diff --git a/.travis.yml b/.travis.yml
index 491ab8d3..1588ee1b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -30,8 +30,7 @@ matrix:
       install:
         - 'pip install .[qa]'
       script:
-        # Ignore F401, which are unused imports. flake8 is a primitive tool and is sometimes wrong.
-        - 'flake8 --extend-ignore F401 jedi setup.py'
+        - 'flake8 jedi setup.py'
         - 'mypy jedi sith.py'
 install:
     - sudo apt-get -y install python3-venv
diff --git a/jedi/inference/compiled/__init__.py b/jedi/inference/compiled/__init__.py
index f4a8691e..09ac19f9 100644
--- a/jedi/inference/compiled/__init__.py
+++ b/jedi/inference/compiled/__init__.py
@@ -1,23 +1,10 @@
+# This file also re-exports symbols for wider use. We configure mypy and flake8
+# to be aware that this file does this.
+
 from jedi.inference.compiled.value import CompiledValue, CompiledName, \
     CompiledValueFilter, CompiledValueName, create_from_access_path
 from jedi.inference.base_value import LazyValueWrapper
 
-__all__ = (
-    'CompiledValue',
-    'CompiledName',
-    'CompiledValueFilter',
-    'CompiledValueName',
-    'create_from_access_path',
-
-    'LazyValueWrapper',
-
-    'builtin_from_name',
-    'ExactValue',
-    'create_simple_object',
-    'get_string_value_set',
-    'load_module',
-)
-
 
 def builtin_from_name(inference_state, string):
     typing_builtins_module = inference_state.builtins_module
diff --git a/jedi/inference/value/__init__.py b/jedi/inference/value/__init__.py
index d35f0647..62164215 100644
--- a/jedi/inference/value/__init__.py
+++ b/jedi/inference/value/__init__.py
@@ -1,21 +1,9 @@
+# Re-export symbols for wider use. We configure mypy and flake8 to be aware that
+# this file does this.
+
 from jedi.inference.value.module import ModuleValue
 from jedi.inference.value.klass import ClassValue
 from jedi.inference.value.function import FunctionValue, \
     MethodValue
 from jedi.inference.value.instance import AnonymousInstance, BoundMethod, \
     CompiledInstance, AbstractInstanceValue, TreeInstance
-
-__all__ = (
-    'ModuleValue',
-
-    'ClassValue',
-
-    'FunctionValue',
-    'MethodValue',
-
-    'AnonymousInstance',
-    'BoundMethod',
-    'CompiledInstance',
-    'AbstractInstanceValue',
-    'TreeInstance',
-)
diff --git a/setup.cfg b/setup.cfg
index 0186cfe8..bc1f1399 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -15,6 +15,12 @@ ignore =
   W503,
   # Single letter loop variables are often fine
   E741,
+per-file-ignores =
+  # Ignore apparently unused imports in files where we're (implicitly)
+  # re-exporting them.
+  jedi/__init__.py:F401
+  jedi/inference/compiled/__init__.py:F401
+  jedi/inference/value/__init__.py:F401
 exclude = jedi/third_party/* .tox/*
 
 [pycodestyle]
@@ -48,8 +54,8 @@ implicit_reexport = False
 
 strict_equality = True
 
-[mypy-jedi]
-# jedi/__init__.py contains only re-exports.
+[mypy-jedi,jedi.inference.compiled,jedi.inference.value]
+# Various __init__.py files which contain re-exports we want to implicitly make.
 implicit_reexport = True
 
 [mypy-jedi.debug]