fix: remove stdout pollution in stdio mode

[chrisdoc]

Use quiet mode for dotenvx to prevent stdout pollution that breaks JSON-RPC communication in stdio mode.

---

Note

Suppresses stdout pollution by using dotenvx quiet mode and stderr logging; consolidates CI to run integration tests in the build job and uploads coverage to Codecov, updating OTEL job dependencies.

• Runtime/Logging:
  • Replace @dotenvx/dotenvx/config with dotenvx.config({ quiet: true }) in src/index.ts and tests/integration/hevy-mcp.integration.test.ts to avoid stdout output.
  • Switch startup messages from console.log to console.error in src/index.ts.
• CI/CD (.github/workflows/build-and-test.yml):
  • Run integration tests within the build job; remove separate integration-tests job.
  • Upload coverage to Codecov after integration tests.
  • Set otel-cicd-action needs to [build].

^{Written by Cursor Bugbot for commit 6cb45f4. This will update automatically on new commits. Configure here.}

✨ PR Description

Purpose: Fix stdout pollution by configuring dotenvx in quiet mode and redirecting log messages to stderr in stdio mode.
Main changes:

• Modified dotenvx import to use config with quiet option to prevent stdout pollution
• Changed console.log calls to console.error to keep stdout clean for IPC
• Simplified CI workflow by merging integration tests into the build job

Generated by LinearB AI and added by gitStream.
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[gemini-code-assist]

Summary of Changes

Hello @chrisdoc, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request resolves an issue where unwanted output to stdout was interfering with JSON-RPC communication in stdio mode. The fix involves configuring dotenvx to operate silently and redirecting all informational log messages from stdout to stderr. These adjustments ensure that stdout is exclusively used for JSON-RPC payloads, thereby stabilizing the communication channel.

Highlights

• Dotenvx Configuration: Configured dotenvx to run in quiet mode by explicitly importing dotenvx and calling dotenvx.config({ quiet: true }). This prevents dotenvx from printing output to stdout.
• Console Output Redirection: Redirected informational console.log messages related to client initialization and server startup to console.error. This ensures that standard output remains clear for JSON-RPC communication.
• Integration Test Consistency: Applied the same dotenvx quiet mode configuration to the integration tests to maintain consistent behavior and prevent potential stdout pollution during testing.

Ignored Files

• Ignored by pattern: .github/workflows/** (1)
  • .github/workflows/build-and-test.yml

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (f232c43) to head (6cb45f4).
⚠️ Report is 9 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff            @@
##              main      #174   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files            1         1           
  Lines            2         2           
=========================================
  Hits             2         2           

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[gemini-code-assist]

Code Review

The pull request correctly addresses the issue of stdout pollution from dotenvx by enabling its quiet mode. This is a good fix for ensuring clean JSON-RPC communication over stdio. The changes to use console.error for logging instead of console.log are also appropriate for this goal. I've added a couple of suggestions to improve code structure by grouping all imports at the top of the files, which is a common best practice for maintainability.

[gemini-code-assist]

For better code organization and adherence to common style practices, it's best to group all import statements at the top of the file, before any executable code. This change splits the import statements with the dotenvx.config() call, which can be confusing for developers and some tooling. Moving the configuration call after all imports will improve readability and maintainability.

Suggested change

	import { fileURLToPath } from "node:url";
	import dotenvx from "@dotenvx/dotenvx";
	// Configure dotenvx with quiet mode to prevent stdout pollution in stdio mode
	dotenvx.config({ quiet: true });
	import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
	import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
	import { z } from "zod";
	import { fileURLToPath } from "node:url";
	import dotenvx from "@dotenvx/dotenvx";
	import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
	import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
	import { z } from "zod";
	// Configure dotenvx with quiet mode to prevent stdout pollution in stdio mode
	dotenvx.config({ quiet: true });

[gemini-code-assist]

Similar to the change in src/index.ts, it's best practice to keep all import statements grouped at the top of the file. This change introduces executable code between import statements. Consolidating imports at the beginning of the file improves code structure and readability.

Suggested change

	import dotenvx from "@dotenvx/dotenvx";
	dotenvx.config({ quiet: true });
	import { Client } from "@modelcontextprotocol/sdk/client/index.js";
	import { InMemoryTransport } from "@modelcontextprotocol/sdk/inMemory.js";
	import dotenvx from "@dotenvx/dotenvx";
	import { Client } from "@modelcontextprotocol/sdk/client/index.js";
	import { InMemoryTransport } from "@modelcontextprotocol/sdk/inMemory.js";
	dotenvx.config({ quiet: true });

[gitstream-cm]

✨ PR Review

LGTM

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