diff --git a/src/common/atlas/apiClient.ts b/src/common/atlas/apiClient.ts
index c45f565d..a587d04a 100644
--- a/src/common/atlas/apiClient.ts
+++ b/src/common/atlas/apiClient.ts
@@ -4,8 +4,8 @@ import { AccessToken, ClientCredentials } from "simple-oauth2";
 import { ApiClientError } from "./apiClientError.js";
 import { paths, operations } from "./openapi.js";
 import { CommonProperties, TelemetryEvent } from "../../telemetry/types.js";
-import { packageInfo } from "../../helpers/packageInfo.js";
-import logger, { LogId } from "../../logger.js";
+import { packageInfo } from "../packageInfo.js";
+import logger, { LogId } from "../logger.js";
 
 const ATLAS_API_VERSION = "2025-03-12";
 
diff --git a/src/common/atlas/cluster.ts b/src/common/atlas/cluster.ts
index 793cd99b..a85e2d6f 100644
--- a/src/common/atlas/cluster.ts
+++ b/src/common/atlas/cluster.ts
@@ -1,6 +1,6 @@
 import { ClusterDescription20240805, FlexClusterDescription20241113 } from "./openapi.js";
 import { ApiClient } from "./apiClient.js";
-import logger, { LogId } from "../../logger.js";
+import logger, { LogId } from "../logger.js";
 
 export interface Cluster {
     name?: string;
diff --git a/src/config.ts b/src/common/config.ts
similarity index 100%
rename from src/config.ts
rename to src/common/config.ts
diff --git a/src/errors.ts b/src/common/errors.ts
similarity index 100%
rename from src/errors.ts
rename to src/common/errors.ts
diff --git a/src/logger.ts b/src/common/logger.ts
similarity index 100%
rename from src/logger.ts
rename to src/common/logger.ts
diff --git a/src/helpers/packageInfo.ts b/src/common/packageInfo.ts
similarity index 100%
rename from src/helpers/packageInfo.ts
rename to src/common/packageInfo.ts
diff --git a/src/session.ts b/src/common/session.ts
similarity index 94%
rename from src/session.ts
rename to src/common/session.ts
index eafec2a2..dfae6ec9 100644
--- a/src/session.ts
+++ b/src/common/session.ts
@@ -1,11 +1,11 @@
 import { NodeDriverServiceProvider } from "@mongosh/service-provider-node-driver";
-import { ApiClient, ApiClientCredentials } from "./common/atlas/apiClient.js";
+import { ApiClient, ApiClientCredentials } from "./atlas/apiClient.js";
 import { Implementation } from "@modelcontextprotocol/sdk/types.js";
 import logger, { LogId } from "./logger.js";
 import EventEmitter from "events";
 import { ConnectOptions } from "./config.js";
-import { setAppNameParamIfMissing } from "./helpers/connectionOptions.js";
-import { packageInfo } from "./helpers/packageInfo.js";
+import { setAppNameParamIfMissing } from "../helpers/connectionOptions.js";
+import { packageInfo } from "./packageInfo.js";
 
 export interface SessionOptions {
     apiBaseUrl: string;
diff --git a/src/common/container.ts b/src/helpers/container.ts
similarity index 100%
rename from src/common/container.ts
rename to src/helpers/container.ts
diff --git a/src/common/atlas/generatePassword.ts b/src/helpers/generatePassword.ts
similarity index 100%
rename from src/common/atlas/generatePassword.ts
rename to src/helpers/generatePassword.ts
diff --git a/src/helpers/indexCheck.ts b/src/helpers/indexCheck.ts
index 22bba447..6b7ba09d 100644
--- a/src/helpers/indexCheck.ts
+++ b/src/helpers/indexCheck.ts
@@ -1,6 +1,6 @@
 import { Document } from "mongodb";
 import { NodeDriverServiceProvider } from "@mongosh/service-provider-node-driver";
-import { ErrorCodes, MongoDBError } from "../errors.js";
+import { ErrorCodes, MongoDBError } from "../common/errors.js";
 
 /**
  * Check if the query plan uses an index
diff --git a/src/index.ts b/src/index.ts
index 02f9ca36..f94c4371 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -1,11 +1,11 @@
 #!/usr/bin/env node
 
-import logger, { LogId } from "./logger.js";
+import logger, { LogId } from "./common/logger.js";
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { config } from "./config.js";
-import { Session } from "./session.js";
+import { config } from "./common/config.js";
+import { Session } from "./common/session.js";
 import { Server } from "./server.js";
-import { packageInfo } from "./helpers/packageInfo.js";
+import { packageInfo } from "./common/packageInfo.js";
 import { Telemetry } from "./telemetry/telemetry.js";
 import { createEJsonTransport } from "./helpers/EJsonTransport.js";
 
diff --git a/src/server.ts b/src/server.ts
index c32dc367..3c65d2e3 100644
--- a/src/server.ts
+++ b/src/server.ts
@@ -1,17 +1,17 @@
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { Session } from "./session.js";
+import { Session } from "./common/session.js";
 import { Transport } from "@modelcontextprotocol/sdk/shared/transport.js";
 import { AtlasTools } from "./tools/atlas/tools.js";
 import { MongoDbTools } from "./tools/mongodb/tools.js";
-import logger, { setStdioPreset, setContainerPreset, LogId } from "./logger.js";
+import logger, { setStdioPreset, setContainerPreset, LogId } from "./common/logger.js";
 import { ObjectId } from "mongodb";
 import { Telemetry } from "./telemetry/telemetry.js";
-import { UserConfig } from "./config.js";
+import { UserConfig } from "./common/config.js";
 import { type ServerEvent } from "./telemetry/types.js";
 import { type ServerCommand } from "./telemetry/types.js";
 import { CallToolRequestSchema, CallToolResult } from "@modelcontextprotocol/sdk/types.js";
 import assert from "assert";
-import { detectContainerEnv } from "./common/container.js";
+import { detectContainerEnv } from "./helpers/container.js";
 import { ToolBase } from "./tools/tool.js";
 
 export interface ServerOptions {
diff --git a/src/telemetry/constants.ts b/src/telemetry/constants.ts
index 9dd1cc76..6b18d0fe 100644
--- a/src/telemetry/constants.ts
+++ b/src/telemetry/constants.ts
@@ -1,4 +1,4 @@
-import { packageInfo } from "../helpers/packageInfo.js";
+import { packageInfo } from "../common/packageInfo.js";
 import { type CommonStaticProperties } from "./types.js";
 
 /**
diff --git a/src/telemetry/telemetry.ts b/src/telemetry/telemetry.ts
index f1e24e20..80385843 100644
--- a/src/telemetry/telemetry.ts
+++ b/src/telemetry/telemetry.ts
@@ -1,13 +1,13 @@
-import { Session } from "../session.js";
+import { Session } from "../common/session.js";
 import { BaseEvent, CommonProperties } from "./types.js";
-import { UserConfig } from "../config.js";
-import logger, { LogId } from "../logger.js";
+import { UserConfig } from "../common/config.js";
+import logger, { LogId } from "../common/logger.js";
 import { ApiClient } from "../common/atlas/apiClient.js";
 import { MACHINE_METADATA } from "./constants.js";
 import { EventCache } from "./eventCache.js";
 import nodeMachineId from "node-machine-id";
 import { getDeviceId } from "@mongodb-js/device-id";
-import { detectContainerEnv } from "../common/container.js";
+import { detectContainerEnv } from "../helpers/container.js";
 
 type EventResult = {
     success: boolean;
diff --git a/src/tools/atlas/atlasTool.ts b/src/tools/atlas/atlasTool.ts
index eb7c2f1f..21ae7e8c 100644
--- a/src/tools/atlas/atlasTool.ts
+++ b/src/tools/atlas/atlasTool.ts
@@ -1,7 +1,7 @@
 import { ToolBase, ToolCategory, TelemetryToolMetadata, ToolArgs } from "../tool.js";
 import { ToolCallback } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
-import logger, { LogId } from "../../logger.js";
+import logger, { LogId } from "../../common/logger.js";
 import { z } from "zod";
 import { ApiClientError } from "../../common/atlas/apiClientError.js";
 
diff --git a/src/tools/atlas/connect/connectCluster.ts b/src/tools/atlas/connect/connectCluster.ts
index 31113e82..d8cda77d 100644
--- a/src/tools/atlas/connect/connectCluster.ts
+++ b/src/tools/atlas/connect/connectCluster.ts
@@ -2,8 +2,8 @@ import { z } from "zod";
 import { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
 import { AtlasToolBase } from "../atlasTool.js";
 import { ToolArgs, OperationType } from "../../tool.js";
-import { generateSecurePassword } from "../../../common/atlas/generatePassword.js";
-import logger, { LogId } from "../../../logger.js";
+import { generateSecurePassword } from "../../../helpers/generatePassword.js";
+import logger, { LogId } from "../../../common/logger.js";
 import { inspectCluster } from "../../../common/atlas/cluster.js";
 
 const EXPIRY_MS = 1000 * 60 * 60 * 12; // 12 hours
diff --git a/src/tools/atlas/create/createDBUser.ts b/src/tools/atlas/create/createDBUser.ts
index fef9d513..d2133a04 100644
--- a/src/tools/atlas/create/createDBUser.ts
+++ b/src/tools/atlas/create/createDBUser.ts
@@ -3,7 +3,7 @@ import { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
 import { AtlasToolBase } from "../atlasTool.js";
 import { ToolArgs, OperationType } from "../../tool.js";
 import { CloudDatabaseUser, DatabaseUserRole } from "../../../common/atlas/openapi.js";
-import { generateSecurePassword } from "../../../common/atlas/generatePassword.js";
+import { generateSecurePassword } from "../../../helpers/generatePassword.js";
 
 export class CreateDBUserTool extends AtlasToolBase {
     public name = "atlas-create-db-user";
diff --git a/src/tools/mongodb/connect/connect.ts b/src/tools/mongodb/connect/connect.ts
index e8de9333..c2100689 100644
--- a/src/tools/mongodb/connect/connect.ts
+++ b/src/tools/mongodb/connect/connect.ts
@@ -3,9 +3,9 @@ import { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
 import { MongoDBToolBase } from "../mongodbTool.js";
 import { ToolArgs, OperationType } from "../../tool.js";
 import assert from "assert";
-import { UserConfig } from "../../../config.js";
+import { UserConfig } from "../../../common/config.js";
 import { Telemetry } from "../../../telemetry/telemetry.js";
-import { Session } from "../../../session.js";
+import { Session } from "../../../common/session.js";
 import { Server } from "../../../server.js";
 
 const disconnectedSchema = z
diff --git a/src/tools/mongodb/mongodbTool.ts b/src/tools/mongodb/mongodbTool.ts
index 2e5c68c7..83fc85ab 100644
--- a/src/tools/mongodb/mongodbTool.ts
+++ b/src/tools/mongodb/mongodbTool.ts
@@ -2,8 +2,8 @@ import { z } from "zod";
 import { ToolArgs, ToolBase, ToolCategory, TelemetryToolMetadata } from "../tool.js";
 import { NodeDriverServiceProvider } from "@mongosh/service-provider-node-driver";
 import { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
-import { ErrorCodes, MongoDBError } from "../../errors.js";
-import logger, { LogId } from "../../logger.js";
+import { ErrorCodes, MongoDBError } from "../../common/errors.js";
+import logger, { LogId } from "../../common/logger.js";
 import { Server } from "../../server.js";
 
 export const DbOperationArgs = {
diff --git a/src/tools/tool.ts b/src/tools/tool.ts
index 551374d6..bb0e0804 100644
--- a/src/tools/tool.ts
+++ b/src/tools/tool.ts
@@ -1,11 +1,11 @@
 import { z, type ZodRawShape, type ZodNever, AnyZodObject } from "zod";
 import type { RegisteredTool, ToolCallback } from "@modelcontextprotocol/sdk/server/mcp.js";
 import type { CallToolResult, ToolAnnotations } from "@modelcontextprotocol/sdk/types.js";
-import { Session } from "../session.js";
-import logger, { LogId } from "../logger.js";
+import { Session } from "../common/session.js";
+import logger, { LogId } from "../common/logger.js";
 import { Telemetry } from "../telemetry/telemetry.js";
 import { type ToolEvent } from "../telemetry/types.js";
-import { UserConfig } from "../config.js";
+import { UserConfig } from "../common/config.js";
 import { Server } from "../server.js";
 
 export type ToolArgs<Args extends ZodRawShape> = z.objectOutputType<Args, ZodNever>;
diff --git a/tests/integration/helpers.ts b/tests/integration/helpers.ts
index e5da149f..10502198 100644
--- a/tests/integration/helpers.ts
+++ b/tests/integration/helpers.ts
@@ -1,12 +1,12 @@
 import { Client } from "@modelcontextprotocol/sdk/client/index.js";
 import { InMemoryTransport } from "./inMemoryTransport.js";
 import { Server } from "../../src/server.js";
-import { UserConfig } from "../../src/config.js";
+import { UserConfig } from "../../src/common/config.js";
 import { McpError } from "@modelcontextprotocol/sdk/types.js";
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { Session } from "../../src/session.js";
+import { Session } from "../../src/common/session.js";
 import { Telemetry } from "../../src/telemetry/telemetry.js";
-import { config } from "../../src/config.js";
+import { config } from "../../src/common/config.js";
 import { jest } from "@jest/globals";
 
 interface ParameterInfo {
diff --git a/tests/integration/telemetry.test.ts b/tests/integration/telemetry.test.ts
index 881a8915..3c180cfa 100644
--- a/tests/integration/telemetry.test.ts
+++ b/tests/integration/telemetry.test.ts
@@ -1,7 +1,7 @@
 import { createHmac } from "crypto";
 import { Telemetry } from "../../src/telemetry/telemetry.js";
-import { Session } from "../../src/session.js";
-import { config } from "../../src/config.js";
+import { Session } from "../../src/common/session.js";
+import { config } from "../../src/common/config.js";
 import nodeMachineId from "node-machine-id";
 
 describe("Telemetry", () => {
diff --git a/tests/integration/tools/atlas/clusters.test.ts b/tests/integration/tools/atlas/clusters.test.ts
index b5f34bdf..3916e511 100644
--- a/tests/integration/tools/atlas/clusters.test.ts
+++ b/tests/integration/tools/atlas/clusters.test.ts
@@ -1,4 +1,4 @@
-import { Session } from "../../../../src/session.js";
+import { Session } from "../../../../src/common/session.js";
 import { expectDefined, getResponseElements } from "../../helpers.js";
 import { describeWithAtlas, withProject, randomId } from "./atlasHelpers.js";
 import { ClusterDescription20240805 } from "../../../../src/common/atlas/openapi.js";
diff --git a/tests/integration/tools/mongodb/connect/connect.test.ts b/tests/integration/tools/mongodb/connect/connect.test.ts
index 857b5747..01aaf3ff 100644
--- a/tests/integration/tools/mongodb/connect/connect.test.ts
+++ b/tests/integration/tools/mongodb/connect/connect.test.ts
@@ -5,7 +5,7 @@ import {
     validateThrowsForInvalidArguments,
     validateToolMetadata,
 } from "../../../helpers.js";
-import { config } from "../../../../../src/config.js";
+import { config } from "../../../../../src/common/config.js";
 import { defaultTestConfig, setupIntegrationTest } from "../../../helpers.js";
 
 describeWithMongoDB(
diff --git a/tests/integration/tools/mongodb/mongodbHelpers.ts b/tests/integration/tools/mongodb/mongodbHelpers.ts
index 935b27db..e139aaa4 100644
--- a/tests/integration/tools/mongodb/mongodbHelpers.ts
+++ b/tests/integration/tools/mongodb/mongodbHelpers.ts
@@ -4,7 +4,7 @@ import { fileURLToPath } from "url";
 import fs from "fs/promises";
 import { MongoClient, ObjectId } from "mongodb";
 import { getResponseContent, IntegrationTest, setupIntegrationTest, defaultTestConfig } from "../../helpers.js";
-import { UserConfig } from "../../../../src/config.js";
+import { UserConfig } from "../../../../src/common/config.js";
 
 const __dirname = path.dirname(fileURLToPath(import.meta.url));
 
diff --git a/tests/unit/session.test.ts b/tests/unit/session.test.ts
index 44126359..fdd4296b 100644
--- a/tests/unit/session.test.ts
+++ b/tests/unit/session.test.ts
@@ -1,7 +1,7 @@
 import { jest } from "@jest/globals";
 import { NodeDriverServiceProvider } from "@mongosh/service-provider-node-driver";
-import { Session } from "../../src/session.js";
-import { config } from "../../src/config.js";
+import { Session } from "../../src/common/session.js";
+import { config } from "../../src/common/config.js";
 
 jest.mock("@mongosh/service-provider-node-driver");
 const MockNodeDriverServiceProvider = NodeDriverServiceProvider as jest.MockedClass<typeof NodeDriverServiceProvider>;
diff --git a/tests/unit/telemetry.test.ts b/tests/unit/telemetry.test.ts
index 1898c4a6..c6d3828f 100644
--- a/tests/unit/telemetry.test.ts
+++ b/tests/unit/telemetry.test.ts
@@ -1,11 +1,11 @@
 import { ApiClient } from "../../src/common/atlas/apiClient.js";
-import { Session } from "../../src/session.js";
+import { Session } from "../../src/common/session.js";
 import { DEVICE_ID_TIMEOUT, Telemetry } from "../../src/telemetry/telemetry.js";
 import { BaseEvent, TelemetryResult } from "../../src/telemetry/types.js";
 import { EventCache } from "../../src/telemetry/eventCache.js";
-import { config } from "../../src/config.js";
+import { config } from "../../src/common/config.js";
 import { jest } from "@jest/globals";
-import logger, { LogId } from "../../src/logger.js";
+import logger, { LogId } from "../../src/common/logger.js";
 import { createHmac } from "crypto";
 
 // Mock the ApiClient to avoid real API calls