Include `__init__.py` During mpy-cross; Include Subfolders; Modularize Package Search

• Removes the exclusion of compiling __init__.py with mpy-cross, for packaged libraries. Zero-byte files are still excluded.

• When creating the list of files to bundle, subfolders weren't traversed inside of a packaged library. This release now includes subfolders (to include subfolders in the examples folder; for now)

• Modularize Package Search

  • Adds a command line argument package_folder_prefix to use for determining which folder(s) to include with packaged libraries. This changes from an exclusive approach to an inclusive approach, while still allowing some flexibility. (could be expanded to use a list of prefixes in the future)