Reorganize monorepo structure with packages/ dir

- Move all packages into packages/ directory for better organization
- Restructure source code within each package under src/ subdirectory
- Update all import paths and configuration files accordingly
- Maintain package functionality while improving repository structure

This addresses https://github.com/fedify-dev/fedify/issues/320 by providing
a cleaner monorepo layout that follows common conventions and makes
the codebase easier to navigate.