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/env-cleaner.ts

@@ -0,0 +1,27 @@
+// Filters npm/pnpm/yarn config env vars that break MCP servers in pnpm projects (#456)
+export const EXCLUDED_ENV_PATTERNS: RegExp[] = [
+  /^NPM_CONFIG_/i,
+  /^npm_config_/,
+  /^YARN_/,
+  /^PNPM_/,
+  /^NO_UPDATE_NOTIFIER$/,
+]
+
+export function createCleanMcpEnvironment(
+  customEnv: Record<string, string> = {}
+): Record<string, string> {
+  const cleanEnv: Record<string, string> = {}
+
+  for (const [key, value] of Object.entries(process.env)) {
+    if (value === undefined) continue
+
+    const shouldExclude = EXCLUDED_ENV_PATTERNS.some((pattern) => pattern.test(key))
+    if (!shouldExclude) {
+      cleanEnv[key] = value
+    }
+  }
+
+  Object.assign(cleanEnv, customEnv)
+
+  return cleanEnv
+}