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When Python is built from source, the "Modules/" subdirectory is added to sys.path on UNIX. I don't understand why: it does not contain .py files nor .so dynamic modules. Dynamic modules are built in "build/lib.linux-x86_64-3.5-pydebug".
A side effect of adding Modules/ subdirectory to sys.path is that Modules subdirectories (ex: _sqlite, _ctypes, _io, _decimal, etc.) can be used as packages.
For example, when the _decimal module cannot be compiled, Lib/decimal.py uses Modules/_decimal as a Python package which is wrong. The decimal becomes an empty module (no symbol, because Modules/_decimal does not contain an __init__.py nor any .so file) because decimal.py uses "import _decimal" at the end (see decimal.py).
Attached patch removes Modules/ from sys.path on UNIX.
Maybe adding Modules/ to sys.path was useful before the introduction of pybuildir.txt? See issue #9589 and the changeset 4742e7aea2f5 (and the issue #586680).

A side effect of this issue is that when the _decimal cannot be build (ex: #22283), the Python implementation of the decimal cannot be used. Extract of buildbot test logs related to #22283:
---
Failed to build these modules:
_decimal
(...)
 File "/usr/home/buildbot/buildarea/3.x.krah-freebsd/build/Lib/test/test_statistics.py", line 15, in <module>
 from decimal import Decimal
ImportError: cannot import name 'Decimal'
---
http://buildbot.python.org/all/builders/AMD64%20FreeBSD%209.0%203.x/builds/7213/steps/test/logs/stdio 

See also issue #22280 for the case of the wrong _decimal package.

The motivation for this feature is that modules built as shared libraries through Modules/Setup end up in Modules, so Modules is added so that they are found.
I'd like to preserve support for building dynamic extension modules through Modules/Setup, but they don't have to live in Modules; putting them into build (say) would be fine as well.

> I'd like to preserve support for building dynamic extension modules through Modules/Setup, but they don't have to live in Modules; putting them into build (say) would be fine as well.
Does it mean that you are ok to commit my patch?

I think we have this behavior since 6c468df214dc and 227ce85bdbe0 (#17095).

Another bug linked to the bad Modules/_ctypes package:
http://buildbot.python.org/all/builders/AMD64%20OpenIndiana%203.x/builds/8549/steps/test/logs/stdio
test test_ctypes crashed -- Traceback (most recent call last):
 File "/export/home/buildbot/64bits/3.x.cea-indiana-amd64/build/Lib/test/regrtest.py", line 1271, in runtest_inner
 the_module = importlib.import_module(abstest)
 File "/export/home/buildbot/64bits/3.x.cea-indiana-amd64/build/Lib/importlib/__init__.py", line 109, in import_module
 return _bootstrap._gcd_import(name[level:], package, level)
 File "<frozen importlib._bootstrap>", line 2203, in _gcd_import
 File "<frozen importlib._bootstrap>", line 2186, in _find_and_load
 File "<frozen importlib._bootstrap>", line 2175, in _find_and_load_unlocked
 File "<frozen importlib._bootstrap>", line 1149, in _load_unlocked
 File "<frozen importlib._bootstrap>", line 1420, in exec_module
 File "<frozen importlib._bootstrap>", line 321, in _call_with_frames_removed
 File "/export/home/buildbot/64bits/3.x.cea-indiana-amd64/build/Lib/test/test_ctypes.py", line 3, in <module>
 from ctypes.test import load_tests
 File "/export/home/buildbot/64bits/3.x.cea-indiana-amd64/build/Lib/ctypes/__init__.py", line 7, in <module>
 from _ctypes import Union, Structure, Array
ImportError: cannot import name 'Union'

> Does it mean that you are ok to commit my patch?
No, because it will break #17095 again. A proper patch would do what you do, plus find some other solution to #17095. Just reverting 6c468df214dc is not ok.

Closing as a duplicate of the re-opened Issue17095 (since the changes there haven't been released yet)