Refactor debug logging to use logger instead of direct process.stderr

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>

Author: Copilot

.github/aw/actions-lock.json

@@ -25,6 +25,11 @@
       "version": "v5.0.2",
       "sha": "8b402f58fbc84540c8b491a91e594a4576fec3d7"
     },
+    "actions/checkout@v5": {
+      "repo": "actions/checkout",
+      "version": "v5",
+      "sha": "93cb6efe18208431cddfb8368fd83d5badbf9bfd"
+    },
     "actions/checkout@v6.0.2": {
       "repo": "actions/checkout",
       "version": "v6.0.2",
@@ -35,11 +40,21 @@
       "version": "v3.0.0-beta.2",
       "sha": "bf559f85448f9380bcfa2899dbdc01eb5b37be3a"
     },
+    "actions/download-artifact@v6": {
+      "repo": "actions/download-artifact",
+      "version": "v6",
+      "sha": "018cc2cf5baa6db3ef3c5f8a56943fffe632ef53"
+    },
     "actions/download-artifact@v7": {
       "repo": "actions/download-artifact",
       "version": "v7",
       "sha": "37930b1c2abaa49bbe596cd826c3c89aef350131"
     },
+    "actions/github-script@v7": {
+      "repo": "actions/github-script",
+      "version": "v7",
+      "sha": "f28e40c7f34bde8b3046d885e986cb6290c5673b"
+    },
     "actions/github-script@v8": {
       "repo": "actions/github-script",
       "version": "v8",
@@ -125,6 +140,11 @@
       "version": "v4.32.0",
       "sha": "e6985fd516cce3b1a0e8db34a4013d2e50a1e252"
     },
+    "github/stale-repos@v3": {
+      "repo": "github/stale-repos",
+      "version": "v3",
+      "sha": "3477b6488008d9411aaf22a0924ec7c1f6a69980"
+    },
     "github/stale-repos@v8.0.4": {
       "repo": "github/stale-repos",
       "version": "v8.0.4",
@@ -145,6 +165,11 @@
       "version": "v1.286.0",
       "sha": "90be1154f987f4dc0fe0dd0feedac9e473aa4ba8"
     },
+    "super-linter/super-linter@v8.2.1": {
+      "repo": "super-linter/super-linter",
+      "version": "v8.2.1",
+      "sha": "2bdd90ed3262e023ac84bf8fe35dc480721fc1f2"
+    },
     "super-linter/super-linter@v8.3.2": {
       "repo": "super-linter/super-linter",
       "version": "v8.3.2",

.github/workflows/go-pattern-detector.lock.yml

@@ -1,8 +1,11 @@
 // @ts-check
 /// <reference types="@actions/github-script" />
 
+const { createLogger } = require("./mcp_logger.cjs");
+const moduleLogger = createLogger("mcp_http_transport");
+
 // Log immediately at module load time
-process.stderr.write("[mcp_http_transport] Module is being loaded\n");
+moduleLogger.debug("Module is being loaded");
 
 /**
  * MCP HTTP Transport Implementation
@@ -77,13 +80,14 @@ class MCPServer {
    * @param {any} transport - Transport instance (must have setServer and start methods)
    */
   async connect(transport) {
-    process.stderr.write("[MCPServer.connect] Starting connect...\n");
+    const logger = createLogger("MCPServer");
+    logger.debug("Starting connect...");
     this.transport = transport;
-    process.stderr.write("[MCPServer.connect] Set transport\n");
+    logger.debug("Set transport");
     transport.setServer(this);
-    process.stderr.write("[MCPServer.connect] Called setServer\n");
+    logger.debug("Called setServer");
     await transport.start();
-    process.stderr.write("[MCPServer.connect] Transport.start() completed\n");
+    logger.debug("Transport.start() completed");
   }
 
   /**
@@ -133,12 +137,13 @@ class MCPHTTPTransport {
    * Start the transport
    */
   async start() {
-    process.stderr.write("[MCPHTTPTransport.start] Called, started=" + this.started + "\n");
+    const logger = createLogger("MCPHTTPTransport");
+    logger.debug(`Called, started=${this.started}`);
     if (this.started) {
       throw new Error("Transport already started");
     }
     this.started = true;
-    process.stderr.write("[MCPHTTPTransport.start] Set started=true\n");
+    logger.debug("Set started=true");
   }
 
   /**

.github/workflows/release.lock.yml

@@ -1,8 +1,11 @@
 // @ts-check
 /// <reference types="@actions/github-script" />
 
+const { createLogger } = require("./mcp_logger.cjs");
+const moduleLogger = createLogger("mcp_server_core");
+
 // Log immediately at module load time
-process.stderr.write("[mcp_server_core] Module is being loaded\n");
+moduleLogger.debug("Module is being loaded");
 
 /**
  * MCP Server Core Module

.github/workflows/stale-repo-identifier.lock.yml

@@ -5,13 +5,15 @@
 // This is the main entry point script for the safe-outputs MCP server
 // It starts the HTTP server on the configured port
 
+const { createLogger } = require("./mcp_logger.cjs");
+const logger = createLogger("safe-outputs-entry");
+
 // Log immediately to verify Node.js execution starts
-process.stderr.write("[safe-outputs-entry] Entry point script executing\n");
-console.error("[safe-outputs-entry] Console.error test - Node.js is running");
+logger.debug("Entry point script executing");
 
 const { startHttpServer } = require("./safe_outputs_mcp_server_http.cjs");
 
-process.stderr.write("[safe-outputs-entry] Successfully required safe_outputs_mcp_server_http.cjs\n");
+logger.debug("Successfully required safe_outputs_mcp_server_http.cjs");
 
 // Start the HTTP server
 // The server reads configuration from /opt/gh-aw/safeoutputs/config.json
@@ -24,19 +26,18 @@ process.stderr.write("[safe-outputs-entry] Successfully required safe_outputs_mc
 // the MCP gateway doesn't perform the MCP protocol initialization handshake.
 // It directly calls methods like tools/list without the Mcp-Session-Id header.
 if (require.main === module) {
-  process.stderr.write("[safe-outputs-entry] In require.main === module block\n");
+  logger.debug("In require.main === module block");
   const port = parseInt(process.env.GH_AW_SAFE_OUTPUTS_PORT || "3001", 10);
   const logDir = process.env.GH_AW_MCP_LOG_DIR;
-  process.stderr.write(`[safe-outputs-entry] Port: ${port}, LogDir: ${logDir}\n`);
-  process.stderr.write("[safe-outputs-entry] Calling startHttpServer...\n");
+  logger.debug(`Port: ${port}, LogDir: ${logDir}`);
+  logger.debug("Calling startHttpServer...");
 
   startHttpServer({ port, logDir, stateless: true }).catch(error => {
-    console.error(`[safe-outputs-entry] Failed to start safe-outputs HTTP server: ${error.message}`);
-    console.error(`[safe-outputs-entry] Error stack: ${error.stack}`);
+    logger.debugError("Failed to start safe-outputs HTTP server: ", error);
     process.exit(1);
   });
 
-  process.stderr.write("[safe-outputs-entry] startHttpServer call initiated (async)\n");
+  logger.debug("startHttpServer call initiated (async)");
 }
 
 module.exports = { startHttpServer };

.github/workflows/super-linter.lock.yml

@@ -1,8 +1,11 @@
 // @ts-check
 /// <reference types="@actions/github-script" />
 
+const { createLogger } = require("./mcp_logger.cjs");
+const moduleLogger = createLogger("safe_outputs_mcp_server_http");
+
 // Log immediately at module load time (before any requires)
-process.stderr.write("[safe_outputs_mcp_server_http] Module is being loaded\n");
+moduleLogger.debug("Module is being loaded");
 
 /**
  * Safe Outputs MCP Server with HTTP Transport
@@ -22,23 +25,23 @@ process.stderr.write("[safe_outputs_mcp_server_http] Module is being loaded\n");
  */
 
 const http = require("http");
-process.stderr.write("[safe_outputs_mcp_server_http] Loaded http\n");
+moduleLogger.debug("Loaded http");
 const { randomUUID } = require("crypto");
-process.stderr.write("[safe_outputs_mcp_server_http] Loaded crypto\n");
+moduleLogger.debug("Loaded crypto");
 const { MCPServer, MCPHTTPTransport } = require("./mcp_http_transport.cjs");
-process.stderr.write("[safe_outputs_mcp_server_http] Loaded mcp_http_transport.cjs\n");
-const { createLogger } = require("./mcp_logger.cjs");
-process.stderr.write("[safe_outputs_mcp_server_http] Loaded mcp_logger.cjs\n");
+moduleLogger.debug("Loaded mcp_http_transport.cjs");
+const { createLogger: createMCPLogger } = require("./mcp_logger.cjs");
+moduleLogger.debug("Loaded mcp_logger.cjs");
 const { bootstrapSafeOutputsServer, cleanupConfigFile } = require("./safe_outputs_bootstrap.cjs");
-process.stderr.write("[safe_outputs_mcp_server_http] Loaded safe_outputs_bootstrap.cjs\n");
+moduleLogger.debug("Loaded safe_outputs_bootstrap.cjs");
 const { createAppendFunction } = require("./safe_outputs_append.cjs");
-process.stderr.write("[safe_outputs_mcp_server_http] Loaded safe_outputs_append.cjs\n");
+moduleLogger.debug("Loaded safe_outputs_append.cjs");
 const { createHandlers } = require("./safe_outputs_handlers.cjs");
-process.stderr.write("[safe_outputs_mcp_server_http] Loaded safe_outputs_handlers.cjs\n");
+moduleLogger.debug("Loaded safe_outputs_handlers.cjs");
 const { attachHandlers, registerPredefinedTools, registerDynamicTools } = require("./safe_outputs_tools_loader.cjs");
-process.stderr.write("[safe_outputs_mcp_server_http] Loaded safe_outputs_tools_loader.cjs\n");
+moduleLogger.debug("Loaded safe_outputs_tools_loader.cjs");
 const { getErrorMessage } = require("./error_helpers.cjs");
-process.stderr.write("[safe_outputs_mcp_server_http] All modules loaded successfully\n");
+moduleLogger.debug("All modules loaded successfully");
 
 /**
  * Create and configure the MCP server with tools
@@ -48,7 +51,7 @@ process.stderr.write("[safe_outputs_mcp_server_http] All modules loaded successf
  */
 function createMCPServer(options = {}) {
   // Create logger early
-  const logger = createLogger("safeoutputs");
+  const logger = createMCPLogger("safeoutputs");
 
   logger.debug(`=== Creating MCP Server ===`);
 
@@ -188,11 +191,9 @@ async function startHttpServer(options = {}) {
   const port = options.port || 3000;
   const stateless = options.stateless || false;
 
-  // Add immediate synchronous logging
-  process.stderr.write(`[safe-outputs-startup] startHttpServer called with port=${port}, stateless=${stateless}\n`);
-
-  const logger = createLogger("safe-outputs-startup");
+  const logger = createMCPLogger("safe-outputs-startup");
 
+  logger.debug(`startHttpServer called with port=${port}, stateless=${stateless}`);
   logger.debug(`=== Starting Safe Outputs MCP HTTP Server ===`);
   logger.debug(`Port: ${port}`);
   logger.debug(`Mode: ${stateless ? "stateless" : "stateful"}`);
@@ -222,9 +223,9 @@ async function startHttpServer(options = {}) {
 
     // Connect server to transport
     logger.debug(`Connecting server to transport...`);
-    process.stderr.write(`[safe-outputs-startup] About to call server.connect(transport)...\n`);
+    logger.debug(`About to call server.connect(transport)...`);
     await server.connect(transport);
-    process.stderr.write(`[safe-outputs-startup] server.connect(transport) completed successfully\n`);
+    logger.debug(`server.connect(transport) completed successfully`);
     logger.debug(`Server connected to transport successfully`);
 
     // Create HTTP server