-regeneration.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-/**
- * Spec Regeneration routes - HTTP API for AI-powered spec generation
- *
- * This file re-exports from the app-spec directory to maintain backward compatibility.
- * The actual implementation has been split into smaller modules in ./app-spec/
- */
-
-export { createSpecRegenerationRoutes } from "./app-spec/index.js";
diff --git a/apps/server/tests/unit/routes/app-spec/common.test.ts b/apps/server/tests/unit/routes/app-spec/common.test.ts
new file mode 100644
index 00000000..39df4e70
--- /dev/null
+++ b/apps/server/tests/unit/routes/app-spec/common.test.ts
@@ -0,0 +1,103 @@
+import { describe, it, expect, beforeEach } from "vitest";
+import {
+  setRunningState,
+  getErrorMessage,
+  isRunning,
+  currentAbortController,
+} from "@/routes/app-spec/common.js";
+
+describe("app-spec/common.ts", () => {
+  beforeEach(() => {
+    // Reset state before each test
+    setRunningState(false, null);
+  });
+
+  describe("setRunningState", () => {
+    it("should set isRunning to true when running is true", () => {
+      setRunningState(true);
+      expect(isRunning).toBe(true);
+    });
+
+    it("should set isRunning to false when running is false", () => {
+      setRunningState(true);
+      setRunningState(false);
+      expect(isRunning).toBe(false);
+    });
+
+    it("should set currentAbortController when provided", () => {
+      const controller = new AbortController();
+      setRunningState(true, controller);
+      expect(currentAbortController).toBe(controller);
+    });
+
+    it("should set currentAbortController to null when not provided", () => {
+      const controller = new AbortController();
+      setRunningState(true, controller);
+      setRunningState(false);
+      expect(currentAbortController).toBe(null);
+    });
+
+    it("should set currentAbortController to null when explicitly passed null", () => {
+      const controller = new AbortController();
+      setRunningState(true, controller);
+      setRunningState(true, null);
+      expect(currentAbortController).toBe(null);
+    });
+
+    it("should update state multiple times correctly", () => {
+      const controller1 = new AbortController();
+      const controller2 = new AbortController();
+
+      setRunningState(true, controller1);
+      expect(isRunning).toBe(true);
+      expect(currentAbortController).toBe(controller1);
+
+      setRunningState(true, controller2);
+      expect(isRunning).toBe(true);
+      expect(currentAbortController).toBe(controller2);
+
+      setRunningState(false, null);
+      expect(isRunning).toBe(false);
+      expect(currentAbortController).toBe(null);
+    });
+  });
+
+  describe("getErrorMessage", () => {
+    it("should return message from Error instance", () => {
+      const error = new Error("Test error message");
+      expect(getErrorMessage(error)).toBe("Test error message");
+    });
+
+    it("should return 'Unknown error' for non-Error objects", () => {
+      expect(getErrorMessage("string error")).toBe("Unknown error");
+      expect(getErrorMessage(123)).toBe("Unknown error");
+      expect(getErrorMessage(null)).toBe("Unknown error");
+      expect(getErrorMessage(undefined)).toBe("Unknown error");
+      expect(getErrorMessage({})).toBe("Unknown error");
+      expect(getErrorMessage([])).toBe("Unknown error");
+    });
+
+    it("should return message from Error with empty message", () => {
+      const error = new Error("");
+      expect(getErrorMessage(error)).toBe("");
+    });
+
+    it("should handle Error objects with custom properties", () => {
+      const error = new Error("Base message");
+      (error as any).customProp = "custom value";
+      expect(getErrorMessage(error)).toBe("Base message");
+    });
+
+    it("should handle Error objects created with different constructors", () => {
+      class CustomError extends Error {
+        constructor(message: string) {
+          super(message);
+          this.name = "CustomError";
+        }
+      }
+
+      const customError = new CustomError("Custom error message");
+      expect(getErrorMessage(customError)).toBe("Custom error message");
+    });
+  });
+});
diff --git a/apps/server/tests/unit/routes/app-spec/parse-and-create-features.test.ts b/apps/server/tests/unit/routes/app-spec/parse-and-create-features.test.ts
new file mode 100644
index 00000000..7b3d0568
--- /dev/null
+++ b/apps/server/tests/unit/routes/app-spec/parse-and-create-features.test.ts
@@ -0,0 +1,244 @@
+import { describe, it, expect } from "vitest";
+
+describe("app-spec/parse-and-create-features.ts - JSON extraction", () => {
+  // Test the JSON extraction regex pattern used in parseAndCreateFeatures
+  const jsonExtractionPattern = /\{[\s\S]*"features"[\s\S]*\}/;
+
+  describe("JSON extraction regex", () => {
+    it("should extract JSON with features array", () => {
+      const content = `Here is the response:
+{
+  "features": [
+    {
+      "id": "feature-1",
+      "title": "Test Feature",
+      "description": "A test feature",
+      "priority": 1,
+      "complexity": "simple",
+      "dependencies": []
+    }
+  ]
+}`;
+
+      const match = content.match(jsonExtractionPattern);
+      expect(match).not.toBeNull();
+      expect(match![0]).toContain('"features"');
+      expect(match![0]).toContain('"id": "feature-1"');
+    });
+
+    it("should extract JSON with multiple features", () => {
+      const content = `Some text before
+{
+  "features": [
+    {
+      "id": "feature-1",
+      "title": "Feature 1"
+    },
+    {
+      "id": "feature-2",
+      "title": "Feature 2"
+    }
+  ]
+}
+Some text after`;
+
+      const match = content.match(jsonExtractionPattern);
+      expect(match).not.toBeNull();
+      expect(match![0]).toContain('"features"');
+      expect(match![0]).toContain('"feature-1"');
+      expect(match![0]).toContain('"feature-2"');
+    });
+
+    it("should extract JSON with nested objects and arrays", () => {
+      const content = `Response:
+{
+  "features": [
+    {
+      "id": "feature-1",
+      "dependencies": ["dep-1", "dep-2"],
+      "metadata": {
+        "tags": ["tag1", "tag2"]
+      }
+    }
+  ]
+}`;
+
+      const match = content.match(jsonExtractionPattern);
+      expect(match).not.toBeNull();
+      expect(match![0]).toContain('"dependencies"');
+      expect(match![0]).toContain('"dep-1"');
+    });
+
+    it("should handle JSON with whitespace and newlines", () => {
+      const content = `Text before
+{
+  "features": [
+    {
+      "id": "feature-1",
+      "title": "Feature",
+      "description": "A feature\nwith newlines"
+    }
+  ]
+}
+Text after`;
+
+      const match = content.match(jsonExtractionPattern);
+      expect(match).not.toBeNull();
+      expect(match![0]).toContain('"features"');
+    });
+
+    it("should extract JSON when features array is empty", () => {
+      const content = `Response:
+{
+  "features": []
+}`;
+
+      const match = content.match(jsonExtractionPattern);
+      expect(match).not.toBeNull();
+      expect(match![0]).toContain('"features"');
+      expect(match![0]).toContain("[]");
+    });
+
+    it("should not match content without features key", () => {
+      const content = `{
+  "otherKey": "value"
+}`;
+
+      const match = content.match(jsonExtractionPattern);
+      expect(match).toBeNull();
+    });
+
+    it("should not match content without JSON structure", () => {
+      const content = "Just plain text with features mentioned";
+      const match = content.match(jsonExtractionPattern);
+      expect(match).toBeNull();
+    });
+
+    it("should extract JSON when features key appears multiple times", () => {
+      const content = `Before:
+{
+  "features": [
+    {
+      "id": "feature-1",
+      "title": "Feature"
+    }
+  ]
+}
+After: The word "features" appears again`;
+
+      const match = content.match(jsonExtractionPattern);
+      expect(match).not.toBeNull();
+      // Should match from first { to last }
+      expect(match![0]).toContain('"features"');
+    });
+
+    it("should handle JSON with escaped quotes", () => {
+      const content = `{
+  "features": [
+    {
+      "id": "feature-1",
+      "description": "A feature with \\"quotes\\""
+    }
+  ]
+}`;
+
+      const match = content.match(jsonExtractionPattern);
+      expect(match).not.toBeNull();
+      expect(match![0]).toContain('"features"');
+    });
+
+    it("should extract JSON with complex nested structure", () => {
+      const content = `Response:
+{
+  "features": [
+    {
+      "id": "feature-1",
+      "dependencies": [
+        {
+          "id": "dep-1",
+          "type": "required"
+        }
+      ],
+      "metadata": {
+        "tags": ["tag1"],
+        "notes": "Some notes"
+      }
+    }
+  ],
+  "metadata": {
+    "version": "1.0"
+  }
+}`;
+
+      const match = content.match(jsonExtractionPattern);
+      expect(match).not.toBeNull();
+      expect(match![0]).toContain('"features"');
+      expect(match![0]).toContain('"metadata"');
+    });
+  });
+
+  describe("JSON parsing validation", () => {
+    it("should parse valid feature JSON structure", () => {
+      const validJson = `{
+  "features": [
+    {
+      "id": "feature-1",
+      "title": "Test Feature",
+      "description": "A test feature",
+      "priority": 1,
+      "complexity": "simple",
+      "dependencies": []
+    }
+  ]
+}`;
+
+      const parsed = JSON.parse(validJson);
+      expect(parsed.features).toBeDefined();
+      expect(Array.isArray(parsed.features)).toBe(true);
+      expect(parsed.features.length).toBe(1);
+      expect(parsed.features[0].id).toBe("feature-1");
+      expect(parsed.features[0].title).toBe("Test Feature");
+    });
+
+    it("should handle features with optional fields", () => {
+      const jsonWithOptionalFields = `{
+  "features": [
+    {
+      "id": "feature-1",
+      "title": "Feature",
+      "priority": 2,
+      "complexity": "moderate"
+    }
+  ]
+}`;
+
+      const parsed = JSON.parse(jsonWithOptionalFields);
+      expect(parsed.features[0].id).toBe("feature-1");
+      expect(parsed.features[0].priority).toBe(2);
+      // description and dependencies are optional
+      expect(parsed.features[0].description).toBeUndefined();
+      expect(parsed.features[0].dependencies).toBeUndefined();
+    });
+
+    it("should handle features with dependencies", () => {
+      const jsonWithDeps = `{
+  "features": [
+    {
+      "id": "feature-1",
+      "title": "Feature 1",
+      "dependencies": []
+    },
+    {
+      "id": "feature-2",
+      "title": "Feature 2",
+      "dependencies": ["feature-1"]
+    }
+  ]
+}`;
+
+      const parsed = JSON.parse(jsonWithDeps);
+      expect(parsed.features[0].dependencies).toEqual([]);
+      expect(parsed.features[1].dependencies).toEqual(["feature-1"]);
+    });
+  });
+});
diff --git a/docs/server/route-organization.md b/docs/server/route-organization.md
new file mode 100644
index 00000000..4f39a5b0
--- /dev/null
+++ b/docs/server/route-organization.md
@@ -0,0 +1,582 @@
+# Route Organization Pattern
+
+This document describes the pattern used for organizing Express routes into modular, maintainable file structures. This pattern is exemplified by the `app-spec` route module and should be applied to other route modules for consistency and maintainability.
+
+---
+
+## Table of Contents
+
+1. [Overview](#overview)
+2. [Directory Structure](#directory-structure)
+3. [File Organization Principles](#file-organization-principles)
+4. [File Types and Their Roles](#file-types-and-their-roles)
+5. [Implementation Guidelines](#implementation-guidelines)
+6. [Example: app-spec Module](#example-app-spec-module)
+7. [Migration Guide](#migration-guide)
+
+---
+
+## Overview
+
+The route organization pattern separates concerns into:
+
+- **Route handlers** - Thin HTTP request/response handlers in `routes/` subdirectory
+- **Business logic** - Extracted into standalone function files
+- **Shared utilities** - Common functions and state in `common.ts`
+- **Route registration** - Centralized in `index.ts`
+
+This pattern improves:
+
+- **Maintainability** - Clear separation of concerns
+- **Testability** - Functions can be tested independently
+- **Reusability** - Business logic can be reused across routes
+- **Readability** - Smaller, focused files are easier to understand
+
+---
+
+## Directory Structure
+
+```
+routes/
+  └── {module-name}/
+      ├── index.ts                    # Route registration & export
+      ├── common.ts                   # Shared utilities & state
+      ├── {business-function}.ts      # Extracted business logic functions
+      └── routes/
+          ├── {endpoint-name}.ts      # Individual route handlers
+          └── ...
+```
+
+### Example Structure
+
+```
+routes/
+  └── app-spec/
+      ├── index.ts                    # createSpecRegenerationRoutes()
+      ├── common.ts                   # Shared state, logging utilities
+      ├── generate-spec.ts            # generateSpec() function
+      ├── generate-features-from-spec.ts  # generateFeaturesFromSpec() function
+      ├── parse-and-create-features.ts   # parseAndCreateFeatures() function
+      └── routes/
+          ├── create.ts               # POST /create handler
+          ├── generate.ts             # POST /generate handler
+          ├── generate-features.ts    # POST /generate-features handler
+          ├── status.ts               # GET /status handler
+          └── stop.ts                 # POST /stop handler
+```
+
+---
+
+## File Organization Principles
+
+### 1. **Single Responsibility**
+
+Each file should have one clear purpose:
+
+- Route handlers handle HTTP concerns (request/response, validation)
+- Business logic files contain domain-specific operations
+- Common files contain shared utilities and state
+
+### 2. **Separation of Concerns**
+
+- **HTTP Layer** (`routes/*.ts`) - Request parsing, response formatting, status codes
+- **Business Logic** (`*.ts` in root) - Core functionality, domain operations
+- **Shared State** (`common.ts`) - Module-level state, cross-cutting utilities
+
+### 3. **File Size Management**
+
+- Extract functions when files exceed ~150-200 lines
+- Extract when a function is reusable across multiple routes
+- Extract when a function has complex logic that deserves its own file
+
+### 4. **Naming Conventions**
+
+- Route handlers: `{verb}-{resource}.ts` or `{action}.ts` (e.g., `create.ts`, `status.ts`)
+- Business logic: `{action}-{noun}.ts` or `{verb}-{noun}.ts` (e.g., `generate-spec.ts`)
+- Common utilities: Always `common.ts`
+
+---
+
+## File Types and Their Roles
+
+### `index.ts` - Route Registration
+
+**Purpose**: Central export point that creates and configures the Express router.
+
+**Responsibilities**:
+
+- Import route handler factories
+- Create Express Router instance
+- Register all routes
+- Export router creation function
+
+**Pattern**:
+
+```typescript
+import { Router } from "express";
+import type { EventEmitter } from "../../lib/events.js";
+import { createCreateHandler } from "./routes/create.js";
+import { createGenerateHandler } from "./routes/generate.js";
+
+export function create{Module}Routes(events: EventEmitter): Router {
+  const router = Router();
+
+  router.post("/create", createCreateHandler(events));
+  router.get("/status", createStatusHandler());
+
+  return router;
+}
+```
+
+**Key Points**:
+
+- Function name: `create{Module}Routes`
+- Accepts dependencies (e.g., `EventEmitter`) as parameters
+- Returns configured Router instance
+- Route handlers are factory functions that accept dependencies
+
+---
+
+### `common.ts` - Shared Utilities & State
+
+**Purpose**: Central location for shared state, utilities, and helper functions used across multiple route handlers and business logic files.
+
+**Common Contents**:
+
+- Module-level state (e.g., `isRunning`, `currentAbortController`)
+- State management functions (e.g., `setRunningState()`)
+- Logging utilities (e.g., `logAuthStatus()`, `logError()`)
+- Error handling utilities (e.g., `getErrorMessage()`)
+- Shared constants
+- Shared types/interfaces
+
+**Pattern**:
+
+```typescript
+import { createLogger } from "../../lib/logger.js";
+
+const logger = createLogger("{ModuleName}");
+
+// Shared state
+export let isRunning = false;
+export let currentAbortController: AbortController | null = null;
+
+// State management
+export function setRunningState(
+  running: boolean,
+  controller: AbortController | null = null
+): void {
+  isRunning = running;
+  currentAbortController = controller;
+}
+
+// Utility functions
+export function logError(error: unknown, context: string): void {
+  logger.error(`❌ ${context}:`, error);
+}
+
+export function getErrorMessage(error: unknown): string {
+  return error instanceof Error ? error.message : "Unknown error";
+}
+```
+
+**Key Points**:
+
+- Export shared state as `let` variables (mutable state)
+- Provide setter functions for state management
+- Keep utilities focused and reusable
+- Use consistent logging patterns
+
+---
+
+### `routes/{endpoint-name}.ts` - Route Handlers
+
+**Purpose**: Thin HTTP request/response handlers that validate input, call business logic, and format responses.
+
+**Responsibilities**:
+
+- Parse and validate request parameters
+- Check preconditions (e.g., `isRunning` state)
+- Call business logic functions
+- Handle errors and format responses
+- Manage background tasks (if applicable)
+
+**Pattern**:
+
+```typescript
+import type { Request, Response } from "express";
+import type { EventEmitter } from "../../../lib/events.js";
+import { createLogger } from "../../../lib/logger.js";
+import {
+  isRunning,
+  setRunningState,
+  logError,
+  getErrorMessage,
+} from "../common.js";
+import { businessLogicFunction } from "../business-logic.js";
+
+const logger = createLogger("{ModuleName}");
+
+export function create{Action}Handler(events: EventEmitter) {
+  return async (req: Request, res: Response): Promise<void> => {
+    logger.info("========== /{endpoint} endpoint called ==========");
+
+    try {
+      // 1. Parse and validate input
+      const { param1, param2 } = req.body as { param1: string; param2?: number };
+
+      if (!param1) {
+        res.status(400).json({ success: false, error: "param1 required" });
+        return;
+      }
+
+      // 2. Check preconditions
+      if (isRunning) {
+        res.json({ success: false, error: "Operation already running" });
+        return;
+      }
+
+      // 3. Set up state
+      const abortController = new AbortController();
+      setRunningState(true, abortController);
+
+      // 4. Call business logic (background if async)
+      businessLogicFunction(param1, param2, events, abortController)
+        .catch((error) => {
+          logError(error, "Operation failed");
+          events.emit("module:event", { type: "error", error: getErrorMessage(error) });
+        })
+        .finally(() => {
+          setRunningState(false, null);
+        });
+
+      // 5. Return immediate response
+      res.json({ success: true });
+    } catch (error) {
+      logger.error("❌ Route handler exception:", error);
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}
+```
+
+**Key Points**:
+
+- Factory function pattern: `create{Action}Handler(dependencies)`
+- Returns async Express handler function
+- Validate input early
+- Use shared utilities from `common.ts`
+- Handle errors consistently
+- For background tasks, return success immediately and handle completion asynchronously
+
+---
+
+### `{business-function}.ts` - Business Logic Files
+
+**Purpose**: Standalone files containing complex business logic functions that can be reused across routes or extracted to reduce file size.
+
+**When to Extract**:
+
+- Function exceeds ~100-150 lines
+- Function is called from multiple route handlers
+- Function has complex logic that deserves its own file
+- Function can be tested independently
+
+**Pattern**:
+
+```typescript
+/**
+ * {Brief description of what this function does}
+ */
+
+import { query, type Options } from "@anthropic-ai/claude-agent-sdk";
+import type { EventEmitter } from "../../lib/events.js";
+import { createLogger } from "../../lib/logger.js";
+import { logAuthStatus } from "./common.js";
+import { anotherBusinessFunction } from "./another-business-function.js";
+
+const logger = createLogger("{ModuleName}");
+
+export async function businessLogicFunction(
+  param1: string,
+  param2: number,
+  events: EventEmitter,
+  abortController: AbortController
+): Promise<void> {
+  logger.debug("========== businessLogicFunction() started ==========");
+
+  try {
+    // Business logic here
+    // ...
+
+    // Can call other business logic functions
+    await anotherBusinessFunction(param1, events, abortController);
+
+    logger.debug("========== businessLogicFunction() completed ==========");
+  } catch (error) {
+    logger.error("❌ businessLogicFunction() failed:", error);
+    throw error;
+  }
+}
+```
+
+**Key Points**:
+
+- Export named functions (not default exports)
+- Include JSDoc comment at top
+- Import shared utilities from `common.ts`
+- Use consistent logging patterns
+- Can import and call other business logic functions
+- Handle errors and re-throw or emit events as appropriate
+
+---
+
+## Implementation Guidelines
+
+### Step 1: Create Directory Structure
+
+```bash
+mkdir -p routes/{module-name}/routes
+```
+
+### Step 2: Create `common.ts`
+
+Start with shared state and utilities:
+
+- Module-level state variables
+- State management functions
+- Logging utilities
+- Error handling utilities
+
+### Step 3: Extract Business Logic
+
+Identify large functions or reusable logic:
+
+- Functions > 150 lines → extract to separate file
+- Functions used by multiple routes → extract to separate file
+- Complex operations → extract to separate file
+
+### Step 4: Create Route Handlers
+
+For each endpoint:
+
+- Create `routes/{endpoint-name}.ts`
+- Implement factory function pattern
+- Keep handlers thin (validation + call business logic)
+- Use utilities from `common.ts`
+
+### Step 5: Create `index.ts`
+
+- Import all route handler factories
+- Create router and register routes
+- Export router creation function
+
+### Step 6: Register Module
+
+In main routes file:
+
+```typescript
+import { create{Module}Routes } from "./{module-name}/index.js";
+
+app.use("/api/{module-name}", create{Module}Routes(events));
+```
+
+---
+
+## Example: app-spec Module
+
+The `app-spec` module demonstrates this pattern:
+
+### File Breakdown
+
+**`index.ts`** (24 lines)
+
+- Creates router
+- Registers 5 endpoints
+- Exports `createSpecRegenerationRoutes()`
+
+**`common.ts`** (74 lines)
+
+- Shared state: `isRunning`, `currentAbortController`
+- State management: `setRunningState()`
+- Utilities: `logAuthStatus()`, `logError()`, `getErrorMessage()`
+
+**`generate-spec.ts`** (204 lines)
+
+- Extracted business logic for spec generation
+- Handles SDK calls, streaming, file I/O
+- Called by both `create.ts` and `generate.ts` routes
+
+**`generate-features-from-spec.ts`** (155 lines)
+
+- Extracted business logic for feature generation
+- Handles SDK calls and streaming
+- Calls `parseAndCreateFeatures()` for final step
+
+**`parse-and-create-features.ts`** (84 lines)
+
+- Extracted parsing and file creation logic
+- Called by `generate-features-from-spec.ts`
+
+**`routes/create.ts`** (96 lines)
+
+- Thin handler for POST /create
+- Validates input, checks state, calls `generateSpec()`
+
+**`routes/generate.ts`** (99 lines)
+
+- Thin handler for POST /generate
+- Similar to `create.ts` but different input parameter
+
+**`routes/generate-features.ts`** (71 lines)
+
+- Thin handler for POST /generate-features
+- Calls `generateFeaturesFromSpec()`
+
+**`routes/status.ts`** (17 lines)
+
+- Simple handler for GET /status
+- Returns current state
+
+**`routes/stop.ts`** (25 lines)
+
+- Simple handler for POST /stop
+- Aborts current operation
+
+### Key Observations
+
+1. **Route handlers are thin** - Most are 70-100 lines, focused on HTTP concerns
+2. **Business logic is extracted** - Complex operations in separate files
+3. **Shared utilities centralized** - Common functions in `common.ts`
+4. **Reusability** - `generateSpec()` used by both `create.ts` and `generate.ts`
+5. **Clear separation** - HTTP layer vs business logic vs shared utilities
+
+---
+
+## Migration Guide
+
+### Migrating an Existing Route Module
+
+1. **Analyze current structure**
+
+   - Identify all endpoints
+   - Identify shared state/utilities
+   - Identify large functions (>150 lines)
+
+2. **Create directory structure**
+
+   ```bash
+   mkdir -p routes/{module-name}/routes
+   ```
+
+3. **Extract common utilities**
+
+   - Move shared state to `common.ts`
+   - Move utility functions to `common.ts`
+   - Update imports in existing files
+
+4. **Extract business logic**
+
+   - Identify functions to extract
+   - Create `{function-name}.ts` files
+   - Move logic, update imports
+
+5. **Create route handlers**
+
+   - Create `routes/{endpoint-name}.ts` for each endpoint
+   - Move HTTP handling logic
+   - Keep handlers thin
+
+6. **Create index.ts**
+
+   - Import route handlers
+   - Register routes
+   - Export router creation function
+
+7. **Update main routes file**
+
+   - Import from new `index.ts`
+   - Update route registration
+
+8. **Test**
+   - Verify all endpoints work
+   - Check error handling
+   - Verify shared state management
+
+### Example Migration
+
+**Before** (monolithic `routes.ts`):
+
+```typescript
+// routes.ts - 500+ lines
+router.post("/create", async (req, res) => {
+  // 200 lines of logic
+});
+
+router.post("/generate", async (req, res) => {
+  // 200 lines of similar logic
+});
+```
+
+**After** (organized structure):
+
+```typescript
+// routes/app-spec/index.ts
+export function createSpecRegenerationRoutes(events) {
+  const router = Router();
+  router.post("/create", createCreateHandler(events));
+  router.post("/generate", createGenerateHandler(events));
+  return router;
+}
+
+// routes/app-spec/routes/create.ts - 96 lines
+export function createCreateHandler(events) {
+  return async (req, res) => {
+    // Thin handler, calls generateSpec()
+  };
+}
+
+// routes/app-spec/generate-spec.ts - 204 lines
+export async function generateSpec(...) {
+  // Business logic extracted here
+}
+```
+
+---
+
+## Best Practices
+
+### ✅ Do
+
+- Keep route handlers thin (< 150 lines)
+- Extract complex business logic to separate files
+- Centralize shared utilities in `common.ts`
+- Use factory function pattern for route handlers
+- Export named functions (not default exports)
+- Use consistent logging patterns
+- Handle errors consistently
+- Document complex functions with JSDoc
+
+### ❌ Don't
+
+- Put business logic directly in route handlers
+- Duplicate utility functions across files
+- Create files with only one small function (< 20 lines)
+- Mix HTTP concerns with business logic
+- Use default exports for route handlers
+- Create deeply nested directory structures
+- Put route handlers in root of module directory
+
+---
+
+## Summary
+
+The route organization pattern provides:
+
+1. **Clear structure** - Easy to find and understand code
+2. **Separation of concerns** - HTTP, business logic, and utilities separated
+3. **Reusability** - Business logic can be shared across routes
+4. **Maintainability** - Smaller, focused files are easier to maintain
+5. **Testability** - Functions can be tested independently
+
+Apply this pattern to all route modules for consistency and improved code quality.