Return similarly named, non-submodule modules

In our setuptools integration command, we were attempting to avoid
checking each submodule in the packages list. This was done without
recognizing that two modules may start with the same prefix, e.g.,

- foo
- foo_bar
- foo_biz

In this case, we only ever checked ``foo``. By appending a '.' to the
end of each package name, we avoid this since we only care about
deduplicating submodules, e.g.,

- foo
- foo.sub
- foo.sub.sub

Closes #295

src/flake8/main/setuptools_command.py

@@ -66,7 +66,7 @@ class Flake8(setuptools.Command):
             if package_directory.startswith(seen_package_directories):
                 continue
 
-            seen_package_directories += (package_directory,)
+            seen_package_directories += (package_directory + '.',)
             yield package_directory
 
     def module_files(self):

tests/unit/test_setuptools_command.py

@@ -0,0 +1,34 @@
+"""Module containing tests for the setuptools command integration."""
+import pytest
+
+from setuptools import dist
+
+from flake8.main import setuptools_command
+
+
+@pytest.fixture
+def distribution():
+    """Create a setuptools Distribution object."""
+    return dist.Distribution({
+        'name': 'foo',
+        'packages': [
+            'foo',
+            'foo.bar',
+            'foo_biz',
+        ],
+    })
+
+
+@pytest.fixture
+def command(distribution):
+    """Create an instance of Flake8's setuptools command."""
+    return setuptools_command.Flake8(distribution)
+
+
+def test_package_files_removes_submodules(command):
+    """Verify that we collect all package files."""
+    package_files = list(command.package_files())
+    assert sorted(package_files) == [
+        'foo',
+        'foo_biz',
+    ]