Replace Bun-specific file operations with Filesystem module:
- Replace Bun.file().json() with Filesystem.readJson<T>()
- Replace Bun.file().text() with Filesystem.readText()
- Replace Bun.file().exists() with Filesystem.exists()
- Replace Bun.write() with Filesystem.write() and Filesystem.writeJson()
All 99 config tests pass.