PyCharm, what is python_stubs?

(1) Yes, you are mostly correct.

The python_stubs file is an automatically generated file that contains dummy definitions for built-in functions. It is used by PyCharm to infer the types of the built-in functions in the case that they weren't hardcoded for the given version.

(3) It isn't always possible to correctly infer the type of a built-in functoin only from his docs. Some docstrings start with the "type signature":

>>> print(min.__doc__)
min(iterable[, key=func]) -> value
min(a, b, c, ...[, key=func]) -> value

but pickle.load() doesn't.

Note that this will probably change in future python versions, because starting with python3.4 the Argument Clinic was introduced which allows better inspection for built-ins defined in C. I'm not sure whether PyCharm is already able to get that information.

(2) Try rebuilding the python skeletons. However, AFAIK, the only real option, if this doesn't work, is to open a ticket on PyCharm's issue tracker.

PEP484 defined these stub files. As per the PEP, they are supposed to be for type-hints and can be used by type-checker.