In T97992#1256635, @XZise wrote:

Do the following inside of the core directory:

Don'tNeedToKnow@Imamadmad /cygdrive/c/core
$ python pwb.py login

pwb.py does add the core directory to the PATH variable so that python sees the pywikibot directory. There are other ways to fix this like adding the core directory (or any directory containing the pywikibot directory) to PATH or PYTHONPATH.

Edit: It's PYTHONPATH not PYTHON_PATH, thanks @jayvdb for the reminder.