refactor: migrate config/config.ts from Bun.file()/Bun.write() to Filesystem module

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.