The ".project" and ".pydevproject" files were added by eclipse, as well as the "pycache" folders.
Run main.py to see the order in which package file content is run. This is something I wasn't aware of until I started playing around with it, so you might find it useful too.
Here's the console output (in case you're curious):
helpers init file
say init file
hello file top level code
goodbye file top level code
running code inside class
running main
hello
goodbye
in class constructor
parameter: 99
in class method