refactor: remove ~80 dead symbols and files across 6 packages

Remove unused code identified post api-server/mcp-transport split:
- api-server: legacy cache helpers, unused logger functions
- ep-admin: basic-commands, pipeline-commands, TUI adapters, unused
  error classes, runtime/index re-export
- ep-cli: execution service, display service, skill-generator,
  config/env, runtime/test, unused error classes
- ep-shared-services: pattern-presentation, normalize-pattern,
  render-card/index-markdown, clean-pattern-service, pattern-types
- mcp-transport: MCP_2_0_IMPROVEMENTS, oauth-client, unused cache
  key helpers
- toolkit: io module, cache/search/validation services, unused
  re-exports

69 files changed, ~8,800 lines removed.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: PaulJPhilp

packages/api-server/src/services/cache/helpers.ts

@@ -22,13 +22,3 @@ export const isExpired = (entry: CacheEntry<unknown>): boolean => {
   return Date.now() - entry.timestamp > entry.ttl;
 };
 
-/**
- * Legacy cache functions (for backward compatibility)
- */
-export function getCacheKey(...parts: string[]): string {
-  return parts.join(":");
-}
-
-export function createCacheKey(prefix: string, id: string): string {
-  return `${prefix}:${id}`;
-}

packages/api-server/src/services/logger/__tests__/logger.test.ts

@@ -1,7 +1,7 @@
 import { Effect, Layer } from "effect";
 import { describe, expect, it } from "vitest";
 import { MCPConfigService } from "../../config";
-import { createLogEntry, logDebug, logError, logInfo, logWarn } from "../helpers";
+import { createLogEntry } from "../helpers";
 import { MCPLoggerService } from "../index";
 
 const TestLayer = Layer.provideMerge(
@@ -291,113 +291,4 @@ describe("Logger Helpers", () => {
 		});
 	});
 
-	describe("Legacy logging functions", () => {
-		// Capture console output without mocks
-		function captureConsoleOutput(
-			method: "log" | "warn" | "error"
-		): { output: string[]; restore: () => void } {
-			const output: string[] = [];
-			const original = console[method];
-			
-			console[method] = ((...args: unknown[]) => {
-				output.push(args.map(String).join(" "));
-			}) as any;
-			
-			return {
-				output,
-				restore: () => {
-					console[method] = original;
-				},
-			};
-		}
-
-		it("logDebug should log debug message", () => {
-			const { output, restore } = captureConsoleOutput("error");
-			const originalDebug = process.env.MCP_DEBUG;
-			try {
-				process.env.MCP_DEBUG = "true";
-				logDebug("Debug message", { key: "value" });
-				expect(output.length).toBeGreaterThan(0);
-				const parsed = JSON.parse(output[0]!);
-				expect(parsed.level).toBe("debug");
-				expect(parsed.message).toBe("Debug message");
-				expect(parsed.data).toEqual({ key: "value" });
-			} finally {
-				restore();
-				if (originalDebug === undefined) {
-					delete process.env.MCP_DEBUG;
-				} else {
-					process.env.MCP_DEBUG = originalDebug;
-				}
-			}
-		});
-
-		it("logInfo should log info message", () => {
-			const { output, restore } = captureConsoleOutput("error");
-			try {
-				logInfo("Info message", { key: "value" });
-				expect(output.length).toBeGreaterThan(0);
-				const parsed = JSON.parse(output[output.length - 1]!);
-				expect(parsed.level).toBe("info");
-				expect(parsed.message).toBe("Info message");
-			} finally {
-				restore();
-			}
-		});
-
-		it("logWarn should log warning message", () => {
-			const { output, restore } = captureConsoleOutput("warn");
-			try {
-				logWarn("Warning message", { key: "value" });
-				expect(output.length).toBeGreaterThan(0);
-				const parsed = JSON.parse(output[0]!);
-				expect(parsed.level).toBe("warn");
-				expect(parsed.message).toBe("Warning message");
-			} finally {
-				restore();
-			}
-		});
-
-		it("logError should log error message with Error object", () => {
-			const { output, restore } = captureConsoleOutput("error");
-			try {
-				const error = new Error("Test error");
-				logError("Error message", error, { key: "value" });
-				expect(output.length).toBeGreaterThan(0);
-				const parsed = JSON.parse(output[0]!);
-				expect(parsed.level).toBe("error");
-				expect(parsed.message).toBe("Error message");
-				expect(parsed.error.name).toBe("Error");
-				expect(parsed.error.message).toBe("Test error");
-			} finally {
-				restore();
-			}
-		});
-
-		it("logError should log error message with unknown error", () => {
-			const { output, restore } = captureConsoleOutput("error");
-			try {
-				logError("Error message", "String error", { key: "value" });
-				expect(output.length).toBeGreaterThan(0);
-				const parsed = JSON.parse(output[0]!);
-				expect(parsed.error.name).toBe("UnknownError");
-				expect(parsed.error.message).toBe("String error");
-			} finally {
-				restore();
-			}
-		});
-
-		it("logError should log error message without error", () => {
-			const { output, restore } = captureConsoleOutput("error");
-			try {
-				logError("Error message", undefined, { key: "value" });
-				expect(output.length).toBeGreaterThan(0);
-				const parsed = JSON.parse(output[0]!);
-				expect(parsed.level).toBe("error");
-				expect(parsed.error).toBeUndefined();
-			} finally {
-				restore();
-			}
-		});
-	});
 });

packages/api-server/src/services/logger/helpers.ts

@@ -51,100 +51,3 @@ export const createLogEntry = (
   return baseEntry;
 };
 
-/**
- * Log levels and their priorities
- */
-const LOG_LEVELS: Record<string, number> = {
-  debug: 0,
-  info: 1,
-  warn: 2,
-  error: 3,
-};
-
-/**
- * Get current log level priority
- */
-function getLogLevelPriority(): number {
-  const defaultLevel = process.env.NODE_ENV === "production" ? "warn" : "info";
-  const level = process.env.LOG_LEVEL || defaultLevel;
-  // MCP_DEBUG=true forces debug level
-  if (process.env.MCP_DEBUG === "true") return LOG_LEVELS.debug;
-  return LOG_LEVELS[level.toLowerCase()] ?? LOG_LEVELS[defaultLevel];
-}
-
-/**
- * Legacy logging functions (for backward compatibility)
- */
-export function logDebug(
-  message: string,
-  data?: Record<string, unknown>
-): void {
-  if (getLogLevelPriority() <= LOG_LEVELS.debug) {
-    console.error(
-      JSON.stringify({
-        timestamp: new Date().toISOString(),
-        level: "debug",
-        message,
-        data,
-      })
-    );
-  }
-}
-
-export function logInfo(message: string, data?: Record<string, unknown>): void {
-  if (getLogLevelPriority() <= LOG_LEVELS.info) {
-    console.error(
-      JSON.stringify({
-        timestamp: new Date().toISOString(),
-        level: "info",
-        message,
-        data,
-      })
-    );
-  }
-}
-
-export function logWarn(message: string, data?: Record<string, unknown>): void {
-  if (getLogLevelPriority() <= LOG_LEVELS.warn) {
-    console.warn(
-      JSON.stringify({
-        timestamp: new Date().toISOString(),
-        level: "warn",
-        message,
-        data,
-      })
-    );
-  }
-}
-
-export function logError(
-  message: string,
-  error?: unknown,
-  data?: Record<string, unknown>
-): void {
-  if (getLogLevelPriority() <= LOG_LEVELS.error) {
-    const logEntry: any = {
-      timestamp: new Date().toISOString(),
-      level: "error",
-      message,
-      data,
-    };
-
-    if (error) {
-      if (error instanceof Error) {
-        logEntry.error = {
-          name: error.name,
-          message: error.message,
-          stack: error.stack,
-        };
-      } else {
-        logEntry.error = {
-          name: "UnknownError",
-          message: String(error),
-        };
-      }
-    }
-
-    console.error(JSON.stringify(logEntry));
-  }
-}

packages/api-server/src/tracing/otlpLayer.ts

@@ -16,7 +16,7 @@ import { Effect } from "effect";
 /**
  * Tracing configuration from environment variables
  */
-export interface TracingConfig {
+interface TracingConfig {
   readonly otlpEndpoint: string;
   readonly otlpHeaders: Record<string, string>;
   readonly serviceName: string;