refactor: move setup scripts out of src/ to reduce build token count

Setup scripts are standalone CLI tools run via tsx with no runtime
imports from the main app. Moving them out of src/ excludes them from
the tsc build output and reduces the compiled bundle size.

- git mv src/setup/ setup/
- Fix imports to use ../src/logger.js and ../src/config.js
- Update package.json, vitest.config.ts, SKILL.md references
- Fix platform tests to be cross-platform (macOS + Linux)

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

vitest.config.ts

@@ -2,6 +2,6 @@ import { defineConfig } from 'vitest/config';
 
 export default defineConfig({
   test: {
-    include: ['src/**/*.test.ts', 'skills-engine/**/*.test.ts'],
+    include: ['src/**/*.test.ts', 'setup/**/*.test.ts', 'skills-engine/**/*.test.ts'],
   },
 });