fix(skill-mcp-manager): filter npm/pnpm/yarn env vars that break MCP servers (#459)

When running in pnpm projects, the .npmrc configuration propagates as
NPM_CONFIG_* environment variables to child processes. This can cause
MCP servers to fail due to registry/proxy conflicts or case sensitivity
issues between uppercase and lowercase variants.

This fix adds a createCleanMcpEnvironment function that filters out:
- NPM_CONFIG_* and npm_config_* (npm/pnpm config)
- YARN_* (yarn config)
- PNPM_* (pnpm config)
- NO_UPDATE_NOTIFIER

Fixes #456

Co-authored-by: sisyphus-dev-ai <sisyphus-dev-ai@users.noreply.github.com>

src/features/skill-mcp-manager/manager.ts

@@ -3,6 +3,7 @@ import { StdioClientTransport } from "@modelcontextprotocol/sdk/client/stdio.js"
 import type { Tool, Resource, Prompt } from "@modelcontextprotocol/sdk/types.js"
 import type { ClaudeCodeMcpServer } from "../claude-code-mcp-loader/types"
 import { expandEnvVarsInObject } from "../claude-code-mcp-loader/env-expander"
+import { createCleanMcpEnvironment } from "./env-cleaner"
 import type { SkillMcpClientInfo, SkillMcpServerContext } from "./types"
 
 interface ManagedClient {
@@ -115,15 +116,7 @@ export class SkillMcpManager {
     const command = config.command
     const args = config.args || []
 
-    // Always inherit parent process environment
-    const mergedEnv: Record<string, string> = {}
-    for (const [key, value] of Object.entries(process.env)) {
-      if (value !== undefined) mergedEnv[key] = value
-    }
-    // Overlay with skill-specific env vars if present
-    if (config.env) {
-      Object.assign(mergedEnv, config.env)
-    }
+    const mergedEnv = createCleanMcpEnvironment(config.env)
 
     this.registerProcessCleanup()