diff --git a/.flake8 b/.flake8
index 2e1bbb9dc..a1288dba5 100644
--- a/.flake8
+++ b/.flake8
@@ -10,14 +10,12 @@
 #   356 E305 expected 2 blank lines
 
 # Nice-to-haves ignored for now
-#   221 E128 continuation line under-indented for visual indent
-#    44 E127 continuation line over-indented for visual indent
+#   152 E128 continuation line under-indented for visual indent
+#    43 E127 continuation line over-indented for visual indent
 
 [flake8]
-ignore = F401, F811, E127, E128, E301, E302, E305, E501, E701, E704, B303
+ignore = F401, F811, F821, E127, E128, E301, E302, E305, E501, E701, E704, E999, B303
 
 # Errors that we need to fix before enabling flake8 by default:
-#   921 F821 undefined name
-#    26 F403 from * import used
-#     7 E999 invalid syntax
-#     5 F405 name undefined or from * imports
+#   936 F821 undefined name - FIXME: re-enable and add missing imports
+#     6 E999 invalid syntax - FIXME: re-enable after flake8 is running from Python 3.6
diff --git a/out/Crypto/Util/Counter.pyi b/out/Crypto/Util/Counter.pyi
index 93cbc4baf..91fa04c48 100644
--- a/out/Crypto/Util/Counter.pyi
+++ b/out/Crypto/Util/Counter.pyi
@@ -3,7 +3,7 @@
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
 from typing import Any
-from Crypto.Util.py21compat import *
-from Crypto.Util.py3compat import *
+from Crypto.Util.py21compat import *  # noqa: F403
+from Crypto.Util.py3compat import *  # noqa: F403
 
 def new(nbits, prefix: Any = ..., suffix: Any = ..., initial_value: int = ..., overflow: int = ..., little_endian: bool = ..., allow_wraparound: bool = ..., disable_shortcut: bool = ...): ...
diff --git a/stdlib/2/posixpath.pyi b/stdlib/2/posixpath.pyi
index 413958b4b..5e5439fa6 100644
--- a/stdlib/2/posixpath.pyi
+++ b/stdlib/2/posixpath.pyi
@@ -3,7 +3,7 @@
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
 from typing import Any, AnyStr, List
-from genericpath import *
+from genericpath import *  # noqa: F403
 
 curdir = ...  # type: Any
 pardir = ...  # type: Any
diff --git a/stdlib/2/sqlite3/__init__.pyi b/stdlib/2/sqlite3/__init__.pyi
index 28bc3bad1..fc22e5d50 100644
--- a/stdlib/2/sqlite3/__init__.pyi
+++ b/stdlib/2/sqlite3/__init__.pyi
@@ -2,4 +2,4 @@
 #
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
-from sqlite3.dbapi2 import *
+from sqlite3.dbapi2 import *  # noqa: F403
diff --git a/stdlib/2/xml/etree/cElementTree.pyi b/stdlib/2/xml/etree/cElementTree.pyi
index a6f4274de..8f689de4b 100644
--- a/stdlib/2/xml/etree/cElementTree.pyi
+++ b/stdlib/2/xml/etree/cElementTree.pyi
@@ -2,4 +2,4 @@
 #
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
-from xml.etree.ElementTree import *
+from xml.etree.ElementTree import *  # noqa: F403
diff --git a/stdlib/3.2/xml/etree/cElementTree.pyi b/stdlib/3.2/xml/etree/cElementTree.pyi
index a6f4274de..8f689de4b 100644
--- a/stdlib/3.2/xml/etree/cElementTree.pyi
+++ b/stdlib/3.2/xml/etree/cElementTree.pyi
@@ -2,4 +2,4 @@
 #
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
-from xml.etree.ElementTree import *
+from xml.etree.ElementTree import *  # noqa: F403
diff --git a/stdlib/3.3/xml/etree/cElementTree.pyi b/stdlib/3.3/xml/etree/cElementTree.pyi
index a6f4274de..8f689de4b 100644
--- a/stdlib/3.3/xml/etree/cElementTree.pyi
+++ b/stdlib/3.3/xml/etree/cElementTree.pyi
@@ -2,4 +2,4 @@
 #
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
-from xml.etree.ElementTree import *
+from xml.etree.ElementTree import *  # noqa: F403
diff --git a/stdlib/3.4/xml/etree/cElementTree.pyi b/stdlib/3.4/xml/etree/cElementTree.pyi
index a6f4274de..8f689de4b 100644
--- a/stdlib/3.4/xml/etree/cElementTree.pyi
+++ b/stdlib/3.4/xml/etree/cElementTree.pyi
@@ -2,4 +2,4 @@
 #
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
-from xml.etree.ElementTree import *
+from xml.etree.ElementTree import *  # noqa: F403
diff --git a/stdlib/3.5/xml/etree/cElementTree.pyi b/stdlib/3.5/xml/etree/cElementTree.pyi
index a6f4274de..8f689de4b 100644
--- a/stdlib/3.5/xml/etree/cElementTree.pyi
+++ b/stdlib/3.5/xml/etree/cElementTree.pyi
@@ -2,4 +2,4 @@
 #
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
-from xml.etree.ElementTree import *
+from xml.etree.ElementTree import *  # noqa: F403
diff --git a/stdlib/3/concurrent/futures/__init__.pyi b/stdlib/3/concurrent/futures/__init__.pyi
index 5b6ab81d6..4439dcadb 100644
--- a/stdlib/3/concurrent/futures/__init__.pyi
+++ b/stdlib/3/concurrent/futures/__init__.pyi
@@ -1,3 +1,3 @@
-from ._base import *
-from .thread import *
-from .process import *
+from ._base import *  # noqa: F403
+from .thread import *  # noqa: F403
+from .process import *  # noqa: F403
diff --git a/stdlib/3/curses/__init__.pyi b/stdlib/3/curses/__init__.pyi
index e60fdf30d..63a4bd9f0 100644
--- a/stdlib/3/curses/__init__.pyi
+++ b/stdlib/3/curses/__init__.pyi
@@ -2,7 +2,7 @@
 #
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
-from _curses import *
+from _curses import *  # noqa: F403
 # Stubgen imports a python version of has_key only if it's not present
 # in _curses (which it is in this stub)
 # from .has_key import has_key as has_key
diff --git a/stdlib/3/sqlite3/__init__.pyi b/stdlib/3/sqlite3/__init__.pyi
index 28bc3bad1..fc22e5d50 100644
--- a/stdlib/3/sqlite3/__init__.pyi
+++ b/stdlib/3/sqlite3/__init__.pyi
@@ -2,4 +2,4 @@
 #
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
-from sqlite3.dbapi2 import *
+from sqlite3.dbapi2 import *  # noqa: F403
diff --git a/stdlib/3/tkinter/__init__.pyi b/stdlib/3/tkinter/__init__.pyi
index 782932df5..ec6124392 100644
--- a/stdlib/3/tkinter/__init__.pyi
+++ b/stdlib/3/tkinter/__init__.pyi
@@ -3,7 +3,7 @@
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
 from typing import Any
-from tkinter.constants import *
+from tkinter.constants import *  # noqa: F403
 
 TclError = ...  # type: Any
 wantobjects = ...  # type: Any
diff --git a/stdlib/3/tokenize.pyi b/stdlib/3/tokenize.pyi
index 2f1a184fe..9849f68ba 100644
--- a/stdlib/3/tokenize.pyi
+++ b/stdlib/3/tokenize.pyi
@@ -4,7 +4,7 @@
 
 from typing import Any, Union, TextIO
 from builtins import open as _builtin_open
-from token import *
+from token import *  # noqa: F403
 
 COMMENT = ...  # type: Any
 NL = ...  # type: Any
diff --git a/stdlib/3/xml/etree/cElementTree.pyi b/stdlib/3/xml/etree/cElementTree.pyi
index a6f4274de..8f689de4b 100644
--- a/stdlib/3/xml/etree/cElementTree.pyi
+++ b/stdlib/3/xml/etree/cElementTree.pyi
@@ -2,4 +2,4 @@
 #
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
-from xml.etree.ElementTree import *
+from xml.etree.ElementTree import *  # noqa: F403
diff --git a/third_party/2/scribe/scribe.pyi b/third_party/2/scribe/scribe.pyi
index 227ec268e..ec2a71f72 100644
--- a/third_party/2/scribe/scribe.pyi
+++ b/third_party/2/scribe/scribe.pyi
@@ -5,7 +5,7 @@
 from typing import Any
 
 import fb303.FacebookService
-from .ttypes import *
+from .ttypes import *  # noqa: F403
 from thrift.Thrift import TProcessor
 
 class Iface(fb303.FacebookService.Iface):
diff --git a/third_party/2/six/moves/cPickle.pyi b/third_party/2/six/moves/cPickle.pyi
index a3c341476..3feedc6ad 100644
--- a/third_party/2/six/moves/cPickle.pyi
+++ b/third_party/2/six/moves/cPickle.pyi
@@ -3,4 +3,4 @@
 #
 # Stubs for six.moves.cPickle (Python 2.7)
 
-from cPickle import *
+from cPickle import *  # noqa: F403
diff --git a/third_party/2/sqlalchemy/databases/mysql.pyi b/third_party/2/sqlalchemy/databases/mysql.pyi
index c218c50b7..4cda14fc4 100644
--- a/third_party/2/sqlalchemy/databases/mysql.pyi
+++ b/third_party/2/sqlalchemy/databases/mysql.pyi
@@ -1 +1 @@
-from sqlalchemy.dialects.mysql.base import *
+from sqlalchemy.dialects.mysql.base import *  # noqa: F403
diff --git a/third_party/2/thrift/protocol/TBinaryProtocol.pyi b/third_party/2/thrift/protocol/TBinaryProtocol.pyi
index e74547204..a1e5e71e2 100644
--- a/third_party/2/thrift/protocol/TBinaryProtocol.pyi
+++ b/third_party/2/thrift/protocol/TBinaryProtocol.pyi
@@ -4,7 +4,8 @@
 
 from typing import Any
 
-from .TProtocol import *
+from .TProtocol import TProtocolBase
+from .TProtocol import *  # noqa: F403
 
 class TBinaryProtocol(TProtocolBase):
     VERSION_MASK = ...  # type: Any
diff --git a/third_party/2/thrift/protocol/TProtocol.pyi b/third_party/2/thrift/protocol/TProtocol.pyi
index 493495881..e59765a0e 100644
--- a/third_party/2/thrift/protocol/TProtocol.pyi
+++ b/third_party/2/thrift/protocol/TProtocol.pyi
@@ -4,7 +4,8 @@
 
 from typing import Any
 
-from thrift.Thrift import *
+from thrift.Thrift import TException
+from thrift.Thrift import *  # noqa: F403
 
 class TProtocolException(TException):
     UNKNOWN = ...  # type: Any
diff --git a/third_party/2/thrift/transport/TSocket.pyi b/third_party/2/thrift/transport/TSocket.pyi
index f7c411ebe..6148117f3 100644
--- a/third_party/2/thrift/transport/TSocket.pyi
+++ b/third_party/2/thrift/transport/TSocket.pyi
@@ -4,7 +4,8 @@
 
 from typing import Any
 
-from .TTransport import *
+from .TTransport import TTransportBase, TServerTransportBase
+from .TTransport import *  # noqa: F403
 
 class TSocketBase(TTransportBase):
     handle = ...  # type: Any
diff --git a/third_party/2and3/Crypto/PublicKey/ElGamal.pyi b/third_party/2and3/Crypto/PublicKey/ElGamal.pyi
index 1695ba1cb..4ed2c5ba5 100644
--- a/third_party/2and3/Crypto/PublicKey/ElGamal.pyi
+++ b/third_party/2and3/Crypto/PublicKey/ElGamal.pyi
@@ -3,7 +3,9 @@
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
 from typing import Any, Optional
-from Crypto.PublicKey.pubkey import *
+
+from Crypto.PublicKey.pubkey import pubkey
+from Crypto.PublicKey.pubkey import *  # noqa: F403
 
 class error(Exception): ...
 
diff --git a/third_party/2and3/Crypto/PublicKey/pubkey.pyi b/third_party/2and3/Crypto/PublicKey/pubkey.pyi
index 7415b32c5..dd34d695a 100644
--- a/third_party/2and3/Crypto/PublicKey/pubkey.pyi
+++ b/third_party/2and3/Crypto/PublicKey/pubkey.pyi
@@ -2,7 +2,7 @@
 #
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
-from Crypto.Util.number import *
+from Crypto.Util.number import *  # noqa: F403
 
 __revision__ = ...  # type: str
 
diff --git a/third_party/3/six/moves/cPickle.pyi b/third_party/3/six/moves/cPickle.pyi
index aa9f2bc80..f2e2e1222 100644
--- a/third_party/3/six/moves/cPickle.pyi
+++ b/third_party/3/six/moves/cPickle.pyi
@@ -3,4 +3,4 @@
 #
 # Stubs for six.moves.cPickle (Python 3.2)
 
-from pickle import *
+from pickle import *  # noqa: F403