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>

package.json

@@ -12,7 +12,7 @@
     "typecheck": "tsc --noEmit",
     "format": "prettier --write \"src/**/*.ts\"",
     "format:check": "prettier --check \"src/**/*.ts\"",
-    "setup": "tsx src/setup/index.ts",
+    "setup": "tsx setup/index.ts",
     "test": "vitest run",
     "test:watch": "vitest"
   },